Contacts of the helix formed by residues 44 - 58 (chain B) in PDB entry 5WRV
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 ASP 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A LYS* 2.7 33.9 + - - +
701A ACT 3.9 6.9 - - - +
15B TRP* 3.7 6.9 + - - -
37B ILE* 5.0 2.8 - - + +
38B LEU* 4.0 0.5 - - - +
41B ASN* 3.2 35.3 + - + +
42B LYS 3.5 1.2 + - - -
43B ASP* 1.3 73.2 - - - +
45B VAL* 1.3 57.6 + - - +
46B THR* 3.1 8.7 + - - -
47B ALA* 2.9 37.8 + - + +
48B LEU* 2.9 30.8 + - - +
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A ACT 3.2 23.5 - - + +
43B ASP 3.1 1.5 + - - +
44B ASP* 1.3 71.4 - - - +
46B THR* 1.3 60.1 + - - +
48B LEU* 3.3 8.9 + - - +
49B HIS* 2.8 30.7 + - + +
74B VAL* 3.6 34.5 - - + +
75B LEU* 4.1 11.9 - - + +
78B ASN* 4.0 33.9 - - + +
80B LEU* 5.4 2.9 - - + -
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Residues in contact with THR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A PRO* 4.0 13.5 - - + -
602A PRO 4.6 4.5 - - - +
603A LEU* 3.6 31.4 - - + -
606A LYS* 3.5 19.3 - - + +
701A ACT 2.9 13.8 + - - -
15B TRP* 3.8 7.2 - - + -
44B ASP* 3.1 8.2 + - - -
45B VAL* 1.3 80.3 - - - +
47B ALA* 1.3 56.4 + - - +
49B HIS* 3.3 6.8 + - - +
50B CYS* 2.9 29.5 + - - -
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Residues in contact with ALA 47 (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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15B TRP* 3.5 20.1 - - + -
34B VAL* 3.3 19.2 - - + +
37B ILE* 4.1 10.1 - - + -
38B LEU* 3.7 23.3 - - + -
44B ASP* 2.9 24.4 + - + +
46B THR* 1.3 73.9 - - - +
48B LEU* 1.3 59.8 + - - +
50B CYS* 3.3 1.2 + - - +
51B LYS* 2.8 25.1 + - - +
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Residues in contact with LEU 48 (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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38B LEU* 3.9 24.7 - - + -
42B LYS 4.5 1.3 - - - +
43B ASP* 4.3 7.0 - - - -
44B ASP 2.9 21.1 + - - +
45B VAL 3.6 4.3 - - - +
47B ALA* 1.3 74.5 - - - +
49B HIS* 1.3 63.0 + - - +
51B LYS* 3.2 6.4 + - + +
52B VAL* 3.0 29.9 + - - +
67B VAL* 3.9 22.2 - - + +
71B HIS* 3.7 46.2 - - + +
74B VAL* 4.0 22.4 - - + -
75B LEU* 4.1 14.6 - - + -
80B LEU* 4.7 0.9 - - + -
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Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A ALA 4.4 2.7 + - - -
601A PRO* 3.6 35.7 - - + +
45B VAL* 2.8 18.6 + - + +
46B THR* 3.4 7.2 - - - +
48B LEU* 1.3 75.4 - - - +
50B CYS* 1.3 62.7 + - - +
52B VAL* 3.3 3.1 + - - +
53B VAL* 3.0 28.7 + - + +
80B LEU* 3.9 33.3 - - + +
83B GLU* 2.7 37.0 + - + -
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Residues in contact with CYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.5 39.9 - - + -
601A PRO* 4.0 7.0 - - - -
603A LEU* 3.9 24.2 - - - -
15B TRP* 4.0 8.7 - - - -
18B VAL* 4.4 1.3 - - - -
34B VAL* 3.8 19.5 - - + -
46B THR 2.9 22.6 + - - +
47B ALA* 3.8 4.3 - - - +
49B HIS* 1.3 73.2 - - - +
51B LYS* 1.3 61.7 + - - +
53B VAL 3.2 1.0 + - - -
54B CYS* 2.9 28.4 + - - -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.7 18.4 - - + -
34B VAL* 3.7 12.3 - - + +
35B ASN* 2.9 32.1 + - - +
38B LEU* 3.7 16.0 - - + +
47B ALA 2.8 20.7 + - - +
48B LEU* 3.2 6.0 + - + +
50B CYS* 1.3 72.0 - - - +
52B VAL* 1.3 64.6 + - - +
54B CYS* 3.2 4.6 + - - +
55B LEU* 3.0 37.1 + - + +
