Contacts of the helix formed by residues 99 - 113 (chain B) in PDB entry 1WZV
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 LYS 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.9 40.3 - - - +
9B GLU* 4.0 17.6 - - + +
94B TRP* 5.5 0.2 - - - -
97B CYS 4.0 7.2 - - - +
98B THR* 1.3 76.6 - - - +
100B THR* 1.3 59.9 + - - +
101B CYS* 3.1 19.5 - - - -
102B GLN* 2.9 43.8 + - - +
103B VAL* 3.3 10.9 + - - +
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Residues in contact with THR 100 (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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9B GLU* 2.9 21.6 + - - -
13B LEU* 4.9 0.7 - - - -
34B TRP* 3.5 32.3 - - + -
54B ILE* 4.5 9.6 - - + -
56B PHE* 3.2 28.1 - - + -
60B TYR* 3.2 7.8 + - - -
65B PRO* 4.7 4.6 - - + +
94B TRP* 5.7 0.2 - - - -
99B LYS* 1.3 71.4 - - - +
101B CYS* 1.3 55.8 + - - +
103B VAL* 3.2 15.2 + - + +
104B LEU* 2.9 40.7 + - + +
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Residues in contact with CYS 101 (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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9B GLU* 4.6 0.6 + - - -
13B LEU* 3.9 33.8 - - + +
20B TYR* 4.4 2.8 + - - -
99B LYS* 3.1 22.4 - - - -
100B THR* 1.3 79.2 - - - +
102B GLN* 1.3 70.6 + - - +
104B LEU* 3.5 4.8 + - - +
105B GLU* 3.0 28.6 + - - +
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Residues in contact with GLN 102 (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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88B ILE* 4.0 18.3 - - + +
97B CYS 3.8 7.9 + - - -
98B THR* 4.0 12.4 + - + +
99B LYS* 2.9 44.8 + - - +
101B CYS* 1.3 86.0 - - - +
103B VAL* 1.3 57.4 + - - +
105B GLU* 3.7 13.8 - - - +
106B ALA* 3.1 26.0 + - - +
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Residues in contact with VAL 103 (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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65B PRO* 4.7 7.0 - - + -
67B ILE* 3.6 28.3 - - + -
86B LEU* 3.7 8.7 - - + +
88B ILE* 4.1 9.6 - - + -
89B ILE* 3.6 34.3 - - + -
94B TRP* 4.1 5.6 - - + -
98B THR* 3.8 17.5 - - + -
99B LYS 3.6 13.2 - - - +
100B THR* 3.2 15.5 + - + +
102B GLN* 1.3 74.5 - - - +
104B LEU* 1.3 60.5 + - + +
106B ALA* 3.1 4.5 + - - +
107B LEU* 2.8 26.3 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.1 15.3 - - + -
18B PRO* 6.0 1.1 - - + -
20B TYR* 3.9 14.6 - - + +
21B LEU* 3.7 30.5 - - + -
24B LEU* 5.5 0.2 - - + -
34B TRP* 4.7 4.0 - - + -
38B LEU* 5.2 2.3 - - + +
52B LEU* 4.1 24.0 - - + -
54B ILE* 4.2 13.0 - - + -
67B ILE* 3.9 23.3 - - + -
100B THR* 2.9 35.7 + - + +
101B CYS* 4.0 4.5 - - - +
103B VAL* 1.3 73.0 - - - +
105B GLU* 1.3 60.6 + - - +
107B LEU* 3.4 8.9 - - + +
108B ASN* 2.8 29.8 + - - +
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Residues in contact with GLU 105 (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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20B TYR* 3.2 26.3 + - + +
101B CYS 3.0 16.9 + - - +
102B GLN* 3.7 13.8 - - - +
103B VAL 3.3 0.2 - - - -
104B LEU* 1.3 74.9 - - - +
106B ALA* 1.3 57.5 + - - +
108B ASN* 3.3 6.0 + - - +
109B VAL* 3.1 37.0 + - + +
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Residues in contact with ALA 106 (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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86B LEU* 3.6 9.8 - - + +
88B ILE* 3.9 26.0 - - + -
