Contacts of the helix formed by residues 4 - 19 (chain A) in PDB entry 2WH6
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 SER 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA 3.7 2.2 + - - -
3A TYR* 1.3 76.1 - - - +
5A THR* 1.3 60.6 + - - +
6A ARG* 3.5 10.8 + - - +
7A GLU* 3.0 36.3 + - - +
8A ILE* 3.0 26.2 + - - +
36A THR* 5.2 0.9 - - - +
141A ASP* 3.9 17.7 - - - -
150A TRP* 4.5 1.3 - - - -
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Residues in contact with THR 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 1.3 68.3 - - - +
6A ARG* 1.3 61.4 + - - +
8A ILE* 3.2 2.0 + - - +
9A LEU* 2.8 29.9 + - - +
105A MET* 3.9 13.7 - - + -
137A SER* 3.4 35.2 - - - +
138A GLU 4.9 0.2 - - - -
140A LEU* 3.7 15.4 - - + +
141A ASP* 2.8 26.7 + - - -
144A ILE* 4.3 0.7 - - - +
150A TRP* 3.0 41.4 + - + +
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Residues in contact with ARG 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.2 9.1 + - - +
5A THR* 1.3 79.1 - - - +
7A GLU* 1.3 56.3 + - - +
9A LEU* 4.8 0.7 - - - -
10A LEU* 2.9 31.5 + - - +
35A GLU 5.0 0.4 + - - -
36A THR* 3.7 39.3 + - + +
134A LEU* 3.7 36.5 - - + +
135A GLU* 5.3 0.8 - - - +
137A SER* 5.0 3.3 + - - -
138A GLU* 3.2 34.3 + - + +
141A ASP* 4.7 0.4 + - - -
1168A GOL 2.5 58.2 + - - +
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA 4.3 2.8 - - - +
3A TYR* 3.6 19.8 - - + -
4A SER* 3.0 41.0 + - - +
6A ARG* 1.3 76.1 - - - +
8A ILE* 1.3 58.9 + - - +
10A LEU* 3.3 1.0 + - - -
11A ALA* 2.9 27.2 + - - +
36A THR* 4.2 9.6 - - + -
37A PRO 4.1 15.3 - - - +
38A LEU* 3.4 22.1 - - + +
39A ARG* 2.9 39.7 + - - +
40A LEU* 3.9 6.2 + - + -
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Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 5.3 2.5 - - + -
4A SER 3.0 11.1 + - - +
5A THR 3.4 8.5 - - - +
7A GLU* 1.3 77.2 - - - +
9A LEU* 1.3 66.8 + - - +
11A ALA* 3.3 1.0 + - - +
12A LEU* 2.9 34.8 + - + +
40A LEU* 3.9 20.6 - - + +
46A VAL* 4.3 11.9 - - + +
47A VAL* 4.6 4.0 - - + -
50A TYR* 3.5 40.4 - - + -
105A MET* 3.8 13.7 - - + -
150A TRP* 3.7 42.8 - - + +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR 2.8 21.7 + - - +
6A ARG* 4.8 0.2 - - - -
8A ILE* 1.3 74.7 - - - +
10A LEU* 1.3 58.3 + - - +
12A LEU* 3.2 9.2 + - + +
13A CYS* 2.9 42.3 + - - -
105A MET* 3.9 43.3 - - + +
108A CYS* 3.9 22.7 - - + -
109A MET* 4.4 4.3 - - + +
133A MET* 4.0 13.5 - - + +
134A LEU* 4.0 17.9 - - + -
137A SER* 3.4 25.6 - - - +
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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
----------------------------------------------------------
6A ARG 2.9 18.3 + - - +
7A GLU 3.9 3.1 - - - +
9A LEU* 1.3 76.6 - - - +
11A ALA* 1.3 64.1 + - - +
13A CYS* 3.2 3.9 + - + +
14A ILE* 2.9 46.1 + - + +
29A LEU* 3.8 25.4 - - + +
32A ALA* 3.6 44.9 - - + +
33A ALA* 3.7 9.6 - - - +
36A THR* 3.7 12.1 - - + +
38A LEU* 4.1 14.1 - - + -
130A VAL* 5.1 0.2 - - + -
134A LEU* 3.8 16.5 - - + +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU 2.9 18.1 + - - +
8A ILE 3.7 3.6 - - - +
