Contacts of the helix formed by residues 114 - 143 (chain D) in PDB entry 1TKP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 114 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 3.3 22.1 - - - +
7C ALA* 5.6 0.2 - - - +
8C ARG* 3.7 14.6 - - + +
113D TYR* 1.3 77.8 - - - +
115D ILE* 1.3 65.4 + - - +
116D ARG* 3.3 13.7 + - - +
117D THR* 2.5 41.7 + - - -
118D SER* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 2.7 22.9 + - - +
174A THR* 3.8 31.0 - - - +
175A LEU* 4.0 9.2 - - + +
51D HIS* 5.1 2.2 - - + +
55D VAL* 3.3 34.3 - - + -
56D GLU 4.7 4.0 - - - +
59D GLU* 4.8 0.2 - - - +
63D LEU* 3.7 22.2 - - + -
67D LEU* 4.5 6.7 - - + -
114D ASP* 1.3 73.2 - - - +
116D ARG* 1.3 66.2 + - - +
118D SER* 4.4 8.5 - - - -
119D LEU* 3.0 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR 4.2 6.1 - - - +
175A LEU* 2.9 44.3 + - + +
176A VAL 4.9 0.9 - - - -
177A THR* 3.6 26.1 - - - +
114D ASP* 3.3 10.0 + - - +
115D ILE* 1.3 78.2 - - - +
117D THR* 1.3 56.7 + - - +
120D ALA* 3.0 28.4 + - - +
169D TYR 4.3 3.8 + - - -
170D LEU* 2.9 63.6 + - + +
171D GLU 4.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D TYR* 3.8 23.3 - - + -
114D ASP* 2.5 32.4 + - - -
115D ILE 3.2 0.6 - - - -
116D ARG* 1.3 76.5 - - - +
118D SER* 1.3 62.1 + - - +
120D ALA* 3.3 3.7 + - - +
121D ASN* 2.8 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D HIS* 3.3 42.2 + - - -
108D GLU* 3.4 13.8 + - - -
112D VAL* 5.9 0.2 - - - +
113D TYR* 3.5 16.5 + - - +
114D ASP 3.0 17.5 + - - -
115D ILE* 3.8 11.8 - - - +
117D THR* 1.3 77.2 - - - +
119D LEU* 1.3 64.6 + - - -
121D ASN* 3.0 5.2 + - - +
122D ASP* 2.9 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.5 31.9 - - + -
51D HIS* 5.1 0.4 - - - +
63D LEU* 4.0 13.7 - - + -
66D PHE* 5.6 0.2 - - + -
67D LEU* 4.1 27.6 - - + -
115D ILE* 3.0 30.4 + - + +
116D ARG 3.8 3.8 - - - +
118D SER* 1.3 80.2 - - - +
120D ALA* 1.3 52.3 + - - +
122D ASP* 3.0 9.5 + - - +
123D MET 2.7 32.1 + - - -
166D ILE* 3.5 24.6 - - + +
169D TYR* 3.9 22.0 - - + -
170D LEU* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ARG 3.0 19.4 + - - +
117D THR* 4.0 4.7 - - - +
119D LEU* 1.3 72.3 - - - +
121D ASN* 1.3 67.0 + - - +
123D MET* 3.6 11.9 - - + +
124D ALA* 3.1 21.8 + - - +
170D LEU* 4.0 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN* 3.8 11.0 - - - +
106D ASP 5.4 0.2 - - - +
108D GLU* 2.5 39.4 + - - +
113D TYR* 4.5 2.8 - - - -
117D THR* 2.8 30.6 + - - +
118D SER 3.0 7.8 + - - +
120D ALA* 1.3 78.6 - - - +
122D ASP* 1.3 60.7 + - - +
124D ALA* 3.3 7.8 + - - +
125D ILE* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 4.7 3.1 - - + +
47D GLN* 2.9 20.6 + - - +
48D LEU* 3.6 24.2 - - + +
51D HIS* 2.5 45.1 + - - +
67D LEU* 4.3 0.2 - - - +
118D SER 2.9 12.0 + - - +
119D LEU* 3.0 14.6 + - - +
121D ASN* 1.3 71.3 - - - +
123D MET* 1.3 68.8 + - - +
125D ILE* 2.9 8.6 + - - +
126D TYR* 2.8 27.7 + - + -
166D ILE* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU 2.7 19.5 + - - +