102B GLN 3.1 15.4 + - - +
103B VAL 3.1 8.3 + - - +
105B GLU* 1.3 73.2 - - - +
107B LEU* 1.3 66.6 + - - +
109B VAL* 3.4 9.1 + - - +
110B LEU* 3.0 23.7 + - - +
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Residues in contact with LEU 107 (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* 4.3 11.4 - - + -
52B LEU* 3.7 40.2 - - + -
67B ILE* 4.0 15.3 - - + -
69B PHE* 4.1 15.9 - - + -
84B ILE* 3.7 28.9 - - + -
86B LEU* 3.8 13.0 - - + +
103B VAL 2.8 14.2 + - - +
104B LEU* 3.4 17.0 - - + +
106B ALA* 1.3 77.8 - - - +
108B ASN* 1.3 60.4 + - - +
110B LEU* 3.3 7.4 + - + +
111B VAL* 3.1 28.8 + - + +
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Residues in contact with ASN 108 (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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20B TYR* 3.2 56.3 - - + +
38B LEU* 3.9 15.8 - - + +
39B LEU 4.3 4.7 - - - +
40B PRO* 4.6 2.6 - - - +
104B LEU 2.8 13.2 + - - +
105B GLU* 3.4 10.8 + - - +
107B LEU* 1.3 77.1 - - - +
109B VAL* 1.3 58.7 + - - +
111B VAL* 3.5 1.4 + - - +
112B ASN* 2.9 55.0 + - - +
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Residues in contact with VAL 109 (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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105B GLU* 3.1 24.0 + - + +
106B ALA* 3.6 9.6 - - - +
108B ASN* 1.3 76.1 - - + +
110B LEU* 1.3 56.3 + - - +
112B ASN* 3.2 4.6 + - - +
113B ARG* 2.7 48.7 + - + +
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Residues in contact with LEU 110 (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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75B HIS* 3.7 5.1 + - - +
77B ASN* 3.7 36.8 - - + +
78B VAL* 6.4 0.7 - - + -
84B ILE* 4.5 15.3 - - + -
85B CYS 4.1 20.0 - - - +
86B LEU* 3.7 25.1 - - + -
87B PRO* 5.5 1.3 - - + -
106B ALA 3.0 14.0 + - - +
107B LEU* 3.3 12.8 + - + +
109B VAL* 1.3 77.1 - - - +
111B VAL* 1.3 66.7 + - + +
113B ARG 3.1 25.5 - - - +
114B PRO 3.6 1.9 - - - -
115B ASN* 4.9 8.5 - - + +
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Residues in contact with VAL 111 (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* 3.7 11.0 - - + -
40B PRO* 3.8 32.1 - - + -
42B GLN* 4.6 0.2 - - - +
45B TYR* 4.6 9.9 - - + -
69B PHE* 3.7 29.2 - - + -
73B ILE* 4.4 11.4 - - + -
75B HIS* 2.8 37.8 - - + +
78B VAL* 5.1 6.3 - - + -
84B ILE* 6.1 0.2 - - + -
107B LEU* 3.1 23.0 + - + +
108B ASN* 4.0 2.7 - - - +
110B LEU* 1.3 78.4 - - + +
112B ASN* 1.3 61.6 + - - +
114B PRO* 3.9 2.1 - - - +
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Residues in contact with ASN 112 (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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40B PRO* 3.5 11.3 - - - +
41B ASP* 2.8 39.6 + - - +
42B GLN* 3.0 49.7 + - + +
108B ASN* 2.9 41.9 + - - +
109B VAL* 3.9 4.4 - - - +
111B VAL* 1.3 77.4 - - - +
113B ARG* 1.3 64.7 + - + +
114B PRO* 3.4 1.8 - - - +
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Residues in contact with ARG 113 (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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42B GLN* 3.9 19.0 - - - +
109B VAL* 2.7 30.5 + - + +
110B LEU* 3.1 13.8 - - - +
112B ASN* 1.3 85.3 + - + +
114B PRO* 1.3 75.8 + - - +
115B ASN* 3.4 4.9 + - - +
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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