Contacts of the helix formed by residues 4 - 20 (chain D) in PDB entry 3DVA
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 THR 4 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D MET* 1.3 78.3 - - - +
5D MET* 1.3 63.5 + - - +
6D VAL* 3.5 7.1 - - - +
7D GLN* 3.1 35.4 + - - +
8D ALA 3.1 16.3 + - - -
150D PRO* 3.6 6.7 - - - +
176D TYR 3.4 11.2 - - - -
177D ARG* 4.1 19.0 - - + +
179D PHE 3.6 14.1 - - - +
180D ARG* 3.5 29.6 - - + +
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Residues in contact with MET 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D THR* 1.3 75.4 - - - +
6D VAL* 1.3 61.8 + - - +
8D ALA* 3.4 2.4 + - - +
9D ILE* 3.1 33.6 + - + +
147D PRO* 4.1 22.0 - - + +
148D SER 4.3 2.9 - - - +
149D THR 3.9 17.7 - - - +
150D PRO* 3.6 18.1 - - + +
153D ALA* 3.6 24.0 - - + -
171D GLU* 4.7 4.5 - - - -
172D HIS 3.8 24.7 - - - +
175D LEU* 3.4 44.5 + - + +
176D TYR* 3.0 18.2 + - + +
179D PHE* 4.5 1.6 + - + -
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Residues in contact with VAL 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D THR* 3.5 12.3 - - - +
5D MET* 1.3 74.4 - - - +
7D GLN* 1.3 67.0 + - + +
9D ILE* 3.3 5.2 + - - +
10D THR* 2.9 34.3 + - - +
37D PHE 3.5 24.5 - - - +
38D ARG* 4.2 3.8 - - + +
39D ALA* 3.7 25.4 - - + +
176D TYR* 3.1 37.6 + - + +
177D ARG* 3.8 19.7 - - + -
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Residues in contact with GLN 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D GLN 4.2 4.2 - - - +
3D MET* 3.6 17.5 - - + +
4D THR* 3.1 42.8 + - - +
5D MET 3.3 0.4 - - - -
6D VAL* 1.3 83.3 - - + +
8D ALA* 1.3 56.4 + - - +
10D THR* 3.4 7.0 + - - -
11D ASP* 2.9 30.4 + - - +
14D ARG* 5.4 0.3 + - - -
180D ARG* 4.7 5.9 + - - +
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Residues in contact with ALA 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D MET* 3.9 19.5 - - - -
4D THR 3.1 16.6 + - - +
5D MET 3.8 4.5 - - - +
7D GLN* 1.3 75.6 - - - +
9D ILE* 1.3 60.1 + - - +
11D ASP* 3.7 2.1 - - - +
12D ALA* 3.0 27.7 + - - +
150D PRO* 3.2 31.9 - - + +
154D LYS* 3.5 17.5 - - + +
183D VAL* 4.6 2.0 - - + -
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Residues in contact with ILE 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D MET* 3.1 27.4 + - + +
6D VAL* 3.5 7.4 - - - +
7D GLN 3.2 0.2 - - - -
8D ALA* 1.3 75.0 - - - +
10D THR* 1.3 60.8 + - - +
12D ALA* 3.1 4.0 + - - +
13D LEU* 2.9 35.1 + - + +
39D ALA* 4.7 5.2 - - + -
115D ARG* 4.0 12.1 - - - +
147D PRO* 5.7 0.2 - - + -
153D ALA* 3.9 15.5 - - + -
154D LYS* 5.2 0.9 - - - +
157D LEU* 3.5 21.1 - - + -
169D PHE* 4.2 8.7 - - + -
171D GLU* 3.5 41.5 - - + +
176D TYR* 4.1 14.1 - - + -
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Residues in contact with THR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D VAL* 2.9 19.1 + - - +
7D GLN* 3.7 7.2 - - - -
9D ILE* 1.3 76.6 - - - +
11D ASP* 1.3 56.4 + - - +
13D LEU* 3.4 5.5 + - - +
14D ARG* 3.0 42.5 + - - +
38D ARG 3.7 5.2 + - - +
39D ALA* 2.8 34.4 + - - +
41D GLU* 4.0 22.4 - - + +
43D LEU* 4.2 7.9 - - + +
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Residues in contact with ASP 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D MET* 3.9 16.2 - - - +
7D GLN 2.9 17.7 + - - +
8D ALA* 3.7 8.3 - - - +
9D ILE 3.2 0.2 - - - -
10D THR* 1.3 76.4 - - - +
12D ALA* 1.3 57.7 + - - +
14D ARG* 3.3 31.0 + - - +
15D ILE* 3.0 40.6 + - - +
154D LYS* 2.7 35.9 + - - +
185D GLU* 5.1 0.6 - - - -
186D GLY 4.9 2.4 + - - -
