Contacts of the helix formed by residues 6 - 17 (chain B) in PDB entry 2W93
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 LEU 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ILE 3.7 0.8 + - - -
5B THR* 1.3 70.9 - - - +
7B GLY* 1.3 63.2 + - - +
9B TYR* 3.2 11.5 - - + +
10B LEU* 3.1 21.7 + - - +
139B ILE* 4.9 0.7 - - + -
142B ILE* 4.0 8.3 - - + -
145B ALA* 3.6 32.3 - - + -
146B PRO* 4.2 10.1 - - + -
149B ILE* 3.6 24.6 - - + +
167B LEU* 4.4 21.7 - - + +
171B LEU* 3.4 36.3 - - + +
172B VAL* 3.4 2.4 + - - -
174B LEU 2.8 13.9 + - - +
176B VAL* 4.3 15.0 - - + -
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Residues in contact with GLY 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 1.3 76.8 - - - +
8B LYS* 1.3 60.7 + - - +
10B LEU* 3.3 12.2 + - - +
11B PHE* 3.1 19.6 - - - -
33B LEU* 3.7 23.1 - - - -
36B LYS* 3.8 13.2 - - - -
167B LEU* 5.6 0.7 - - - -
172B VAL* 2.9 23.2 + - - +
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.6 25.0 - - + +
5B THR* 3.2 21.5 + - - +
7B GLY* 1.3 71.7 - - - +
9B TYR* 1.3 61.5 + - - +
11B PHE* 3.1 4.9 + - - +
12B GLU* 2.8 50.0 + - - +
36B LYS* 3.6 16.1 - - + +
39B GLU* 3.4 45.6 + - - +
40B VAL* 3.7 12.6 - - + -
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Residues in contact with TYR 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.9 15.5 - - + +
5B THR 2.9 13.2 + - - +
6B LEU* 3.2 15.3 - - + +
8B LYS* 1.3 75.0 - - - +
10B LEU* 1.3 64.3 + - - +
12B GLU* 3.3 3.8 + - - +
13B ARG* 2.9 41.3 + - + +
146B PRO* 3.5 31.5 + - + +
149B ILE* 4.0 19.1 - - + -
150B ASP* 2.8 39.7 + - - -
176B VAL* 4.0 17.0 - - + -
180B LEU* 3.9 21.6 - - + +
181B LEU* 3.6 27.7 - - + +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU 3.1 11.9 + - - +
7B GLY* 3.4 10.3 - - - +
8B LYS 3.2 0.4 - - - -
9B TYR* 1.3 83.7 - - - +
11B PHE* 1.3 70.5 + - + +
13B ARG* 3.2 3.1 + - - +
14B LEU* 3.0 44.5 + - + +
33B LEU* 4.1 21.1 - - + -
71B ILE* 4.7 2.5 - - + -
96B LEU* 4.4 16.2 - - + -
98B VAL* 4.2 26.7 - - + -
149B ILE* 3.8 28.9 - - + -
153B ILE* 4.5 1.6 - - + -
165B LEU* 4.7 4.5 - - + -
167B LEU* 4.5 5.6 - - + -
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLY 3.1 24.0 - - - -
8B LYS* 3.1 3.1 + - - +
10B LEU* 1.3 77.6 - - + +
12B GLU* 1.3 66.0 + - - +
14B LEU* 3.2 20.5 + - + +
15B LYS* 3.0 23.4 + - - +
22B VAL* 3.9 14.6 - - + -
33B LEU* 3.3 35.9 - - + -
36B LYS* 3.8 13.2 - - + -
37B ILE* 3.3 34.8 - - + -
40B VAL* 3.8 24.0 - - + -
43B MET* 4.0 12.4 - - + +
71B ILE* 3.6 31.4 - - + -
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.7 19.0 - - + +
8B LYS* 2.8 43.0 + - + +
9B TYR 3.7 4.0 - - - +
11B PHE* 1.3 75.2 - - - +
13B ARG* 1.3 62.3 + - - +
15B LYS* 3.3 16.2 + - - +
16B GLN* 3.1 30.2 + - - +
40B VAL* 3.8 20.4 - - + +
181B LEU* 3.8 18.8 - - + -
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 2.9 34.9 + - + +
10B LEU* 3.5 9.0 - - - +
12B GLU* 1.3 74.3 - - - +
14B LEU* 1.3 65.0 + - - +
16B GLN* 2.8 45.2 + - - +
17B VAL* 3.2 17.7 + - - +
149B ILE* 4.7 0.2 - - + -
150B ASP* 2.8 43.0 + - - +
153B ILE* 3.6 19.7 - - + -
180B LEU* 3.4 13.8 + - - +
181B LEU* 3.5 21.5 + - + +
183B THR* 2.8 30.9 + - - -
184B PRO* 3.9 3.8 - - - +
185B ILE* 3.7 19.3 - - + +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.0 29.7 + - + +
11B PHE* 3.2 29.4 + - + +
13B ARG* 1.3 77.2 - - - +
15B LYS* 1.3 61.8 + - - +
17B VAL* 3.0 16.5 + - + +
19B VAL* 3.0 36.9 + - + +
22B VAL* 4.5 6.1 - - + -
43B MET* 4.9 2.5 - - + -
67B MET* 4.2 22.2 - - + -
69B CYS* 3.9 40.2 - - + -
96B LEU* 4.3 6.3 - - + -
153B ILE* 4.3 12.1 - - + -
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE 3.0 12.6 + - - +
12B GLU* 3.4 19.2 + - - +
14B LEU* 1.3 76.8 - - - +
16B GLN* 1.3 61.8 + - + +
18B ASN* 3.1 14.6 + - - -
19B VAL 3.6 10.6 + - - -
20B ASN* 4.3 16.1 + - - +
40B VAL* 3.8 15.1 - - + +
41B GLU* 3.0 39.9 + - - +
42B GLY* 4.8 4.0 - - - -
43B MET* 4.1 5.4 - - - -
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU* 3.1 17.6 + - - +
13B ARG* 2.8 41.7 + - - +
15B LYS* 1.3 76.7 - - + +
17B VAL* 1.3 62.9 + - + +
18B ASN 3.4 1.2 + - - -
181B LEU* 3.0 35.5 + - - +
184B PRO* 4.6 7.6 - - + +
185B ILE* 4.8 2.4 + - + +
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG 3.2 12.1 + - - +
14B LEU* 3.0 24.3 + - + +
16B GLN* 1.3 81.7 - - + +
18B ASN* 1.3 68.4 + - - +
19B VAL* 3.3 11.4 + - + +
65B LYS 5.2 1.4 - - - +
66B GLY* 6.1 0.2 - - - -
67B MET* 3.9 33.2 + - + +
153B ILE* 3.8 13.2 - - + -
157B TYR* 5.9 2.3 - - + -
185B ILE* 4.6 7.4 - - + -
187B MET* 3.5 31.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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