Contacts of the helix formed by residues 22 - 35 (chain G) in PDB entry 1WR6
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 THR 22 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G SER 3.7 1.7 + - - +
21G ASP* 1.3 76.5 - - - +
23G ILE* 1.3 65.4 + - - +
24G GLU* 3.7 5.2 + - - +
25G ASN* 3.2 23.6 + - - +
26G VAL* 3.1 22.5 + - - +
52G ASP 3.6 10.8 - - - +
53G GLY* 3.2 20.6 - - - +
54G ARG 3.3 6.1 - - - -
55G THR* 3.6 14.4 - - + +
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Residues in contact with ILE 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G THR* 1.3 73.7 - - - +
24G GLU* 1.3 62.8 + - - +
26G VAL* 3.1 7.5 + - + +
27G LYS* 3.0 32.5 + - - +
43G LEU* 4.3 8.7 - - + -
50G LEU* 3.7 49.6 - - + +
51G GLU 3.0 28.9 - - - +
52G ASP* 3.4 12.8 + - - +
54G ARG 2.9 15.5 + - - +
56G LEU* 4.1 24.7 - - + +
59G TYR* 4.0 13.5 - - + -
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Residues in contact with GLU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G THR* 3.2 6.7 - - - +
23G ILE* 1.3 77.7 - - - +
25G ASN* 1.3 57.6 + - - +
27G LYS* 3.3 8.9 + - + +
28G ALA* 2.9 25.6 + - + +
38G PRO* 5.5 5.3 - - + +
52G ASP* 3.2 39.8 + - + +
53G GLY* 6.0 0.5 - - - -
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Residues in contact with ASN 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASP* 2.9 26.7 + - - +
22G THR* 3.2 23.6 + - - +
24G GLU* 1.3 79.2 - - - +
26G VAL* 1.3 65.7 + - - +
28G ALA* 3.1 12.0 + - - +
29G LYS* 3.0 55.2 + - - +
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Residues in contact with VAL 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ILE* 4.2 10.8 - - + -
5G VAL* 5.0 0.4 - - + -
15G LEU* 3.7 22.2 - - + -
17G VAL* 4.3 8.7 - - + -
21G ASP* 4.6 3.6 - - + -
22G THR 3.1 16.7 + - - +
23G ILE* 3.1 10.3 + - + +
25G ASN* 1.3 74.4 - - - +
27G LYS* 1.3 62.9 + - - +
29G LYS* 3.2 11.2 + - - +
30G ILE* 3.1 24.1 + - + +
43G LEU* 4.1 19.1 - - + -
56G LEU* 3.9 35.4 - - + -
67G LEU* 4.5 5.2 - - + -
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Residues in contact with LYS 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ILE* 3.0 25.7 + - - +
24G GLU* 3.4 9.6 - - + +
26G VAL* 1.3 78.1 - - - +
28G ALA* 1.3 55.9 + - - +
30G ILE* 3.1 2.1 + - - +
31G GLN* 2.8 26.0 + - - +
38G PRO* 4.3 23.0 + - + +
41G GLN* 3.3 63.0 + - + +
42G ARG* 4.3 9.1 - - - +
43G LEU* 4.0 17.5 - - + +
50G LEU 4.3 7.1 + - - -
52G ASP* 2.7 34.6 + - - +
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Residues in contact with ALA 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLU* 2.9 14.5 + - + +
25G ASN* 3.1 19.9 + - - +
27G LYS* 1.3 78.3 - - - +
29G LYS* 1.3 56.2 + - + +
31G GLN* 3.2 15.7 + - - +
32G ASP* 2.8 34.2 + - - +
38G PRO* 4.8 5.1 - - + +
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Residues in contact with LYS 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 3.8 20.2 - - + -
16G GLU 3.5 27.4 + - - +
17G VAL* 4.0 15.0 - - + -
21G ASP* 3.8 12.6 + - - -
25G ASN* 3.0 47.5 + - - +
26G VAL* 3.6 7.9 - - - +
28G ALA* 1.3 72.2 - - + +
30G ILE* 1.3 62.7 + - - +
32G ASP* 2.8 29.6 + - + +
33G LYS* 2.9 17.8 + - + +
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Residues in contact with ILE 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G VAL* 4.1 29.4 - - + -
13G ILE* 4.7 20.6 - - + -
15G LEU* 3.8 19.7 - - + -
26G VAL* 3.1 18.5 + - + +
27G LYS* 3.1 4.0 + - - +
29G LYS* 1.3 74.5 - - - +
31G GLN* 1.3 62.7 + - - +
33G LYS* 3.3 3.0 + - - +
34G GLU* 2.9 27.8 + - + +
35G GLY 3.8 0.2 + - - -
36G ILE* 4.6 8.5 - - + -
41G GLN* 3.2 36.6 - - + +
43G LEU* 4.2 17.9 - - + -
69G LEU* 4.6 9.0 - - + -
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Residues in contact with GLN 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G LYS 2.8 12.6 + - - +
28G ALA* 3.4 13.8 - - - +
30G ILE* 1.3 75.6 - - - +
32G ASP* 1.3 64.1 + - - +
35G GLY* 2.8 33.0 + - - -
36G ILE 3.2 27.8 - - - +
37G PRO* 4.2 10.3 - - - +
38G PRO* 3.7 26.7 - - + +
41G GLN* 3.9 0.9 - - - +
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Residues in contact with ASP 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ALA* 2.8 18.3 + - - +
29G LYS* 2.8 21.5 + - - +
31G GLN* 1.3 82.7 - - - +
33G LYS* 1.3 60.0 + - + +
35G GLY 4.7 0.7 + - - -
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Residues in contact with LYS 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ILE* 4.5 9.6 - - + -
14G THR* 3.2 23.4 + - - +
15G LEU* 3.8 23.3 - - + -
29G LYS* 2.9 19.1 + - + +
30G ILE* 4.2 3.4 - - - +
32G ASP* 1.3 78.8 - - + +
34G GLU* 1.3 77.7 + - + +
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Residues in contact with GLU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B GLY* 5.0 11.3 - - - +
301B VAL* 5.8 1.2 - - - +
13G ILE* 3.8 37.0 - - + +
30G ILE* 2.9 17.2 + - + +
33G LYS* 1.3 93.1 - - + +
35G GLY* 1.3 62.3 + - - +
36G ILE* 3.5 26.6 + - + +
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Residues in contact with GLY 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G GLN* 2.8 25.1 + - - +
32G ASP 4.6 0.6 + - - -
33G LYS 3.7 0.8 - - - -
34G GLU* 1.3 79.0 - - - +
36G ILE* 1.3 63.1 + - - +
37G PRO* 3.4 10.6 - - - +
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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