120D ALA* 3.6 11.4 - - + +
122D ASP* 1.3 75.6 - - - +
124D ALA* 1.3 61.8 + - - +
126D TYR* 3.2 12.0 + - + +
127D GLY* 3.0 19.1 + - - -
163D ALA* 4.7 7.6 - - + +
166D ILE* 3.9 14.1 - - + +
167D GLU* 4.0 43.1 - - + +
170D LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ASP* 6.6 0.4 - - + -
120D ALA 3.1 11.5 + - - +
121D ASN* 3.3 9.4 + - - +
122D ASP 3.1 0.2 - - - -
123D MET* 1.3 77.6 - - - +
125D ILE* 1.3 65.8 + - + +
127D GLY* 3.3 2.4 + - - +
128D ASP* 3.2 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D VAL* 4.7 3.8 - - + -
44D LEU* 3.6 43.1 - - + -
47D GLN* 3.6 29.2 - - + +
105D VAL* 4.0 30.3 - - + -
106D ASP* 3.3 27.6 - - + +
107D VAL* 5.3 0.4 - - - -
121D ASN 3.2 9.2 + - - +
122D ASP* 2.9 8.5 + - - +
124D ALA* 1.3 74.4 - - + +
126D TYR* 1.3 67.2 + - - +
127D GLY 3.2 0.2 + - - -
128D ASP* 3.2 4.0 + - - +
129D ILE* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 3.8 33.4 - - + -
48D LEU* 3.3 22.7 - - + +
70D ALA* 3.4 20.1 + - - +
74D ALA* 5.6 0.4 - - + +
122D ASP* 2.8 31.3 + - + -
123D MET* 3.2 6.5 + - - +
125D ILE* 1.3 73.8 - - - +
127D GLY* 1.3 52.3 + - - +
129D ILE* 3.1 6.5 + - + +
130D ILE* 2.7 41.0 + - + +
159D LEU* 3.7 35.0 - - + -
162D ASP* 3.4 22.4 + - + +
163D ALA* 3.6 21.5 - - + -
166D ILE* 3.3 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D MET 3.0 13.7 + - - -
124D ALA* 3.3 3.3 + - - -
125D ILE 3.2 0.4 - - - -
126D TYR* 1.3 77.3 - - - +
128D ASP* 1.3 64.1 + - - +
130D ILE* 3.8 9.0 - - - +
131D GLU* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ASN* 5.9 2.0 - - - +
104D SER* 5.1 2.9 - - - +
105D VAL* 3.6 35.3 - - + +
106D ASP* 5.1 3.8 + - - +
124D ALA* 3.2 19.2 + - - +
125D ILE 3.7 1.6 - - - +
127D GLY* 1.3 79.1 - - - +
129D ILE* 1.3 55.8 - - - +
131D GLU* 3.8 12.6 - - - +
132D ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP* 5.4 7.2 - - + +
40D ASN* 3.7 36.8 - - + +
41D VAL* 3.9 16.6 - - + -
44D LEU* 3.8 20.6 - - + -
105D VAL* 4.7 2.5 - - + -
125D ILE* 3.0 37.4 + - + +
126D TYR* 3.5 8.1 - - - +
128D ASP* 1.3 72.3 - - - +
130D ILE* 1.3 65.7 + - + +
132D ALA* 3.4 5.1 + - - +
133D THR* 2.8 40.9 + - - +
159D LEU* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D TYR* 2.7 26.0 + - + +
127D GLY* 3.2 8.0 + - - +
129D ILE* 1.3 76.0 - - + +
131D GLU* 1.3 59.4 + - + +
133D THR* 3.2 2.4 + - - -
134D ARG* 2.9 69.3 + - - +
156D LEU* 4.0 10.3 - - + +
159D LEU* 4.2 12.8 - - + +
160D GLU* 3.7 31.6 - - + +
163D ALA* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D GLY 3.1 23.7 + - - +
128D ASP* 3.8 11.4 - - - +
130D ILE* 1.3 78.5 - - + +
132D ALA* 1.3 65.0 + - - +
134D ARG* 3.4 21.5 + - - +
135D GLU* 3.2 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP* 3.8 8.3 - - - +
40D ASN* 5.5 6.7 - - - +
128D ASP 3.0 15.3 + - - +
129D ILE* 4.0 4.7 - - - +
131D GLU* 1.3 80.4 - - - +
133D THR* 1.3 57.4 + - - +
135D GLU* 3.1 12.0 + - - +
136D HIS* 2.8 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP* 4.3 9.3 + - - -
