Contacts of the helix formed by residues 49 - 62 (chain G) in PDB entry 6WNX
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 49 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45G ILE 3.4 0.4 + - - -
46G SER 3.3 5.4 + - - +
47G GLU* 3.1 16.0 - - - +
48G GLY* 1.3 78.5 - - - +
50G LEU* 1.3 59.5 + - - +
51G TRP 3.4 2.5 - - - -
52G LYS* 3.5 21.3 + - + +
53G LYS* 3.1 32.4 + - + +
87G PRO 3.8 22.7 - - - +
88G PRO* 4.9 0.7 - - + -
89G ASN* 3.5 37.2 - - - +
92G TYR* 4.0 18.2 - - + -
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Residues in contact with LEU 50 (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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20G GLU* 3.7 21.1 - - + +
23G LEU* 3.9 13.0 - - + +
24G SER* 3.6 39.9 - - - +
31G LEU* 4.3 13.7 - - + +
44G VAL 3.8 7.0 - - - +
45G ILE* 3.2 34.2 + - + +
48G GLY* 3.5 26.2 - - - +
49G MET* 1.3 73.4 - - - +
51G TRP* 1.3 61.6 + - - +
53G LYS* 3.4 10.6 + - + +
54G LEU* 2.9 28.2 + - - +
89G ASN* 3.6 0.6 - - - +
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Residues in contact with TRP 51 (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* 3.8 13.7 - - + -
31G LEU* 3.5 26.9 - - + -
32G CYS* 3.5 35.2 - - - -
35G GLU* 3.0 28.1 + - - -
45G ILE* 3.8 13.9 - - + +
49G MET 3.4 0.4 - - - -
50G LEU* 1.3 74.0 - - - +
52G LYS* 1.3 66.2 + - - +
54G LEU* 3.1 10.7 + - + +
55G ILE* 3.0 29.1 + - + +
89G ASN* 3.6 15.7 - - - +
92G TYR* 3.9 4.7 - - - +
93G ARG* 3.5 46.4 - - + +
96G TYR* 3.7 46.7 - + + -
97G PRO* 5.8 0.4 - - + -
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Residues in contact with LYS 52 (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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49G MET* 3.5 30.5 + - + +
50G LEU 3.5 0.2 - - - -
51G TRP* 1.3 76.3 - - - +
53G LYS* 1.3 57.5 + - + +
55G ILE* 3.3 4.1 + - - +
56G GLU* 2.9 62.3 + - - +
77G TYR 3.7 8.7 - - - -
78G LEU* 4.6 3.1 - - + +
79G PHE* 3.3 23.5 - - - +
89G ASN* 4.2 1.0 - - - +
92G TYR* 3.5 62.4 - - + +
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Residues in contact with LYS 53 (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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20G GLU* 3.6 24.9 + - - +
21G ASN* 5.1 6.3 + - - -
24G SER* 5.3 10.7 - - - -
48G GLY 3.1 27.4 + - - +
49G MET* 3.1 15.9 + - + +
50G LEU* 3.5 20.6 - - + +
51G TRP 3.2 0.2 - - - -
52G LYS* 1.3 76.8 - - + +
54G LEU* 1.3 58.0 + - - +
56G GLU* 3.4 17.3 + - - +
57G ARG* 3.0 26.7 + - - +
60G ARG* 4.8 2.3 + - - -
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Residues in contact with LEU 54 (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 SER 6.1 0.2 - - - -
26G LEU 4.0 3.4 - - - +
27G ASP* 4.5 1.3 - - - -
28G ALA* 3.8 28.5 - - - +
31G LEU* 4.0 10.8 - - + -
50G LEU 2.9 17.9 + - - +
51G TRP* 3.1 17.7 + - + +
53G LYS* 1.3 73.4 - - - +
55G ILE* 1.3 52.7 - - - +
57G ARG* 2.9 43.7 + - + +
58G MET* 2.7 47.9 + - + +
96G TYR* 3.5 27.4 - - + -
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Residues in contact with ILE 55 (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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51G TRP 3.0 14.2 + - - +
52G LYS* 3.5 7.9 - - - +
54G LEU* 1.3 75.6 - - - +
