Contacts of the helix formed by residues 5 - 20 (chain D) in PDB entry 2OZL
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 5 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D THR* 1.3 72.7 - - - +
6D ARG* 1.3 63.8 + - - +
8D ALA* 3.1 2.1 + - - +
9D ILE* 3.0 33.1 + - + +
147D PRO* 6.0 2.5 - - + -
148D TRP 3.9 11.4 - - - +
149D ASN 3.8 5.8 - - - +
150D SER* 3.2 30.0 + - - +
153D ALA* 3.7 21.8 - - + -
172D ASN 5.8 0.2 - - - +
175D MET* 3.3 31.9 - - + +
176D TYR* 3.5 5.5 + - + -
178D VAL 3.3 8.5 + - - +
180D PHE* 3.9 9.9 - - + -
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Residues in contact with ARG 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D THR* 3.9 5.3 + - - +
5D VAL* 1.3 78.2 - - - +
7D ASP* 1.3 73.5 + - - +
9D ILE* 3.4 6.2 + - - +
10D ASN* 3.1 20.9 + - + +
37D TYR* 2.8 30.1 + - - +
38D LYS* 3.6 28.6 - - - +
39D VAL* 4.1 12.4 - - + +
41D ARG* 4.6 9.8 - - - +
173D GLU* 5.4 4.4 + - - -
176D TYR* 3.0 62.2 + - + +
177D GLY* 3.8 12.9 - - - +
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Residues in contact with ASP 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D VAL* 3.8 15.3 - - + -
4D THR* 3.1 23.6 + - - +
6D ARG* 1.3 87.5 - - - +
8D ALA* 1.3 60.2 + - - +
10D ASN* 3.3 9.4 + - - +
11D GLN* 2.9 33.9 + - - +
41D ARG* 4.3 12.3 + - - -
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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 VAL* 3.8 6.5 - - + +
4D THR 2.9 12.8 + - - +
5D VAL 3.1 8.3 + - - +
7D ASP* 1.3 73.1 - - - +
9D ILE* 1.3 65.2 + - - +
11D GLN* 3.3 6.0 + - - +
12D GLY 3.1 18.0 + - - -
150D SER* 3.3 37.5 - - - +
153D ALA* 4.4 0.7 - - + -
154D LYS* 3.5 21.1 - - + +
182D PHE* 4.2 8.5 - - + -
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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 VAL* 3.0 23.3 + - + +
6D ARG* 3.7 5.8 - - - +
8D ALA* 1.3 76.0 - - - +
10D ASN* 1.3 63.7 + - - +
13D MET* 3.0 16.7 + - + +
39D VAL* 3.6 20.0 - - + -
115D ARG* 4.3 6.3 - - - +
147D PRO* 5.9 0.9 - - + -
153D ALA* 3.6 17.5 - - + -
157D ILE* 2.9 46.6 - - + +
171D GLU* 3.7 37.9 - - + +
176D TYR* 3.9 18.2 - - + -
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Residues in contact with ASN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ARG* 3.1 11.3 + - + +
7D ASP* 3.5 14.8 - - - +
8D ALA 3.2 0.2 - - - -
9D ILE* 1.3 77.6 - - - +
11D GLN* 1.3 59.7 + - - +
13D MET* 3.4 6.0 + - - +
14D ASP* 2.9 32.2 + - - +
38D LYS 5.1 0.4 + - - +
39D VAL 3.0 27.2 + - - +
40D SER* 3.7 4.0 - - - +
41D ARG* 3.0 32.5 + - - +
43D LEU* 4.1 13.7 - - - +
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Residues in contact with GLN 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D VAL* 3.9 30.9 - - - +
7D ASP* 2.9 16.2 + - + +
8D ALA* 3.6 8.7 - - - +
9D ILE 3.3 0.2 - - - -
10D ASN* 1.3 77.4 + - - +
12D GLY* 1.3 64.4 + - - +
14D ASP* 3.3 6.1 + - - +
15D GLU* 2.9 35.7 + - - +
154D LYS* 2.9 29.7 + - - +
182D PHE* 3.8 14.8 - - - -
187D GLN* 4.4 6.3 - - - +
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Residues in contact with GLY 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ALA 3.1 9.0 + - - -
9D ILE 3.3 0.4 + - - -
11D GLN* 1.3 80.1 - - - +
13D MET* 1.3 61.3 + - - +
15D GLU* 3.4 2.8 + - - +
16D GLU* 3.1 29.1 + - - +
154D LYS* 4.0 5.8 - - - +
157D ILE* 3.3 20.6 - - - -
