Contacts of the helix formed by residues 6 - 17 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C ILE 3.8 0.2 + - - -
5C THR* 1.3 71.8 - - - +
7C GLY* 1.3 63.5 + - - +
9C TYR* 3.3 9.3 + - + +
10C LEU* 3.1 20.8 + - - +
139C ILE* 4.8 1.6 - - + -
142C ILE* 4.0 9.2 - - + -
145C ALA* 3.6 31.0 - - + -
146C PRO* 4.3 6.1 - - + -
149C ILE* 3.5 28.3 - - + +
167C LEU* 4.5 19.0 - - + +
171C LEU* 3.5 40.6 - - + +
172C VAL* 3.4 5.8 + - + +
174C LEU 2.9 11.9 + - - +
176C VAL* 4.1 16.1 - - + +
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Residues in contact with GLY 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 1.3 77.0 - - - +
8C LYS* 1.3 61.7 + - - +
10C LEU* 3.1 13.7 + - - +
11C PHE* 3.2 17.8 - - - -
33C LEU* 3.6 25.4 - - - -
36C LYS* 3.7 13.5 - - - -
167C LEU* 5.9 0.4 - - - -
172C VAL* 2.9 19.2 + - - -
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Residues in contact with LYS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 3.6 27.2 - - + +
5C THR* 3.2 21.4 + - - +
7C GLY* 1.3 74.8 - - - +
9C TYR* 1.3 63.1 + - - +
11C PHE* 3.1 4.6 + - - +
12C GLU* 2.9 42.5 + - + +
36C LYS* 3.6 11.5 - - + +
39C GLU* 3.4 50.8 + - + +
40C VAL* 3.8 11.4 - - + -
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Residues in contact with TYR 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 4.0 12.5 - - + +
5C THR 2.9 13.8 + - - +
6C LEU* 3.3 11.2 - - + +
8C LYS* 1.3 75.5 - - - +
10C LEU* 1.3 65.0 - - - +
12C GLU* 3.3 3.8 + - - +
13C ARG* 3.0 39.5 + - + +
146C PRO* 3.6 30.9 + - + +
149C ILE* 3.9 20.4 - - + -
150C ASP* 2.7 40.4 + - - -
176C VAL* 4.0 22.0 - - + -
177C PRO 5.1 0.9 - - - -
180C LEU* 3.9 24.8 - - + +
181C LEU* 3.7 26.4 - - + +
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Residues in contact with LEU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU 3.1 10.5 + - - +
7C GLY* 3.1 12.1 + - - +
9C TYR* 1.3 81.4 - - - +
11C PHE* 1.3 72.8 + - + +
13C ARG* 3.2 5.0 + - - +
14C LEU* 2.9 45.9 + - + +
33C LEU* 4.3 12.3 - - + -
71C ILE* 4.8 1.8 - - + -
96C LEU* 4.4 16.8 - - + -
98C VAL* 4.2 17.5 - - + -
149C ILE* 3.9 27.8 - - + -
153C ILE* 4.4 1.6 - - + -
165C LEU* 4.5 7.4 - - + -
167C LEU* 4.1 22.9 - - + -
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Residues in contact with PHE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLY 3.2 22.9 + - - -
8C LYS 3.1 3.0 + - - +
10C LEU* 1.3 79.2 - - + +
12C GLU* 1.3 59.1 - - - +
14C LEU* 3.3 21.2 + - + +
15C LYS* 2.9 29.5 + - - +
22C VAL* 4.0 8.5 - - + -
33C LEU* 3.3 35.7 - - + -
36C LYS* 3.8 5.2 - - + +
37C ILE* 3.2 44.4 - - + -
40C VAL* 3.7 24.1 - - + +
43C MET* 3.7 16.3 - - + +
71C ILE* 3.5 31.9 - - + -
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 3.7 19.5 - - + +
8C LYS* 2.9 40.1 + - - +
9C TYR 3.7 2.0 - - - +
11C PHE* 1.3 77.6 - - - +
13C ARG* 1.3 60.2 + - - +
15C LYS* 3.3 12.3 + - - +
16C GLN* 3.0 31.7 + - - +
39C GLU 4.7 0.2 - - - +
40C VAL* 3.6 26.4 - - + +
41C GLU 5.4 0.2 + - - -
181C LEU* 3.7 24.0 - - + -
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C TYR* 3.0 42.0 + - + +
10C LEU* 3.5 8.1 - - - +
12C GLU* 1.3 74.4 - - - +
14C LEU* 1.3 65.6 + - - +
16C GLN* 2.8 45.3 + - - +
17C VAL* 3.2 18.1 + - - +
149C ILE* 4.6 0.2 - - + -
150C ASP* 2.9 36.9 + - - +
153C ILE* 3.6 18.8 - - + -
180C LEU* 3.3 14.7 + - - +
181C LEU* 3.6 21.1 + - + +
183C THR* 2.8 30.5 + - - -
184C PRO* 4.1 4.2 + - - +
185C ILE* 3.5 19.9 - - + +
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 2.9 25.5 + - + +
11C PHE* 3.3 31.6 + - + +
13C ARG* 1.3 76.3 - - - +
15C LYS* 1.3 61.2 + - - +
17C VAL* 3.1 11.8 + - + +
18C ASN 3.2 0.2 + - - -
19C VAL* 2.9 46.8 + - + +
22C VAL* 4.4 6.5 - - + -
43C MET* 3.8 9.2 - - + -
67C MET* 4.5 6.7 - - + -
69C CYS* 3.8 35.9 - - + -
96C LEU* 4.3 10.1 - - + -
153C ILE* 4.1 18.2 - - + -
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE 2.9 16.9 + - - +
12C GLU* 3.5 13.4 + - - +
13C ARG 3.2 0.2 - - - -
14C LEU* 1.3 75.7 - - - +
16C GLN* 1.3 64.2 + - + +
18C ASN* 3.1 14.6 + - - -
19C VAL 3.7 8.9 + - - -
20C ASN* 4.2 14.8 + - - +
40C VAL* 3.7 13.2 - - + +
41C GLU* 2.9 51.6 + - - +
43C MET* 3.8 9.4 - - - -
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Residues in contact with GLN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLU* 3.0 23.9 + - - +
13C ARG* 2.8 41.5 + - - +
15C LYS* 1.3 78.1 - - + +
17C VAL* 1.3 62.7 + - + +
18C ASN* 3.3 1.1 + - - +
181C LEU* 3.0 35.7 + - - +
184C PRO* 4.8 6.7 - - - +
185C ILE* 5.0 2.0 + - + +
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG 3.2 12.5 + - - +
14C LEU* 3.1 19.0 + - + +
16C GLN* 1.3 82.1 - - + +
18C ASN* 1.3 70.8 + - - +
19C VAL* 3.3 9.8 + - + +
65C LYS 5.7 0.2 - - - +
67C MET* 4.1 21.1 - - - +
153C ILE* 3.9 17.0 - - + -
157C TYR* 6.2 0.9 - - + -
185C ILE* 4.8 5.4 - - + -
187C MET* 3.1 41.7 - - + -
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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