129D ILE* 2.8 39.3 + - - +
130D ILE* 3.6 3.8 - - - -
132D ALA* 1.3 71.7 - - - +
134D ARG* 1.3 64.7 + - - +
136D HIS* 3.0 8.1 + - - +
137D THR* 2.7 33.7 + - + +
152D LEU* 3.6 24.8 - - + +
156D LEU* 3.6 36.3 - - + -
159D LEU* 4.7 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ILE* 2.9 37.2 + - - +
131D GLU* 3.7 19.6 - - - +
133D THR* 1.3 78.6 - - - +
135D GLU* 1.3 60.4 + - - +
137D THR* 3.2 21.3 + - - -
138D GLU* 3.2 21.3 + - - +
156D LEU* 4.1 15.5 - - + +
160D GLU* 3.1 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D GLU* 3.2 18.0 + - - +
132D ALA* 3.1 13.0 + - - +
134D ARG* 1.3 77.0 - - - +
136D HIS* 1.3 66.9 + - + +
138D GLU* 3.4 19.8 + - - +
139D LEU* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ALA* 3.3 39.9 - - + +
34D LEU* 5.6 0.9 - - + -
36D ALA* 5.2 4.9 - - + -
37D ASP* 2.6 42.0 + - - +
132D ALA* 2.8 33.2 + - + +
133D THR 3.0 3.8 + - - +
135D GLU* 1.3 79.4 + - + +
137D THR* 1.3 62.6 + - - +
139D LEU* 3.0 10.7 + - + +
140D ALA* 2.7 31.9 + - - +
152D LEU* 3.7 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D THR* 2.7 30.6 + - + +
134D ARG* 3.2 10.0 + - - +
136D HIS* 1.3 77.8 - - - +
138D GLU* 1.3 61.2 + - - +
140D ALA* 3.1 3.7 + - - +
141D GLU* 2.8 28.6 + - - +
149D ALA* 3.8 16.0 - - - +
152D LEU* 3.5 30.7 - - + +
153D ARG* 4.3 21.8 + - + +
156D LEU* 5.0 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ARG* 3.2 22.7 + - - +
135D GLU* 3.6 16.9 - - - +
137D THR* 1.3 81.4 + - - +
139D LEU* 1.3 58.2 + - - +
141D GLU* 3.2 5.4 + - - +
142D ASN* 2.9 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLN* 3.9 43.7 - - + +
30D CYS* 4.8 2.9 - - - -
33D ALA* 4.1 19.1 - - + -
135D GLU 3.0 17.3 + - - +
136D HIS* 3.0 9.6 + - + +
138D GLU* 1.3 77.5 - - - +
140D ALA* 1.3 64.6 + - - +
142D ASN* 3.3 9.9 + - + +
143D LEU* 3.1 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D CYS* 4.4 14.1 - - - -
136D HIS 2.7 19.6 + - - +
137D THR* 3.5 4.0 - - - +
139D LEU* 1.3 71.9 - - - +
141D GLU* 1.3 66.1 + - - +
143D LEU* 3.1 6.3 + - - +
145D ASP* 2.9 41.4 + - + +
148D THR* 4.0 17.3 - - + -
149D ALA* 3.7 15.7 - - + +
152D LEU* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D THR 2.8 17.1 + - - +
138D GLU* 4.0 5.6 - - - +
140D ALA* 1.3 72.8 - - - +
142D ASN* 1.3 61.5 + - - +
144D GLY* 2.8 20.1 + - - -
145D ASP 4.9 0.2 - - - -
146D HIS* 2.1 56.1 + - - +
149D ALA* 3.6 11.0 - - + +
153D ARG* 3.1 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D GLU* 2.9 26.3 + - - +
139D LEU* 3.5 11.8 - - + +
141D GLU* 1.3 82.7 - - - +
143D LEU* 1.3 63.4 + - + +
144D GLY 3.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D MET* 6.1 0.2 - - - -
26D ARG* 3.0 58.3 + - + +
29D GLN* 3.5 53.2 - - + +
30D CYS* 3.6 18.6 - - - -
139D LEU* 3.1 23.2 + - + +
140D ALA* 3.1 7.8 + - - +
142D ASN* 1.3 81.1 - - + +
144D GLY* 1.4 58.1 + - - +
145D ASP* 3.5 5.3 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il