158D LYS* 3.8 18.6 - - - +
161D ILE* 5.2 0.2 - - - -
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Residues in contact with MET 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 3.0 20.8 + - + +
10D ASN* 3.9 3.4 - - - +
12D GLY* 1.3 72.2 - - - +
14D ASP* 1.3 66.3 + - - +
16D GLU* 3.3 1.9 + - - +
17D LEU* 3.0 33.4 + - + +
23D VAL* 5.6 0.2 - - - +
25D LEU* 4.3 17.9 - - + -
39D VAL* 4.1 31.6 - - + +
40D SER* 4.4 2.9 - - - -
43D LEU* 3.9 24.0 - - + -
77D ILE* 4.2 26.0 - - + -
115D ARG* 4.1 27.6 - - - +
157D ILE* 3.6 9.1 - - + +
161D ILE* 4.6 11.4 - - + +
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Residues in contact with ASP 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASN* 2.9 22.9 + - - +
11D GLN* 3.6 8.0 - - - +
13D MET* 1.3 77.0 - - - +
15D GLU* 1.3 63.7 + - + +
17D LEU* 3.4 3.9 + - - +
18D GLU* 3.1 9.4 + - - +
43D LEU* 4.0 21.8 - - + +
46D LYS* 2.8 26.5 + - - +
47D TYR* 2.7 42.3 + - - -
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Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLN* 2.9 25.6 + - - +
12D GLY 3.8 0.9 - - - +
14D ASP* 1.3 79.1 - - + +
16D GLU* 1.3 59.6 + - - +
18D GLU* 3.3 10.2 + - - +
19D ARG* 3.0 28.5 + - - +
154D LYS* 2.9 35.7 + - - -
158D LYS* 2.8 31.5 + - - +
187D GLN 3.8 5.7 - - - +
189D LYS* 3.4 28.3 + - + +
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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
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12D GLY 3.1 17.4 + - - +
13D MET 4.0 1.6 - - - +
15D GLU* 1.3 74.5 - - - +
17D LEU* 1.3 65.2 + - - +
19D ARG* 3.3 15.3 + - - +
20D ASP* 3.0 26.7 + - - +
23D VAL* 4.0 6.8 - - + +
158D LYS* 2.7 45.9 + - + +
161D ILE* 3.8 39.3 - - + +
162D ARG* 3.0 41.4 + - - +
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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
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13D MET* 3.0 33.4 + - + +
14D ASP* 3.6 4.9 - - - +
16D GLU* 1.3 77.3 - - - +
18D GLU* 1.3 63.3 + - - +
20D ASP 3.3 8.5 + - - +
21D GLU* 4.4 0.7 + - - -
23D VAL* 3.6 37.4 - - + +
24D PHE* 4.0 10.3 - - - -
25D LEU* 4.7 2.0 - - + +
43D LEU* 4.2 11.4 - - + -
47D TYR* 3.7 34.5 - - + -
51D ARG* 2.9 35.5 + - + +
52D ILE* 4.0 22.4 - - + -
77D ILE* 5.4 3.1 - - + -
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ASP* 3.1 11.7 + - - +
15D GLU* 3.6 8.5 - - - +
17D LEU* 1.3 78.9 - - - +
19D ARG* 1.3 60.2 + - - +
20D ASP* 4.9 0.3 - - - -
21D GLU 5.4 0.5 + - - -
46D LYS* 3.5 24.3 + - - -
47D TYR* 3.4 17.4 + - + +
189D LYS* 5.6 5.4 - - - +
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Residues in contact with ARG 19 (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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15D GLU 3.0 16.7 + - - +
16D GLU* 3.7 20.1 + - - +
17D LEU 3.2 0.2 - - - -
18D GLU* 1.3 78.6 - - - +
20D ASP* 1.3 71.1 + - - +
21D GLU 4.2 0.6 + - - -
162D ARG* 3.5 54.1 - - - +
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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* 3.0 6.3 + - - +
17D LEU 3.3 4.7 - - - +
19D ARG* 1.3 94.4 + - - +
21D GLU* 1.3 65.9 + - - +
22D LYS* 2.9 32.4 + - - +
23D VAL* 3.1 26.5 + - + +
51D ARG* 3.1 10.2 + - - -
75D ARG* 3.2 27.0 + - - -
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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