Contacts of the helix formed by residues 90 - 109 (chain J) in PDB entry 6VVT
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 SER 90 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86J LEU* 5.0 0.9 - - - -
88J ARG 3.9 1.4 + - - -
89J ARG* 1.3 74.5 - - - +
91J VAL* 1.3 68.3 + - - +
92J GLU* 2.6 31.2 + - - -
93J GLU* 2.5 35.9 + - - +
94J LEU* 3.1 9.6 + - - +
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Residues in contact with VAL 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F TYR* 4.1 15.0 + - + +
82J TRP* 6.2 0.7 - - + -
86J LEU* 4.2 20.2 - - + -
89J ARG 3.8 1.0 + - - -
90J SER* 1.3 75.4 + - - +
92J GLU* 1.3 76.3 + - + +
94J LEU* 3.4 13.4 + - + +
95J GLU* 2.9 29.2 + - + +
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Residues in contact with GLU 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J SER* 2.6 25.3 + - - +
91J VAL* 1.3 86.9 - - + +
93J GLU* 1.3 66.9 + - + +
95J GLU* 3.1 7.9 + - - +
96J GLU* 2.9 24.9 + - - +
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Residues in contact with GLU 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J ARG 3.9 4.9 - - - +
89J ARG* 3.3 23.9 - - - -
90J SER* 2.5 48.3 + - - +
92J GLU* 1.3 74.7 - - + +
94J LEU* 1.3 61.0 + - - +
96J GLU* 3.4 9.1 + - - +
97J LEU* 3.1 22.5 + - - +
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Residues in contact with LEU 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F GLU* 4.3 10.5 - - + +
193F ALA* 6.2 0.2 - - - -
196F TYR* 3.6 38.5 - - + +
82J TRP* 3.9 20.2 - - + -
85J LEU* 4.1 19.5 - - + -
86J LEU* 4.5 5.2 - - + -
89J ARG* 3.3 48.0 - - + +
90J SER 3.1 6.3 + - - +
91J VAL* 3.7 12.1 - - - +
93J GLU* 1.3 74.6 - - - +
95J GLU* 1.3 64.8 + - - +
97J LEU* 3.3 9.5 + - + +
98J LEU* 2.9 24.1 + - - +
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Residues in contact with GLU 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F TYR* 3.5 28.1 + - - +
219F MET* 5.6 0.9 - - - +
91J VAL* 2.9 19.3 + - + +
92J GLU* 3.5 8.1 - - - +
94J LEU* 1.3 76.0 - - - +
96J GLU* 1.3 62.0 + - - +
98J LEU* 3.3 12.8 + - - +
99J LYS* 3.0 23.3 + - + +
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Residues in contact with GLU 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J GLU 2.9 15.3 + - - +
93J GLU* 3.8 9.5 - - - +
95J GLU* 1.3 76.0 - - - +
97J LEU* 1.3 63.7 + - - +
99J LYS* 3.2 8.5 + - + +
100J GLU* 3.1 44.0 + - + +
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Residues in contact with LEU 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F LYS* 3.9 36.3 - - + +
192F GLU* 4.1 20.2 - - + +
193F ALA* 4.3 7.2 - - + +
275F TYR* 3.5 25.1 - - - +
93J GLU 3.1 14.9 + - - +
94J LEU* 3.3 12.5 + - + +
96J GLU* 1.3 76.5 - - - +
98J LEU* 1.3 62.6 + - - +
100J GLU* 3.0 20.2 + - + +
101J ARG* 3.0 44.8 + - + +
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Residues in contact with LEU 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F ALA* 4.4 12.9 - - + +
196F TYR* 3.8 26.2 - - + -
197F ALA* 4.4 24.5 - - + -
200F LYS* 5.2 1.6 - - + -
219F MET* 3.2 32.3 - - + -
222F ILE* 4.5 10.3 - - + -
94J LEU 2.9 16.7 + - - +
95J GLU* 3.7 12.6 - - - +
96J GLU 3.3 0.2 - - - -
97J LEU* 1.3 76.6 - - - +
99J LYS* 1.3 57.0 + - - +
101J ARG* 3.3 6.0 + - + +
102J LEU* 2.8 58.8 + - + +
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Residues in contact with LYS 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J GLU* 3.0 14.4 + - - +
96J GLU* 3.5 11.7 - - + +
97J LEU 3.2 0.2 - - - -
98J LEU* 1.3 74.1 - - - +
100J GLU* 1.3 55.8 + - + +
