Contacts of the helix formed by residues 99 - 113 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS* 6.3 1.6 - - - +
9A GLU* 4.0 26.1 + - - +
12A ASP* 5.7 3.9 + - - -
60A TYR* 4.5 0.9 - - - -
94A TRP* 5.7 0.2 - - - -
97A CYS 3.9 10.8 - - - +
98A THR* 1.3 74.8 - - - +
100A THR* 1.3 60.4 + - - +
101A CYS* 3.2 25.6 - - - -
102A GLN* 2.9 33.6 + - - +
103A VAL* 3.2 14.1 + - - +
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Residues in contact with THR 100 (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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9A GLU* 2.8 21.8 + - - -
13A LEU* 4.5 3.8 - - - -
34A TRP* 4.0 18.4 - - + -
54A ILE* 4.5 10.5 - - + -
56A PHE* 3.3 32.1 - - + -
60A TYR* 3.2 13.3 + - - -
65A PRO* 5.1 2.9 - - + +
99A LYS* 1.3 68.8 - - - +
101A CYS* 1.3 60.2 + - - +
103A VAL* 3.6 15.9 - - + -
104A LEU* 2.9 43.2 + - + +
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Residues in contact with CYS 101 (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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9A GLU* 4.6 0.4 + - - -
13A LEU* 4.1 30.2 - - + +
20A TYR* 4.3 3.1 + - - -
99A LYS* 3.7 32.5 - - - -
100A THR* 1.3 78.7 - - - +
102A GLN* 1.3 63.0 + - - +
104A LEU* 3.5 3.8 + - - +
105A GLU* 3.0 27.9 + - - +
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Residues in contact with GLN 102 (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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88A ILE* 4.0 15.8 - - + +
97A CYS 3.8 5.2 - - - +
98A THR* 3.5 16.2 + - - +
99A LYS* 2.9 40.5 + - + +
101A CYS* 1.3 78.3 - - - +
103A VAL* 1.3 60.5 + - - +
105A GLU* 3.4 14.2 + - - +
106A ALA* 3.0 30.0 + - - +
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Residues in contact with VAL 103 (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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65A PRO* 4.6 8.3 - - + -
67A ILE* 3.3 29.8 - - + -
86A LEU* 3.6 11.4 - - + +
88A ILE* 4.2 8.1 - - + -
89A ILE* 3.6 31.4 - - + -
94A TRP* 4.2 6.3 - - + -
98A THR* 3.8 18.4 - - + -
99A LYS 3.5 13.7 - - - +
100A THR* 3.2 16.9 + - + +
102A GLN* 1.3 78.1 - - - +
104A LEU* 1.3 55.8 + - - +
106A ALA* 3.4 0.7 + - - +
107A LEU* 3.0 22.5 + - - +
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Residues in contact with LEU 104 (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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13A LEU* 3.8 19.7 - - + -
18A PRO* 5.8 1.1 - - + -
20A TYR* 3.8 14.4 - - + +
21A LEU* 3.5 35.4 - - + -
34A TRP* 4.9 0.7 - - + -
38A LEU* 5.0 1.6 - - + +
52A LEU* 4.0 16.8 - - + -
54A ILE* 3.9 27.4 - - + -
67A ILE* 4.4 10.5 - - + -
100A THR* 2.9 30.5 + - + +
101A CYS* 4.1 4.3 - - - +
103A VAL* 1.3 74.1 - - - +
105A GLU* 1.3 61.6 + - - +
107A LEU* 3.4 16.3 + - + +
108A ASN* 2.9 27.4 + - - +
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Residues in contact with GLU 105 (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 TYR* 3.2 27.4 + - + +
101A CYS 3.0 16.4 + - - +
102A GLN* 3.6 13.6 - - - +
104A LEU* 1.3 77.9 - - - +
106A ALA* 1.3 56.2 + - - +
108A ASN* 3.2 6.7 + - + +
109A VAL* 3.0 33.5 + - + +
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Residues in contact with ALA 106 (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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86A LEU* 3.5 12.3 - - + +
88A ILE* 3.8 27.1 - - + -
