Contacts of the helix formed by residues 135 - 155 (chain D) in PDB entry 4FZX
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 ARG 135 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLU* 4.0 0.4 - - - -
18D GLU* 2.9 37.2 + - - +
36D LEU* 4.0 16.6 - - - +
51D HIS 3.5 21.1 - - - -
52D ARG 5.7 1.0 + - - -
53D ILE* 3.8 10.5 - - - +
57D MSE 3.9 23.3 - - - +
130D GLY 5.1 2.6 + - - -
131D LEU* 4.1 35.9 - - + +
132D HIS* 3.1 46.7 + - + +
133D HIS 3.3 0.2 - - - -
134D HIS* 1.3 80.1 - - - +
136D ALA* 1.3 65.0 + - - +
137D LEU 3.3 1.1 - - - -
138D TYR* 3.3 3.6 + - + +
139D ASP* 3.1 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ASP* 3.4 34.9 - - - +
8D GLU* 3.9 5.4 - - + +
18D GLU* 2.9 35.1 + - + +
19D ILE* 3.9 0.9 - - - -
20D ALA* 3.4 20.2 - - + +
135D ARG* 1.3 71.9 - - - +
137D LEU* 1.3 62.6 + - - +
139D ASP 3.3 1.6 + - - -
140D CYS* 3.1 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 4.9 2.3 + - - +
20D ALA* 3.3 10.4 - - + +
21D SER 3.9 9.2 - - - +
22D VAL* 4.1 3.1 - - + -
32D PRO* 3.8 22.4 - - + -
33D MSE 3.8 20.6 - - - +
34D SER* 4.1 16.2 - - - +
128D PRO* 4.2 13.7 - - + -
131D LEU* 3.7 22.6 - - + +
135D ARG 3.3 0.4 - - - -
136D ALA* 1.3 76.2 - - - +
138D TYR* 1.3 67.5 + - - +
140D CYS* 3.2 11.1 + - + +
141D TYR* 3.0 40.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D MSE 4.1 13.0 - - + +
127D THR* 3.8 29.3 + - + +
128D PRO* 4.0 29.4 - - + -
131D LEU* 4.0 13.4 - - + +
132D HIS* 3.2 35.2 - - - +
133D HIS* 3.8 16.2 - - + -
135D ARG 3.3 4.4 + - - +
137D LEU* 1.3 78.9 - - - +
139D ASP* 1.3 73.8 + - - +
141D TYR* 3.2 14.9 + - - +
142D ILE* 3.3 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A T 5.2 0.5 + - - -
6D ASP* 3.7 11.7 - - - +
114D ASN* 3.5 10.2 + - - +
133D HIS* 2.8 34.8 + - - -
134D HIS* 3.0 25.4 + - - -
135D ARG 3.1 8.4 + - - +
136D ALA 3.3 2.0 + - - +
138D TYR* 1.3 86.0 - - - +
140D CYS* 1.3 56.5 + - - +
142D ILE* 3.2 7.8 + - - +
143D THR* 2.9 34.5 + - - -
201D NA 2.3 32.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.6 18.7 - - + +
5D ILE 4.0 1.1 - - - -
6D ASP* 3.6 16.8 - - - +
20D ALA* 3.3 35.0 - - - -
21D SER* 3.7 7.9 - - - -
22D VAL* 3.7 17.7 - - + +
136D ALA 3.1 17.9 + - - -
137D LEU* 3.2 11.9 - - - +
139D ASP* 1.3 74.0 - - - +
141D TYR* 1.3 61.0 + - - +
143D THR* 3.4 0.6 + - - -
144D ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D VAL* 3.8 9.9 - - + -
29D ILE* 3.8 34.3 - - + +
32D PRO* 3.1 29.8 - - - +
125D VAL* 3.8 14.6 - - + +
126D GLN 3.4 21.8 - - - +
127D THR* 4.6 4.5 - - + -
128D PRO* 3.5 36.7 - - + +
137D LEU* 3.0 41.3 + - + +
138D TYR 3.2 7.6 + - - +
140D CYS* 1.3 77.6 - - - +
142D ILE* 1.3 63.6 + - - +
144D ALA* 3.3 5.1 + - - +
145D ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ASN* 3.6 29.4 - - + +
115D MSE 4.1 17.9 - - + -
118D TYR* 3.7 56.5 - - + +
127D THR* 4.4 12.6 - - + -
133D HIS* 5.3 0.4 - - + +
138D TYR* 3.6 38.8 - - + +
139D ASP* 3.2 10.6 + - - +
141D TYR* 1.3 79.1 - - - +
143D THR* 1.3 60.9 + - - +
145D ALA* 3.4 3.6 + - - +
146D LEU* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.8 22.7 - - + -
5D ILE 5.9 0.2 - - - +
6D ASP* 5.4 2.4 + - - +
78D VAL* 4.3 6.3 - - + -
79D ALA* 4.6 0.4 - - - -
80D HIS* 4.0 15.8 + - + +
99D THR* 3.7 30.1 - - + +
114D ASN* 2.9 30.2 + - - +
139D ASP* 2.9 13.6 + - - +
140D CYS* 4.6 0.2 - - - -
142D ILE* 1.3 73.8 - - - +
144D ALA* 1.3 62.0 + - - +
146D LEU* 3.3 4.2 + - + +
147D LEU* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.7 13.6 - - + +
22D VAL* 3.6 21.3 - - + -
24D VAL* 3.7 16.8 - - + +
29D ILE* 3.9 11.9 - - + -