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Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ALA 3.0 18.6 + - - +
9D ILE 3.4 4.7 - - - +
11D ASP* 1.3 79.0 + - - +
13D LEU* 1.3 61.9 + - - +
15D ILE* 3.3 8.0 + - - +
16D GLU* 3.1 27.1 + - - +
154D LYS* 3.7 28.0 - - + +
157D LEU* 4.0 17.3 - - + -
158D ILE* 3.8 14.2 - - + +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 2.9 23.7 + - + +
10D THR 3.7 3.8 - - - +
12D ALA* 1.3 73.2 - - - +
14D ARG* 1.3 60.4 + - - +
16D GLU* 3.3 4.3 + - - +
17D LEU* 3.0 35.9 + - - +
23D VAL* 5.4 0.4 - - + +
25D ILE* 4.0 17.4 - - + +
39D ALA 3.8 22.7 - - - +
40D THR* 4.2 10.8 - - + -
43D LEU* 3.8 18.2 - - + -
77D VAL* 4.2 5.2 - - + -
115D ARG* 4.1 25.6 - - - +
157D LEU* 3.8 12.3 - - + -
161D ILE* 3.7 25.4 - - + -
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Residues in contact with ARG 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLN 5.4 0.2 + - - -
10D THR* 3.0 27.9 + - - +
11D ASP* 3.4 38.6 + - - +
13D LEU* 1.3 78.0 - - - +
15D ILE* 1.3 64.8 + - + +
17D LEU 3.4 0.3 + - - -
18D LYS* 3.0 24.6 + - + +
41D GLU 5.3 2.8 + - - -
42D GLY 6.1 1.0 - - - -
43D LEU* 3.9 18.2 - - + +
46D GLU* 3.3 34.2 + - - +
47D PHE* 3.6 9.0 - - + -
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASP* 3.0 36.8 + - - +
12D ALA* 3.5 10.8 - - - +
13D LEU 3.2 0.2 - - - -
14D ARG* 1.3 81.8 - - + +
16D GLU* 1.3 68.6 + - - +
18D LYS* 3.7 5.1 - - + +
19D ASN* 2.9 31.1 + - + +
154D LYS* 4.7 3.8 - - - -
158D ILE* 4.3 7.4 - - + -
162D ARG* 5.3 0.4 - - - +
186D GLY* 4.4 20.4 - - - +
187D GLU* 3.5 29.2 - - + +
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Residues in contact with GLU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA 3.1 16.0 + - - +
13D LEU 3.9 2.7 - - - +
15D ILE* 1.3 82.0 - - - +
17D LEU* 1.3 60.7 + - - +
19D ASN* 4.4 8.9 - - - +
20D ASP* 2.9 35.3 + - - +
23D VAL* 3.7 13.3 - - + +
75D ARG* 5.3 1.2 - - - -
158D ILE* 3.4 30.1 - - - +
161D ILE* 3.6 45.3 - - + +
162D ARG* 3.6 33.0 + - - +
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU 3.0 20.2 + - - +
16D GLU* 1.3 77.3 - - - +
18D LYS* 1.3 62.6 + - - +
20D ASP 3.7 4.2 - - - +
21D PRO* 4.4 0.5 - - - +
23D VAL* 3.5 34.3 - - + +
25D ILE* 3.7 28.0 - - + -
43D LEU* 4.1 12.1 - - + -
47D PHE* 3.5 41.0 - - + -
51D ARG* 3.1 47.1 + - + +
52D VAL* 4.1 10.5 - - + -
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Residues in contact with LYS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG* 3.0 20.0 + - + +
15D ILE* 3.7 5.8 - - + +
17D LEU* 1.3 81.2 - - - +
19D ASN* 1.3 64.6 + - - +
20D ASP* 4.6 1.0 - - - -
21D PRO* 5.0 2.4 - - - +
46D GLU* 5.1 6.9 + - - +
47D PHE* 3.5 19.5 - - + -
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Residues in contact with ASN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 2.9 23.8 + - + +
16D GLU* 4.0 12.1 - - - +
18D LYS* 1.3 81.0 - - - +
20D ASP* 1.3 65.0 + - - +
21D PRO* 3.7 6.5 - - - +
162D ARG* 4.1 22.7 + - - +
187D GLU* 6.2 0.8 - - - +
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Residues in contact with ASP 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLU* 2.9 24.9 + - - +
17D LEU 4.0 1.8 - - - -
19D ASN* 1.3 83.4 - - - +
21D PRO* 1.3 64.0 - - - +
22D ASN* 2.8 31.6 + - - +
23D VAL* 3.0 25.9 + - + +
51D ARG* 3.1 10.4 + - - -
75D ARG* 3.2 29.8 + - - -
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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) + - + + + + + -
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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