102J LEU* 4.4 6.7 - - - +
103J ASP* 2.7 50.3 + - - +
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Residues in contact with GLU 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F LYS* 4.6 14.2 + - - +
96J GLU* 3.1 38.6 + - + +
97J LEU* 3.0 23.5 + - + +
99J LYS* 1.3 75.9 - - - +
101J ARG* 1.3 60.2 + - + +
103J ASP* 3.7 7.0 - - - +
104J LEU* 2.9 29.8 + - - +
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Residues in contact with ARG 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F GLU* 2.5 41.0 + - - -
189F LYS* 3.7 21.8 - - - +
190F ARG* 3.7 27.4 - - - +
193F ALA* 3.8 26.2 - - + -
222F ILE* 4.7 10.7 - - + +
97J LEU* 3.0 27.2 + - + +
98J LEU* 3.7 9.4 - - + +
100J GLU* 1.3 78.2 - - - +
102J LEU* 1.3 64.6 + - + +
104J LEU* 3.0 27.3 + - - +
105J ILE* 2.9 28.9 + - - +
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Residues in contact with LEU 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F GLN* 3.4 38.4 - - + +
218F ASP* 5.1 6.1 - - + -
219F MET* 4.4 15.0 - - + +
222F ILE* 4.1 20.2 - - + -
98J LEU* 2.8 54.4 + - + +
99J LYS* 3.9 6.1 - - - +
101J ARG* 1.3 71.7 - - - +
103J ASP* 1.3 63.4 + - - +
104J LEU 3.0 1.3 - - - -
105J ILE* 2.9 25.4 - - + +
106J LYS* 2.9 30.2 + - + +
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Residues in contact with ASP 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J LYS* 2.7 34.5 + - - +
100J GLU* 3.7 6.6 + - - +
102J LEU* 1.3 74.0 - - - +
104J LEU* 1.3 58.4 + - - +
106J LYS* 4.1 13.8 + - - +
107J ALA* 3.4 20.6 + - - +
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Residues in contact with LEU 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F GLU* 4.8 3.1 - - - +
100J GLU 2.9 13.4 + - - +
101J ARG* 3.0 41.0 + - - +
103J ASP* 1.3 77.0 - - - +
105J ILE* 1.3 65.3 + - - +
107J ALA* 3.3 7.4 + - + +
108J LYS* 3.2 22.9 + - + +
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Residues in contact with ILE 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F ASP* 3.0 47.3 - - + +
221F TRP* 5.2 17.5 - - + -
222F ILE* 4.9 7.2 - - + -
101J ARG 2.9 15.3 + - - +
102J LEU* 2.9 34.3 - - + +
104J LEU* 1.3 71.7 - - - +
106J LYS* 1.3 67.6 + - + +
108J LYS* 3.2 23.0 + - - +
109J ARG* 3.5 20.0 + - - +
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Residues in contact with LYS 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F GLN* 5.9 1.1 - - - -
215F GLN* 5.1 18.0 - - - +
218F ASP* 4.1 17.3 - - - +
102J LEU* 2.9 33.9 + - - +
103J ASP* 4.1 15.5 + - - +
105J ILE* 1.3 80.0 - - + +
107J ALA* 1.3 63.1 + - - +
109J ARG* 3.1 47.6 + - - +
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Residues in contact with ALA 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J ASP 3.4 12.9 + - - +
104J LEU* 3.3 13.1 + - + +
105J ILE 3.3 0.6 - - - -
106J LYS* 1.3 78.3 - - - +
108J LYS* 1.3 62.5 + - - +
109J ARG 3.3 6.4 + - - +
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Residues in contact with LYS 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J LEU* 3.2 17.2 + - + +
105J ILE* 3.5 20.9 - - - +
106J LYS 3.2 0.4 - - - -
107J ALA* 1.3 77.0 - - - +
109J ARG* 1.3 80.8 + - - +
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Residues in contact with ARG 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F GLN* 2.2 43.5 + - - +
218F ASP* 2.6 36.3 + - - -
105J ILE* 3.5 15.4 + - - +
106J LYS* 3.1 40.5 + - - +
107J ALA 3.9 6.8 - - - +
108J LYS* 1.3 98.9 - - - +
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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