140D CYS 2.9 19.7 + - - +
141D TYR 3.7 3.8 - - - +
143D THR* 1.3 76.0 - - - +
145D ALA* 1.3 63.6 + - - +
147D LEU* 3.3 2.8 + - - +
148D ILE* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 4.4 0.8 - - - +
118D TYR* 3.9 19.3 - - + -
123D LEU* 3.8 10.0 - - + +
125D VAL* 3.5 28.7 - - + -
141D TYR 3.0 13.8 + - - +
142D ILE 3.5 9.2 - - - +
144D ALA* 1.3 77.4 - - - +
146D LEU* 1.3 62.8 + - - +
148D ILE* 3.3 9.6 + - - +
149D ASP* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D HIS* 3.6 34.1 - - + +
99D THR* 4.0 11.2 - - - +
103D ALA* 5.0 0.2 - - + -
107D TRP* 4.3 14.4 - - + -
114D ASN* 4.0 13.2 - - - +
117D LEU* 3.7 35.9 - - + -
118D TYR* 5.6 2.0 - - - +
121D ARG* 4.8 1.8 - - + -
123D LEU* 3.7 18.9 - - + +
142D ILE 3.2 10.0 + - - +
143D THR 3.3 7.4 + - - +
145D ALA* 1.3 79.5 - - - +
147D LEU* 1.3 56.7 + - - +
149D ASP* 3.1 3.3 + - - +
150D ILE* 2.8 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 4.1 16.2 - - + -
4D ILE* 4.1 12.8 - - + -
24D VAL* 4.4 9.2 - - + -
78D VAL* 4.0 28.7 - - + -
97D ILE* 4.9 0.7 - - + -
99D THR* 4.1 22.4 - - + +
102D LEU* 4.8 4.7 - - + -
143D THR 2.8 19.1 + - - +
144D ALA* 3.6 5.6 - - - +
146D LEU* 1.3 73.2 - - - +
148D ILE* 1.3 57.2 + - - +
150D ILE* 3.1 7.4 + - + +
151D MSE 2.8 43.3 + - + +
161D MSE 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL* 3.7 23.8 - - + -
27D GLY* 3.5 36.1 - - - +
29D ILE* 3.9 26.9 - - + -
125D VAL* 5.8 1.8 - - + -
144D ALA 3.0 20.6 + - - +
145D ALA* 3.6 8.1 - - - +
147D LEU* 1.3 74.3 - - - +
149D ASP* 1.3 57.8 + - - +
151D MSE 3.2 10.1 + - - +
152D ASN* 3.1 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D TRP* 3.7 5.0 - - - -
121D ARG* 2.7 52.8 + - - +
123D LEU* 3.8 24.6 - - + +
145D ALA 3.0 13.1 + - - +
146D LEU* 3.5 7.7 - - - +
148D ILE* 1.3 76.6 - - - +
150D ILE* 1.3 63.4 + - - +
152D ASN* 4.1 5.8 - - - +
153D THR* 2.8 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D THR* 3.7 33.7 - - + +
102D LEU* 4.0 31.6 - - + -
103D ALA* 4.3 3.8 - - + +
106D LEU* 3.8 20.4 - - + +
107D TRP* 3.9 21.8 - - + -
146D LEU* 2.8 38.9 + - + +
147D LEU* 3.4 7.9 - - - +
149D ASP* 1.3 73.9 - - - +
151D MSE 1.3 56.1 + - - +
153D THR* 3.9 0.5 - - - -
154D SER* 2.9 33.0 + - - +
156D TRP* 4.2 9.6 - - + -
161D MSE 4.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 3.9 26.0 - - + -
24D VAL* 5.2 6.1 - - + -
147D LEU* 2.8 31.0 + - + +
148D ILE* 3.5 12.1 - - - +
149D ASP 3.2 0.2 - - - -
150D ILE* 1.3 75.2 - - - +
152D ASN* 1.3 63.1 + - - +
154D SER* 4.1 4.3 - - - -
155D GLY* 2.8 30.1 + - - -
156D TRP 4.4 11.2 - - - +
157D THR* 6.0 0.4 - - - -
158D ALA* 5.6 3.6 - - + +
161D MSE 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ILE* 3.1 29.7 + - - +
149D ASP* 4.2 6.6 - - - +
151D MSE 1.3 81.6 + - - +
153D THR* 1.3 66.4 + - - +
154D SER 3.5 0.2 + - - -
155D GLY* 3.9 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 4.2 24.2 - - + -
107D TRP* 4.1 15.4 - - + +
121D ARG* 3.3 22.5 + - - +
149D ASP* 2.8 22.6 + - - -
150D ILE 3.9 3.4 - - - -
152D ASN* 1.3 80.5 - - - +
154D SER* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 4.0 14.1 - - - -
150D ILE* 2.9 20.4 + - - +
151D MSE 3.8 1.6 + - - -
153D THR* 1.3 82.3 - - - +
155D GLY* 1.3 61.6 + - - +
156D TRP* 2.6 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D MSE 2.8 15.8 + - - -
152D ASN 3.9 3.8 + - - -
153D THR 3.5 1.4 - - - -
154D SER* 1.3 78.5 + - - +
156D TRP* 1.3 65.4 + - - +
157D THR* 3.6 6.6 + - - +
160D GLN* 4.6 2.1 - - - +
----------------------------------------------------------
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