56G GLU* 1.3 56.9 + - - +
58G MET* 3.2 9.3 + - - +
59G VAL* 2.9 28.3 + - + +
65G TRP* 4.3 5.8 - - + -
74G TRP* 3.9 17.7 - - + -
78G LEU* 3.9 28.7 - - + -
92G TYR* 3.7 32.3 - - + +
95G LEU* 4.0 24.9 - - + -
96G TYR* 3.6 25.1 - - + +
99G ILE* 4.3 4.7 - - + -
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Residues in contact with GLU 56 (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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52G LYS* 2.9 48.5 + - - +
53G LYS* 3.6 25.4 - - - +
54G LEU 3.2 0.2 - - - -
55G ILE* 1.3 75.7 - - - +
57G ARG* 1.3 57.1 + - - +
59G VAL* 3.1 7.1 + - - +
60G ARG* 2.9 41.3 + - - +
78G LEU* 4.4 13.9 - - + -
79G PHE* 3.2 48.6 + - + -
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Residues in contact with ARG 57 (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 SER 3.5 21.4 + - - -
25G TYR* 3.6 13.4 + - - -
26G LEU 2.8 30.1 + - - -
27G ASP* 4.3 2.4 - - - +
53G LYS 3.0 11.9 + - - +
54G LEU* 2.9 30.3 + - + +
56G GLU* 1.3 75.6 - - - +
58G MET* 1.3 66.5 + - - +
60G ARG* 3.5 20.1 + - - +
61G THR* 3.1 42.7 + - + +
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Residues in contact with MET 58 (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 ASP* 5.7 4.9 - - + -
28G ALA* 5.3 4.7 - - + +
54G LEU* 2.7 32.2 + - + +
55G ILE 3.5 4.3 - - - +
57G ARG* 1.3 79.7 - - - +
59G VAL* 1.3 56.1 + - - +
61G THR* 4.0 8.1 - - - -
62G ASP* 2.7 40.9 + - - +
65G TRP* 3.4 46.0 - - + +
96G TYR* 3.2 30.3 - - + +
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Residues in contact with VAL 59 (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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55G ILE 2.9 17.2 + - - +
56G GLU* 3.1 9.8 + - - +
58G MET* 1.3 76.4 - - - +
60G ARG* 1.3 64.1 + - + +
61G THR 3.3 1.0 + - - -
62G ASP 3.6 10.2 + - - +
65G TRP* 3.9 27.1 - - + +
66G LYS* 3.7 34.3 - - + +
69G SER* 4.1 8.1 - - - +
74G TRP* 3.9 22.0 - - + -
78G LEU* 4.0 10.8 - - + -
79G PHE* 4.9 15.7 - - + -
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Residues in contact with ARG 60 (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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53G LYS 4.8 1.8 + - - -
56G GLU* 2.9 23.8 + - - +
57G ARG* 3.8 31.3 - - - +
58G MET 3.3 0.2 - - - -
59G VAL* 1.3 77.8 - - + +
61G THR* 1.3 64.7 + - + +
66G LYS* 6.1 0.2 - - - -
79G PHE* 3.7 33.0 - - + -
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Residues in contact with THR 61 (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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57G ARG* 3.1 31.5 + - + +
58G MET* 3.5 11.1 + - - -
59G VAL 4.3 0.2 - - - -
60G ARG* 1.3 85.3 - - + +
62G ASP* 1.3 63.7 + - - +
63G PRO* 3.4 12.0 - - - +
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Residues in contact with ASP 62 (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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58G MET* 2.7 26.1 + - - +
59G VAL 3.6 3.9 - - - +
61G THR* 1.3 73.3 + - - +
63G PRO* 1.4 67.8 - - - +
64G LEU* 3.1 25.1 + - - +
65G TRP* 3.0 41.8 + - + -
66G LYS 3.1 9.0 + - - -
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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