Contacts of the helix formed by residues 6 - 17 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ILE 3.7 0.4 + - - -
5A THR* 1.3 72.2 - - - +
7A GLY* 1.3 63.3 + - - +
9A TYR* 3.3 9.3 + - + +
10A LEU* 3.0 22.2 + - - +
139A ILE* 4.6 1.6 - - + -
142A ILE* 3.9 13.7 - - + -
145A ALA* 3.6 31.4 - - + -
146A PRO* 4.2 9.0 - - + -
149A ILE* 3.5 27.5 - - + +
167A LEU* 4.3 21.9 - - + +
171A LEU* 3.6 36.6 - - + +
172A VAL* 3.5 3.5 + - + +
174A LEU 2.9 9.5 + - - -
176A VAL* 4.2 13.4 - - + +
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Residues in contact with GLY 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 1.3 77.3 - - - +
8A LYS* 1.3 62.9 + - - +
10A LEU* 3.2 11.3 + - - +
11A PHE* 3.2 19.4 - - - -
33A LEU* 3.6 24.9 - - - -
36A LYS* 3.7 11.9 - - - -
167A LEU* 5.9 0.9 - - - -
172A VAL* 2.9 21.2 + - - +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.5 26.3 - - + +
5A THR* 3.0 20.2 + - - +
7A GLY* 1.3 75.2 - - - +
9A TYR* 1.3 58.3 + - - +
11A PHE* 3.1 4.3 + - - +
12A GLU* 2.8 50.2 + - - +
36A LYS* 3.6 9.0 - - + +
39A GLU* 3.5 50.2 + - + +
40A VAL* 3.7 12.3 - - + -
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Residues in contact with TYR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.8 12.2 - - + +
5A THR 2.9 12.2 + - - +
6A LEU* 3.3 14.1 - - + +
8A LYS* 1.3 75.4 - - - +
10A LEU* 1.3 66.2 + - - +
12A GLU* 3.2 4.7 + - - +
13A ARG* 3.0 40.4 + - + +
146A PRO* 3.6 30.7 + - + +
149A ILE* 3.9 20.4 - - + -
150A ASP* 2.7 39.7 + - - -
176A VAL* 4.0 20.4 - - + -
177A PRO 5.0 0.7 - - - -
180A LEU* 3.9 24.4 - - + +
181A LEU* 3.6 25.7 - - + +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU 3.0 12.9 + - - +
7A GLY* 3.4 10.5 - - - +
8A LYS 3.2 0.2 - - - -
9A TYR* 1.3 82.3 - - - +
11A PHE* 1.3 79.7 + - + +
13A ARG* 3.3 2.4 + - - +
14A LEU* 3.0 45.0 + - + +
33A LEU* 4.3 15.7 - - + -
69A CYS* 5.3 0.2 - - - -
71A ILE* 4.8 2.0 - - + -
96A LEU* 4.5 11.0 - - + -
98A VAL* 4.4 13.9 - - + -
149A ILE* 4.0 29.2 - - + -
153A ILE* 4.5 1.8 - - + -
165A LEU* 4.5 13.2 - - + -
167A LEU* 4.3 14.8 - - + -
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Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY 3.2 23.5 + - - -
8A LYS 3.1 3.4 + - - +
10A LEU* 1.3 82.2 - - + +
12A GLU* 1.3 66.7 + - - +
14A LEU* 3.8 17.6 - - + +
15A LYS* 3.0 24.4 + - - +
22A VAL* 4.0 14.6 - - + -
33A LEU* 3.2 35.4 - - + -
36A LYS* 3.7 12.8 - - + +
37A ILE* 3.4 34.1 - - + -
40A VAL* 3.9 21.9 - - + +
43A MET* 4.1 11.7 - - + +
71A ILE* 3.5 32.1 - - + -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.9 8.4 - - + +
8A LYS* 2.8 44.4 + - - +
9A TYR 3.7 1.8 - - - +
11A PHE* 1.3 77.8 - - - +
13A ARG* 1.3 61.2 + - - +
15A LYS* 3.4 14.4 + - - +
16A GLN* 3.0 29.8 + - - +
39A GLU 4.9 0.5 - - - +
40A VAL* 3.6 22.2 - - + +
181A LEU* 3.6 33.9 - - + -
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.0 39.8 + - + +
10A LEU* 3.6 7.4 - - - +
12A GLU* 1.3 74.5 - - - +
14A LEU* 1.3 65.5 + - - +
16A GLN* 2.9 35.1 + - - +
17A VAL* 3.1 18.8 + - - +
149A ILE* 4.7 0.4 - - + -
150A ASP* 2.9 36.7 + - - +
153A ILE* 3.7 19.1 - - + -
180A LEU* 3.3 14.4 + - - +
181A LEU* 3.5 23.7 + - + +
183A THR* 2.8 31.1 + - - -
184A PRO 4.5 0.4 - - - -
185A ILE* 3.5 21.9 - - + +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.0 32.8 + - + +
11A PHE* 3.3 26.0 + - + +
13A ARG* 1.3 75.7 - - - +
15A LYS* 1.3 64.4 + - - +
17A VAL* 3.1 7.2 + - + +
18A ASN 3.1 5.2 + - - -
19A VAL* 2.9 55.0 + - + +
22A VAL* 4.6 6.1 - - + -
43A MET* 4.2 3.1 - - + -
67A MET* 4.3 12.3 - - + -
69A CYS* 3.9 33.7 - - + -
96A LEU* 4.4 6.1 - - + -
153A ILE* 4.2 16.4 - - + -
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE 3.0 13.6 + - - +
12A GLU* 3.4 17.8 + - - +
14A LEU* 1.3 77.1 - - - +
16A GLN* 1.3 63.9 + - + +
18A ASN* 3.0 14.9 + - - -
19A VAL 3.7 9.3 + - - -
20A ASN* 4.3 15.6 + - - +
40A VAL* 3.7 14.1 - - + +
41A GLU* 2.8 46.5 + - - +
42A GLY* 5.0 2.5 - - - -
43A MET* 3.9 7.4 - - + -
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Residues in contact with GLN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU* 3.0 20.5 + - - +
13A ARG* 2.9 41.7 + - - +
15A LYS* 1.3 77.6 - - + +
17A VAL* 1.3 61.7 + - + +
18A ASN 3.3 0.7 - - - -
181A LEU* 2.9 36.7 + - - +
184A PRO* 4.7 7.0 - - + +
185A ILE* 4.8 1.7 + - - +
604A PY0 3.3 19.4 + - - +
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG 3.1 15.3 + - - +
14A LEU* 3.1 17.6 + - + +
16A GLN* 1.3 82.6 - - + +
18A ASN* 1.3 68.3 + - - +
19A VAL* 3.4 8.3 + - + +
67A MET* 4.1 18.4 - - - +
153A ILE* 3.9 21.5 - - + -
185A ILE* 4.5 11.2 - - + +
187A MET* 3.8 32.8 - - + -
604A PY0 3.7 23.9 + - - +
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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