Contacts of the helix formed by residues 118 - 142 (chain D) in PDB entry 3H90
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 VAL 118 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 2.8 15.5 + - + +
117D GLY* 1.3 67.9 - - - -
119D ILE* 1.3 66.0 + - + +
120D VAL* 3.1 6.9 + - - -
121D THR* 3.3 31.7 + - + +
122D ILE* 3.3 23.2 + - + +
162D GLY* 5.1 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D GLY* 3.0 28.7 - - - +
118D VAL* 1.3 80.9 - - + +
120D VAL* 1.3 68.9 + - + +
122D ILE* 3.2 28.4 - - + +
123D VAL* 3.2 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ALA 3.4 25.8 - - - +
31D TRP* 4.6 9.0 - - - -
32D TRP* 5.3 2.5 - - + +
40D LEU* 6.0 4.3 - - + -
117D GLY 3.5 17.7 - - - +
118D VAL* 4.4 1.1 - - - -
119D ILE* 1.3 84.6 - - + +
121D THR* 1.3 71.1 + - + +
123D VAL* 3.0 7.9 + - - +
124D ALA* 2.6 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 5.4 11.7 - - + -
42D ALA* 6.0 3.4 - - + -
118D VAL* 3.3 28.0 + - + +
120D VAL* 1.3 88.7 - - + +
122D ILE* 1.3 61.5 + - - +
124D ALA* 3.8 9.2 - - - +
125D LEU* 3.0 26.9 + - - +
160D MET* 4.0 29.8 - - + +
161D ASN 5.5 0.7 - - - -
162D GLY* 4.9 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D VAL* 3.3 21.7 + - + +
119D ILE* 3.2 36.1 - - + +
121D THR* 1.3 80.0 + - - +
123D VAL* 1.3 67.1 + - + +
125D LEU* 3.7 8.6 - - + +
126D ILE* 3.3 27.5 + - - +
162D GLY* 6.0 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 5.6 2.0 - - + -
30D ALA* 4.9 16.8 - - + -
119D ILE* 3.2 15.6 + - + +
120D VAL* 3.0 10.2 + - - +
122D ILE* 1.3 77.0 - - + +
124D ALA* 1.3 66.4 + - - +
126D ILE* 3.1 7.9 + - - +
127D CYS* 3.0 44.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
27D LYS* 3.8 38.8 - - + +
120D VAL 2.6 21.6 + - - +
121D THR* 3.8 12.1 - - - +
123D VAL* 1.3 72.9 - - - +
125D LEU* 1.3 61.0 + - - +
127D CYS* 3.5 1.3 + - - +
128D THR* 2.7 33.2 + - - +
160D MET* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D THR 3.0 19.0 + - - +
122D ILE* 3.7 10.5 - - + +
123D VAL 3.2 0.2 - - - -
124D ALA* 1.3 75.1 - - - +
126D ILE* 1.3 60.1 + - + +
128D THR* 3.7 4.1 - - - -
129D ILE* 2.8 57.2 + - + +
157D ASP 5.8 0.2 - - - -
158D VAL* 3.3 28.4 - - - +
160D MET* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ILE 3.3 14.6 + - - +
123D VAL* 3.1 9.7 + - - +
125D LEU* 1.3 84.3 - - + +
127D CYS* 1.3 68.9 + - - +
129D ILE* 3.1 11.1 + - + +
130D ILE* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 4.0 27.9 - - + +
26D ILE* 5.1 13.5 - - - -
27D LYS* 5.0 9.0 - - + -
123D VAL* 3.0 40.4 + - - +
124D ALA* 3.9 5.4 - - - +
126D ILE* 1.3 79.8 - - - +
128D THR* 1.3 58.1 + - - +
130D ILE* 3.4 11.6 - - - +
131D LEU* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 5.6 1.1 - - - -
24D LEU* 4.5 7.4 - - + +
27D LYS* 4.5 10.9 + - - +
124D ALA* 2.7 24.7 + - - +
125D LEU* 3.7 3.6 - - - -
127D CYS* 1.3 73.6 - - - +
129D ILE* 1.3 61.1 + - - +
131D LEU* 3.3 7.1 + - + +
132D VAL* 2.8 30.7 + - - +
154D TYR* 3.6 34.5 - - + +
157D ASP* 4.1 15.9 - - + +
158D VAL* 3.6 19.3 - - + +
160D MET* 6.0 0.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
125D LEU* 2.8 52.5 + - + +
126D ILE* 3.4 13.2 - - + +
128D THR* 1.3 71.2 - - - +
130D ILE* 1.3 65.8 + - + +
132D VAL* 3.5 4.5 + - - +
133D SER* 3.1 31.8 + - - +
158D VAL* 3.6 31.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
23D LEU* 5.0 9.2 - - + -
126D ILE* 2.9 33.6 + - + +
127D CYS* 3.4 13.0 - - - +
129D ILE* 1.3 77.8 - - + +
131D LEU* 1.3 67.3 + - - +
133D SER* 2.9 18.1 + - - -
