Contacts of the helix formed by residues 49 - 62 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ILE 3.3 0.6 + - - -
46A SER 3.3 21.1 + - - +
47A GLU* 3.1 17.8 - - - +
48A GLY* 1.3 79.8 - - - +
50A LEU* 1.3 58.6 + - - +
51A TRP 3.3 2.6 + - - -
52A LYS* 3.5 27.1 + - + +
53A LYS* 3.1 32.1 + - + +
87A PRO 4.7 3.8 - - - +
88A PRO* 4.2 4.0 - - + -
89A ASN* 3.5 43.3 - - + +
92A TYR* 4.7 6.5 - - - -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 3.7 23.8 - - + +
23A LEU* 3.9 14.4 - - + +
24A SER* 3.6 37.5 - - - +
31A LEU* 4.3 13.4 - - + +
44A VAL 3.9 2.2 - - - +
45A ILE* 3.2 40.9 + - + +
48A GLY* 3.5 26.0 - - - +
49A MET* 1.3 74.7 - - - +
51A TRP* 1.3 60.4 + - - +
53A LYS* 3.4 10.3 + - + +
54A LEU* 2.9 28.1 + - - +
89A ASN* 3.6 0.6 + - - -
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Residues in contact with TRP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.7 15.7 - - + -
31A LEU* 3.5 23.5 - - + +
32A CYS* 3.6 33.4 - - - -
35A GLU* 3.0 27.9 + - - -
45A ILE* 3.9 13.6 - - + +
49A MET 3.3 0.4 - - - -
50A LEU* 1.3 75.1 - - - +
52A LYS* 1.3 66.7 + - - +
54A LEU* 3.1 14.3 + - + +
55A ILE* 3.0 28.3 + - - +
89A ASN* 3.6 18.8 + - - +
92A TYR* 3.9 4.7 - - - -
93A ARG* 3.6 46.3 - - + +
96A TYR* 3.8 43.5 - + + -
139B ASN* 5.6 0.4 - - - -
141B TRP* 4.2 5.6 - + - -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A MET* 3.5 29.5 + - + +
51A TRP* 1.3 76.8 - - - +
53A LYS* 1.3 59.0 + - + +
55A ILE* 3.3 3.8 + - - +
56A GLU* 2.9 62.6 + - - +
77A TYR 3.6 19.7 - - - -
78A LEU* 4.5 2.6 - - + +
79A PHE* 3.0 24.8 + - - +
81A ASN* 5.2 6.4 + - - +
89A ASN* 4.3 0.8 + - - -
92A TYR* 3.6 49.7 - - + +
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 3.6 24.6 + - + +
24A SER* 5.4 10.5 - - - -
48A GLY* 2.5 30.1 + - - +
49A MET* 3.1 15.1 + - + +
50A LEU* 3.5 21.3 - - + +
51A TRP 3.2 0.2 - - - -
52A LYS* 1.3 77.1 - - + +
54A LEU* 1.3 57.8 + - - +
56A GLU* 3.4 18.2 + - - +
57A ARG* 3.0 26.3 + - - +
60A ARG* 4.7 1.0 + - - -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER 6.1 0.2 - - - -
26A LEU 4.0 7.4 - - - +
28A ALA* 3.8 28.3 - - - +
31A LEU* 4.1 11.2 - - + -
50A LEU 2.9 17.3 + - - +
51A TRP* 3.1 18.4 + - + +
53A LYS* 1.3 75.1 - - - +
55A ILE* 1.3 53.4 + - - +
57A ARG* 2.8 44.6 + - - +
58A MET* 2.8 44.7 + - + +
96A TYR* 3.4 28.3 - - + -
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TRP 3.0 16.0 + - - +
52A LYS 3.5 6.3 - - - +
54A LEU* 1.3 77.0 - - - +
56A GLU* 1.3 57.3 + - - +
58A MET* 3.2 9.2 + - - +
59A VAL* 2.9 28.1 + - + +
65A TRP* 4.4 6.7 - - + -
74A TRP* 3.8 29.8 - - + -
78A LEU* 3.8 17.9 - - + -
92A TYR* 3.6 33.7 - - + +
95A LEU* 4.0 24.5 - - + -
96A TYR* 3.7 23.8 - - + +
99A ILE* 4.4 4.3 - - + -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS* 2.9 35.5 + - - +
53A LYS* 3.6 24.9 + - - +
55A ILE* 1.3 75.7 - - - +
57A ARG* 1.3 55.9 + - - +
59A VAL* 3.1 10.2 + - - +
60A ARG* 2.9 39.1 + - - +
78A LEU* 3.8 14.3 - - + -
79A PHE* 2.7 59.9 + - + -
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER 2.4 35.8 + - - -
25A TYR* 3.4 22.3 + - - +
26A LEU 3.6 18.6 + - - -
27A ASP* 4.3 6.9 - - - +
53A LYS 3.0 13.0 + - - +
54A LEU* 2.8 31.6 + - - +
56A GLU* 1.3 72.0 - - - +
58A MET* 1.3 72.4 + - - +
60A ARG* 3.2 18.8 + - - +
61A THR* 3.1 41.7 + - + +
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Residues in contact with MET 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP* 5.8 4.0 - - + -
28A ALA 5.6 2.7 - - - +
54A LEU* 2.8 32.1 + - + +
55A ILE 3.5 3.8 - - - +
57A ARG* 1.3 84.9 - - - +
59A VAL* 1.3 53.7 + - - +
61A THR* 4.0 7.4 - - - -
62A ASP* 2.7 41.3 + - - +
65A TRP* 3.4 47.1 - - + +
96A TYR* 3.1 30.1 - - + +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE 2.9 16.8 + - - +
56A GLU* 3.1 9.8 + - - +
58A MET* 1.3 76.1 - - - +
60A ARG* 1.3 63.9 + - + +
61A THR 3.3 0.9 + - - -
62A ASP 3.5 10.6 + - - +
65A TRP* 3.9 21.5 - - + +
66A LYS* 3.8 34.2 - - + +
69A SER* 4.1 7.2 - - - +
74A TRP* 3.9 27.8 - - + -
78A LEU* 4.0 10.3 - - + -
79A PHE* 4.6 17.5 - - + -
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS 4.7 1.2 + - - -
56A GLU* 2.9 17.2 + - - +
57A ARG* 3.2 45.5 - - - +
58A MET 3.3 0.2 - - - -
59A VAL* 1.3 77.3 - - + +
61A THR* 1.3 64.6 + - + +
66A LYS* 6.1 0.2 - - - -
79A PHE* 3.7 31.6 - - + -
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.1 30.9 + - + +
58A MET* 3.4 10.4 + - - -
59A VAL 4.2 0.2 - - - -
60A ARG* 1.3 85.0 - - + +
62A ASP* 1.3 65.9 + - - +
63A PRO* 3.4 9.2 - - - +
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A MET* 2.7 24.8 + - + +
59A VAL 3.5 5.1 - - - +
61A THR* 1.3 74.2 + - - +
63A PRO* 1.4 72.0 - - - +
64A LEU* 3.1 23.9 + - - +
65A TRP* 3.0 37.1 + - + -
66A LYS 3.1 9.5 + - - -
389A GLU* 4.5 2.6 - - - +
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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