63B GLU* 4.7 9.1 + - - -
67B VAL* 3.9 28.3 - - + +
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Residues in contact with VAL 52 (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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48B LEU 3.0 17.2 + - - +
49B HIS 3.5 7.6 - - - +
51B LYS* 1.3 76.5 - - - +
53B VAL* 1.3 61.3 + - - +
55B LEU* 3.3 4.3 + - - +
56B ILE* 3.0 32.6 + - + +
64B ALA* 3.9 16.1 - - + +
67B VAL* 3.8 19.5 - - + -
68B ILE* 3.8 30.1 - - + -
80B LEU* 3.9 10.1 - - + -
83B GLU* 3.6 32.5 - - + -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A VAL* 3.9 20.0 - - + +
599A ALA* 3.5 41.3 - - - +
600A PHE* 3.6 24.2 - - + +
27B PHE* 4.2 10.3 - - + -
49B HIS* 3.0 26.3 + - + +
50B CYS 3.2 7.2 + - - +
52B VAL* 1.3 75.1 - - - +
54B CYS* 1.3 63.4 + - - +
56B ILE* 3.3 2.8 + - - +
57B GLN* 2.9 24.1 + - + +
83B GLU* 4.2 9.2 - - + +
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Residues in contact with CYS 54 (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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600A PHE* 3.7 23.3 - - - -
27B PHE* 3.5 37.4 - - - +
30B ALA* 3.7 5.2 - - - -
31B LEU* 3.6 29.8 - - + -
34B VAL* 5.0 1.6 - - - -
50B CYS 2.9 20.0 + - - -
51B LYS* 3.2 8.0 + - - +
53B VAL* 1.3 76.0 - - - +
55B LEU* 1.3 64.0 + - - +
57B GLN* 3.3 3.3 + - - +
58B ASN* 3.0 27.8 + - - +
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Residues in contact with LEU 55 (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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31B LEU* 3.8 23.3 - - + -
51B LYS* 3.0 41.3 + - + +
52B VAL 3.6 3.6 - - - +
54B CYS* 1.3 75.5 - - - +
56B ILE* 1.3 60.3 + - - +
58B ASN* 3.2 6.2 + - + -
59B GLY 3.1 4.7 + - - -
60B SER* 2.8 52.7 + - - +
63B GLU* 3.5 37.7 - - + +
64B ALA* 3.7 24.5 - - + +
67B VAL* 3.9 8.5 - - + -
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Residues in contact with ILE 56 (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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595A LEU* 4.5 7.7 - - + +
598A VAL* 3.7 22.0 - - + -
52B VAL* 3.0 35.0 + - + +
53B VAL 3.7 3.8 - - - +
55B LEU* 1.3 74.3 - - - +
57B GLN* 1.3 59.2 + - - +
59B GLY* 2.9 19.8 + - - -
61B PHE* 3.6 16.4 - - + -
64B ALA* 3.9 3.1 - - + -
83B GLU* 3.9 22.2 - - + +
86B TYR* 3.6 33.9 - - + -
87B CYS* 3.7 32.8 - - - -
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Residues in contact with GLN 57 (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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595A LEU* 4.1 14.0 + - - +
598A VAL* 2.9 34.7 + - + +
27B PHE* 3.5 51.1 - - + -
53B VAL* 2.9 23.5 + - + +
54B CYS 3.6 4.9 - - - +
56B ILE* 1.3 76.0 - - - +
58B ASN* 1.3 61.7 + - - +
59B GLY 3.3 0.8 + - - -
204B ACT 3.2 26.3 + - - +
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Residues in contact with ASN 58 (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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27B PHE* 4.1 13.0 + - - +
28B THR* 3.0 42.2 + - - +
31B LEU* 5.1 8.6 - - + +
54B CYS 3.0 16.9 + - - +
55B LEU* 4.0 5.4 - - + +
56B ILE 3.1 0.4 - - - -
57B GLN* 1.3 80.3 - - - +
59B GLY* 1.3 61.4 + - - +
60B SER* 3.3 9.6 + - - +
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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