134D PHE* 3.1 13.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ALA* 3.3 39.3 - - + +
21D SER* 3.8 10.3 - - - +
23D LEU* 4.4 13.0 - - + -
24D LEU* 5.2 7.4 - - + -
127D CYS 3.0 14.8 + - - +
128D THR* 3.3 10.5 + - + +
130D ILE* 1.3 77.1 - - - +
132D VAL* 1.3 64.4 + - - +
134D PHE* 2.9 9.0 + - + +
135D GLN* 2.9 45.2 + - + +
154D TYR* 3.7 45.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D THR 2.8 22.0 + - - +
129D ILE* 3.7 7.0 - - - +
131D LEU* 1.3 72.3 - - - +
133D SER* 1.3 53.8 + - - +
135D GLN* 3.7 10.8 - - - +
136D ARG* 2.7 41.1 + - + +
151D MET* 3.9 8.1 - - + +
154D TYR* 3.6 44.2 - - + +
155D GLN* 3.8 22.9 - - + +
158D VAL* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ILE* 3.1 19.1 + - - +
130D ILE* 2.9 13.1 + - - -
132D VAL* 1.3 76.8 - - - +
134D PHE* 1.3 59.1 + - - +
136D ARG* 3.3 10.2 + - - +
137D TRP* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ALA* 4.3 16.4 - - + -
17D THR* 3.9 17.5 - - - -
20D ALA* 3.5 34.1 - - + -
130D ILE* 3.1 10.6 + - + +
131D LEU* 2.9 11.7 + - + +
133D SER* 1.3 75.6 - - - +
135D GLN* 1.3 59.9 + - - +
137D TRP* 2.9 39.1 + + + +
138D VAL* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D THR* 3.2 26.4 + - + +
21D SER* 3.0 25.5 + - - -
131D LEU* 2.9 27.5 + - + +
132D VAL* 3.7 15.3 - - - +
134D PHE* 1.3 76.9 - - + +
136D ARG* 1.3 51.7 - - - +
138D VAL* 3.0 5.2 + - - +
139D VAL* 2.7 40.4 + - + +
147D VAL* 4.5 5.8 + - + +
150D ASP* 3.9 10.3 + - - +
151D MET* 3.3 39.9 - - + +
154D TYR* 3.7 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D VAL* 2.7 29.5 + - + +
133D SER* 3.5 9.9 - - - +
135D GLN* 1.3 72.8 - - - +
137D TRP* 1.3 60.1 + - - +
139D VAL* 4.0 4.4 - - + +
140D ARG* 3.2 55.0 + - - +
151D MET* 3.6 20.1 - - + -
155D GLN* 5.5 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 5.9 6.3 - - + -
13D ALA* 5.5 8.3 - - + -
133D SER 2.8 13.8 + - - +
134D PHE* 2.9 41.5 + + + +
136D ARG* 1.3 76.3 - - - +
138D VAL* 1.3 72.8 + - + +
140D ARG* 3.4 16.8 + - + +
141D ARG* 3.0 69.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA* 3.3 31.0 - - + +
14D ILE* 4.0 5.4 - - + -
17D THR* 3.5 26.5 - - + -
134D PHE* 2.8 38.5 + - + +
135D GLN 3.6 5.8 - - - +
137D TRP* 1.3 83.5 - - + +
139D VAL* 1.3 54.1 + - - +
141D ARG* 3.2 4.7 + - - -
142D THR* 2.8 56.7 + - + +
147D VAL* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLN 2.7 27.6 + - - +
136D ARG* 4.0 6.7 - - + +
138D VAL* 1.3 73.3 - - - +
140D ARG* 1.3 59.7 + - - +
141D ARG 3.3 0.2 + - - -
142D THR 3.2 16.2 - - - +
143D GLN* 3.0 30.0 - - - +
144D SER 4.9 2.7 - - - +
147D VAL* 3.5 24.5 - - + -
148D ARG* 3.9 40.4 - - + -
151D MET* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ARG* 3.2 71.4 + - - +
137D TRP* 3.8 16.5 - - + +
138D VAL 3.3 0.4 - - - -
139D VAL* 1.3 79.7 - - - +
141D ARG* 1.3 58.6 + - - +
143D GLN* 4.3 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 4.0 33.7 - - - +
9D VAL* 4.6 9.0 + - - +
13D ALA* 5.7 5.6 - - + -
137D TRP* 3.0 59.9 + - + +
138D VAL* 3.6 7.0 - - - +
139D VAL 3.2 0.4 - - - -
140D ARG* 1.3 78.1 - - - +
142D THR* 1.3 64.5 + - + +
143D GLN* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D SER 5.6 1.1 - - - -
11D ARG* 2.8 39.8 + - + +
13D ALA* 4.1 15.5 - - + -
14D ILE* 3.6 11.5 - - + +
138D VAL* 2.8 49.3 + - + +
139D VAL* 3.2 9.4 - - - +
141D ARG* 1.3 80.7 - - + +
143D GLN* 1.3 54.8 + - - +
144D SER* 2.7 17.0 + - - -
----------------------------------------------------------
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