Contacts of the helix formed by residues 34 - 46 (chain B) in PDB entry 2WP9
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 MET 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A THR* 3.6 41.1 - - + +
337A PHE* 3.9 18.4 - - + -
339A HIS* 6.2 0.4 - - + +
33B MET* 1.3 78.1 - - - +
35B LEU* 1.3 68.0 + - - +
36B LEU* 3.1 4.0 - - + +
37B ASP* 2.8 32.1 + - - +
38B ALA* 3.3 8.3 + - - +
74B ALA 3.8 4.5 - - - +
75B CYS* 3.3 20.4 - - - +
76B ILE* 3.7 14.1 - - - +
77B THR 3.5 1.1 - - - -
78B PRO* 3.7 30.7 - - + -
79B ILE* 4.1 2.9 - - - +
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Residues in contact with LEU 35 (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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5B PHE* 3.9 19.1 - - + -
34B MET* 1.3 72.5 - - - +
36B LEU* 1.3 58.2 + - - +
38B ALA* 3.0 6.4 + - + +
39B LEU* 2.9 29.2 + - + +
65B LEU* 4.2 7.4 - - + -
67B MET* 3.3 36.3 - - + -
74B ALA* 3.2 20.8 + - + +
77B THR* 2.8 17.9 + - - +
79B ILE* 4.0 14.1 - - + +
82B LEU* 4.3 14.6 - - + -
89B ILE* 4.6 0.4 - - + -
91B ILE* 3.6 34.3 - - + -
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B MET* 3.1 2.1 - - + -
35B LEU* 1.3 74.5 - - - +
37B ASP* 1.3 65.2 + - - +
39B LEU* 3.2 7.8 + - + -
40B ILE* 2.9 36.5 + - + +
51B PHE* 4.0 19.7 - - + -
53B ARG* 3.6 39.9 - - + -
56B ARG* 3.7 31.2 - - + -
63B ASP* 4.2 6.5 - - + +
74B ALA* 3.2 11.1 + - + -
75B CYS* 3.7 31.0 - - + +
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Residues in contact with ASP 37 (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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33B MET* 3.5 21.0 - - + +
34B MET* 2.8 40.2 + - - +
36B LEU* 1.3 79.0 - - - +
38B ALA* 1.3 62.4 + - - +
40B ILE* 3.5 9.6 + - - +
41B GLN* 3.0 34.0 + - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.8 32.1 - - + -
25B LEU* 3.9 16.5 - - + +
33B MET* 4.4 7.0 - - + -
34B MET 3.3 4.3 + - - +
35B LEU* 3.0 13.8 + - + +
37B ASP* 1.3 77.7 - - - +
39B LEU* 1.3 55.4 + - - +
41B GLN* 3.0 4.0 + - - +
42B LEU* 2.7 40.2 + - + +
79B ILE* 4.3 8.1 - - + -
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Residues in contact with LEU 39 (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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7B ILE* 4.2 24.9 - - + -
35B LEU* 2.9 20.1 + - + +
36B LEU* 3.6 9.9 - - + +
38B ALA* 1.3 76.3 - - - +
40B ILE* 1.3 62.8 + - - +
42B LEU* 3.1 8.5 + - + +
43B LYS* 3.0 23.6 + - - +
49B LEU* 4.4 12.0 - - + +
51B PHE* 3.8 35.5 - - + -
63B ASP* 6.3 0.7 - - + -
65B LEU* 3.8 28.9 - - + -
74B ALA* 4.2 14.4 - - + -
91B ILE* 4.6 10.5 - - + -
103B LEU* 4.5 12.3 - - + -
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Residues in contact with ILE 40 (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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216A HIS* 3.6 35.7 - - + +
36B LEU* 2.9 43.7 + - + +
37B ASP* 3.8 8.3 - - - +
39B LEU* 1.3 76.8 - - - +
41B GLN* 1.3 64.5 + - + +
43B LYS* 3.3 12.4 + - - +
44B GLU* 3.4 24.2 + - + +
51B PHE* 4.1 13.5 - - + -
53B ARG* 4.8 7.6 - - + +
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Residues in contact with GLN 41 (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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25B LEU* 3.7 34.0 - - + +
26B GLU 4.8 4.0 - - - +
33B MET* 4.4 15.4 - - - +
37B ASP* 3.0 21.9 + - - +
38B ALA 3.0 9.2 + - - +
40B ILE* 1.3 77.9 - - + +
42B LEU* 1.3 65.9 + - - +
44B GLU* 3.1 34.2 + - - +
45B LYS* 3.5 6.2 + - - +
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Residues in contact with LEU 42 (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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5B PHE* 3.9 23.3 - - + -
7B ILE* 3.6 30.7 - - + -
23B TYR* 3.9 25.6 - - + -
24B THR 3.8 21.3 - - - +
25B LEU* 4.3 17.0 - - + -
38B ALA 2.7 23.2 + - - +
39B LEU* 3.5 12.6 - - + +
41B GLN* 1.3 71.8 - - - +
43B LYS* 1.3 52.3 + - - +
45B LYS* 3.0 13.0 + - + +
46B ASP* 2.7 35.8 + - - +
49B LEU* 4.1 12.1 - - + -
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Residues in contact with LYS 43 (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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501A ASP* 5.6 0.4 + - - -
508A THR* 2.8 25.2 + - - -
509A GLN* 3.2 29.5 + - - +
512A GLU* 3.8 22.2 - - - +
39B LEU 3.0 12.2 + - - +
40B ILE* 3.6 10.8 - - - +
41B GLN 3.1 0.4 - - - -
42B LEU* 1.3 74.1 - - - +
44B GLU* 1.3 64.3 + - - +
46B ASP 3.4 11.2 - - - +
47B PRO* 3.0 44.0 + - - +
48B SER 4.4 0.6 - - - -
49B LEU* 2.6 33.7 + - + +
50B SER* 4.6 1.0 + - - -
51B PHE* 4.3 17.3 - - + -
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Residues in contact with GLU 44 (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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455A ASP* 5.7 1.0 - - - +
457A VAL* 3.8 40.5 - - + +
460A ARG* 5.8 1.1 + - - +
461A LYS* 3.5 28.0 + - - -
40B ILE* 3.8 23.0 - - + +
41B GLN* 3.1 22.8 + - - +
43B LYS* 1.3 77.7 - - - +
45B LYS* 1.3 58.9 + - + +
47B PRO* 4.4 8.0 - - - +
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Residues in contact with LYS 45 (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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23B TYR* 5.8 4.9 - - + -
24B THR 5.1 11.2 - - - +
25B LEU* 6.5 1.8 - - + -
41B GLN 3.5 5.5 + - - +
42B LEU* 3.0 15.4 + - + +
44B GLU* 1.3 82.8 - - + +
46B ASP* 1.3 58.7 + - + +
47B PRO* 3.7 6.1 - - - +
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.0 15.9 + - - -
21B GLN* 4.2 5.3 + - - +
23B TYR* 2.7 39.4 + - + -
42B LEU 2.7 15.0 + - - +
43B LYS* 3.1 15.3 - - - +
45B LYS* 1.3 73.7 - - + +
47B PRO* 1.3 65.6 - - - +
48B SER* 2.9 23.7 + - - -
49B LEU* 3.2 11.3 + - + +
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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