102A GLN 3.0 17.6 + - - +
103A VAL 3.7 5.4 - - - +
105A GLU* 1.3 75.7 - - - +
107A LEU* 1.3 58.7 + - - +
109A VAL* 3.3 11.5 + - - +
110A LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 107 (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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38A LEU* 4.4 11.4 - - + -
52A LEU* 3.8 28.7 - - + -
67A ILE* 4.1 17.3 - - + -
69A PHE* 3.8 22.0 - - + -
84A ILE* 3.4 30.7 - - + -
86A LEU* 3.7 13.6 - - + +
103A VAL 3.0 15.5 + - - +
104A LEU* 3.6 18.8 - - + +
105A GLU 3.3 0.2 - - - -
106A ALA* 1.3 73.9 - - - +
108A ASN* 1.3 65.8 + - - +
110A LEU* 3.0 21.2 + - + +
111A VAL* 3.1 12.8 + - - +
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Residues in contact with ASN 108 (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 TYR* 3.3 53.5 - - + +
38A LEU* 3.7 17.9 - - + +
39A LEU 4.3 5.2 - - - +
40A PRO* 4.5 2.1 - - - +
41A ASP* 5.7 2.2 + - - -
104A LEU 2.9 14.2 + - - +
105A GLU* 3.2 11.5 + - - +
107A LEU* 1.3 75.5 - - - +
109A VAL* 1.3 64.5 + - - +
111A VAL* 3.4 2.1 + - - +
112A ASN* 3.0 49.7 + - - +
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Residues in contact with VAL 109 (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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105A GLU* 3.0 24.4 + - + +
106A ALA* 3.4 12.3 - - - +
108A ASN* 1.3 77.7 - - + +
110A LEU* 1.3 58.8 + - - +
112A ASN* 4.6 4.9 - - - +
113A ARG* 2.8 45.5 + - + +
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Residues in contact with LEU 110 (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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75A HIS* 3.5 13.0 - - + -
77A ASN* 4.0 33.1 + - + +
78A VAL* 4.4 4.7 - - + -
84A ILE* 4.2 24.5 - - + -
85A CYS 4.0 18.4 - - - +
86A LEU* 3.9 24.5 - - + -
87A PRO* 4.9 3.4 - - + -
106A ALA 2.9 13.9 + - - +
107A LEU* 3.0 12.3 + - + +
109A VAL* 1.3 77.5 - - - +
111A VAL* 1.3 77.7 + - + +
113A ARG 3.6 13.4 - - - +
114A PRO* 4.2 1.0 - - - +
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Residues in contact with VAL 111 (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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38A LEU* 3.8 10.3 - - + -
40A PRO* 3.9 29.6 - - + -
42A GLN* 4.6 4.3 - - - +
45A TYR* 4.7 6.6 - - + -
69A PHE* 3.6 31.0 - - + -
73A ILE* 4.1 13.9 - - + -
75A HIS* 2.8 37.9 + - + +
78A VAL* 5.1 0.7 - - + -
107A LEU 3.1 15.6 + - - +
108A ASN 4.0 2.9 - - - +
110A LEU* 1.3 87.6 - - + +
112A ASN* 1.3 63.3 + - - +
113A ARG 3.4 0.2 + - - -
114A PRO* 4.0 2.6 - - - +
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Residues in contact with ASN 112 (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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40A PRO* 3.6 6.7 - - - +
41A ASP* 2.9 37.8 + - - +
42A GLN* 3.1 40.2 + - + +
108A ASN* 3.0 46.8 + - - +
109A VAL* 3.2 4.4 + - - +
111A VAL* 1.3 77.8 - - - +
113A ARG* 1.3 67.5 + - + +
114A PRO* 3.4 7.0 - - - +
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Residues in contact with ARG 113 (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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42A GLN* 5.4 7.8 - - - +
109A VAL* 2.8 28.7 + - + +
110A LEU* 3.6 10.4 - - - +
112A ASN* 1.3 89.9 + - + +
114A PRO* 1.3 71.7 - - - +
115A ASN* 3.4 4.7 + - - +
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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