10A LEU* 1.3 74.9 - - - +
12A LEU* 1.3 57.9 + - - +
14A ILE* 3.3 8.7 + - - +
15A ARG* 2.9 31.2 + - - +
38A LEU* 4.2 5.1 - - + +
40A LEU* 4.0 22.0 - - + +
42A PRO* 3.7 9.2 - - + +
47A VAL* 3.7 27.1 - - + -
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 2.9 36.4 + - + +
9A LEU* 3.5 11.7 - - + +
11A ALA* 1.3 76.8 - - - +
13A CYS* 1.3 56.6 + - - +
15A ARG* 3.5 1.8 + - - +
16A ASP* 2.8 30.8 + - - +
47A VAL* 3.5 20.9 - - + +
50A TYR* 3.8 12.6 - - + -
51A HIS* 3.4 40.2 - - + +
54A LEU* 3.7 24.2 - - + -
105A MET* 4.2 13.5 - - + -
109A MET* 3.9 14.0 - - + +
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Residues in contact with CYS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 2.9 31.7 + - - +
10A LEU* 3.2 6.9 + - - +
12A LEU* 1.3 76.9 - - - +
14A ILE* 1.3 59.7 + - - +
16A ASP* 3.4 6.6 + - - +
17A SER* 3.0 30.3 + - - -
29A LEU* 4.2 11.6 - - + +
109A MET* 4.1 18.8 - - - -
112A CYS* 3.7 40.0 - - - -
130A VAL* 6.2 1.3 - - - -
133A MET* 4.3 9.6 - - - -
134A LEU* 5.9 1.1 - - - -
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 2.9 39.6 + - + +
11A ALA* 3.7 4.0 - - - +
13A CYS* 1.3 73.7 - - - +
15A ARG* 1.3 66.6 + - - +
17A SER* 3.1 4.0 + - - -
18A ARG* 2.8 29.8 + - + +
25A LEU* 3.7 30.1 - - + -
29A LEU* 4.2 25.4 - - + +
33A ALA* 4.5 5.2 - - + -
38A LEU* 3.7 28.9 - - + -
42A PRO* 3.8 22.0 - - + -
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 2.9 20.1 + - - +
12A LEU* 3.8 4.0 - - - +
14A ILE* 1.3 72.7 - - - +
16A ASP* 1.3 65.0 + - - +
18A ARG* 2.9 24.3 + - - +
19A VAL* 3.1 40.9 + - - +
42A PRO* 3.5 28.9 - - - +
43A GLU* 3.3 33.1 + - - +
47A VAL* 4.0 8.1 - - + -
48A LEU* 3.3 27.0 - - + +
51A HIS* 4.3 21.4 + - + +
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Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU 2.8 22.9 + - - +
13A CYS* 3.7 5.2 - - - +
14A ILE 3.2 0.2 - - - -
15A ARG* 1.3 73.0 - - - +
17A SER* 1.3 61.5 + - - +
19A VAL* 3.3 2.8 + - - -
20A HIS* 2.8 37.3 + - - -
51A HIS* 2.6 32.0 + - + +
109A MET* 4.0 15.4 - - + +
113A ARG* 2.8 58.4 + - - +
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A CYS 3.0 16.0 + - - -
14A ILE 3.1 8.3 + - - -
16A ASP* 1.3 72.7 - - - +
18A ARG* 1.3 57.4 + - - +
19A VAL 3.0 5.4 - - - -
20A HIS* 3.0 28.4 - - - +
23A GLY* 3.3 9.3 - - - -
24A THR 3.9 10.8 + - - +
25A LEU* 3.7 18.6 - - - -
26A HIS 5.3 0.3 + - - -
29A LEU* 3.5 14.7 - - - +
112A CYS* 5.3 1.4 - - - -
113A ARG* 6.0 1.7 - - - -
116A CYS* 4.6 14.7 - - - +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 2.8 28.5 + - + +
15A ARG* 2.9 19.9 + - - +
17A SER* 1.3 75.2 - - - +
19A VAL* 1.3 63.7 + - + +
20A HIS 3.6 0.2 - - - -
23A GLY* 2.8 36.0 + - - -
24A THR* 4.1 2.2 - - - +
25A LEU* 3.4 42.4 - - + +
30A GLU* 4.9 3.6 + - - -
42A PRO* 5.5 5.4 - - + +
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.1 47.6 + - - +
16A ASP* 3.4 16.4 - - - +
17A SER 3.0 0.6 - - - -
18A ARG* 1.3 83.4 - - + +
20A HIS* 1.3 71.4 + - + +
51A HIS* 3.9 18.4 - - + -
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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