Contacts of the helix formed by residues 91 - 100 (chain J) in PDB entry 1VQ7
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 91 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6150 G 3.7 27.8 + - - +
6160 U 4.5 18.4 + - - -
11050 C 3.9 19.2 + - - -
88J PRO* 3.0 23.9 + - + +
90J LYS* 1.3 81.7 - - - +
92J GLN* 1.3 67.5 + - - +
93J ARG* 4.3 13.2 - - + +
94J GLY 3.2 6.4 + - - +
95J ARG* 2.9 23.5 + - - +
9302J CL 4.3 5.8 - - + -
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Residues in contact with GLN 92 (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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6130 C 4.4 13.9 + - - -
6140 U 3.8 37.1 + - - +
91J LYS* 1.3 73.6 - - - +
93J ARG* 1.3 67.3 + - - +
95J ARG* 3.3 5.1 + - - +
96J GLU* 3.1 45.5 + - + +
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Residues in contact with ARG 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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6150 G 4.9 6.5 + - - -
11040 C 5.7 0.6 + - - -
11050 C 3.3 27.1 + - - -
11060 A 5.6 2.0 + - - -
31J LEU* 4.2 37.7 + - + +
88J PRO* 4.3 14.5 - - - +
91J LYS* 3.3 16.3 - - + +
92J GLN* 1.3 84.2 - - - +
94J GLY* 1.3 61.6 + - - +
96J GLU* 3.2 13.5 + - - +
97J ALA* 3.0 23.2 + - + +
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Residues in contact with GLY 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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31J LEU* 4.7 2.0 - - - -
87J LEU* 4.4 2.6 - - - +
88J PRO* 3.2 38.5 + - - -
89J HIS* 4.0 4.6 - - - -
91J LYS* 3.2 7.1 + - - +
93J ARG* 1.3 81.8 - - - +
95J ARG* 1.3 59.9 + - - +
97J ALA* 3.4 5.8 + - - +
98J PHE* 3.0 25.6 + - - +
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Residues in contact with ARG 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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5330 U 2.7 65.1 + - - -
5340 C 3.8 13.7 + - - -
28140 A 3.2 28.7 + - - -
89J HIS* 3.9 18.0 - - - +
90J LYS 5.7 0.4 - - - -
91J LYS 2.9 20.5 + - - +
92J GLN* 3.8 4.9 - - - +
94J GLY* 1.3 71.9 - - - +
96J GLU* 1.3 58.3 + - + +
98J PHE* 3.8 8.5 - - + +
99J GLU* 2.8 58.9 + - - +
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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 GLN* 3.1 46.9 + - + +
93J ARG* 3.2 12.7 + - - +
95J ARG* 1.3 76.9 - - + +
97J ALA* 1.3 63.7 + - - +
99J GLU* 3.1 8.1 + - - +
100J SER* 2.9 25.6 + - - -
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Residues in contact with ALA 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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30J ALA* 3.5 35.7 - - + +
31J LEU* 3.7 18.6 - - + -
87J LEU* 4.1 5.8 - - + -
93J ARG* 3.0 9.8 + - + +
94J GLY 3.7 7.4 - - - +
96J GLU* 1.3 79.0 - - - +
98J PHE* 1.3 63.6 + - - +
100J SER* 2.7 24.7 + - - -
101J VAL* 3.3 13.0 - - - +
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Residues in contact with PHE 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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28150 G 5.5 5.2 - - - -
80J LYS* 3.5 47.5 - - + -
81J ARG* 5.7 0.4 - - - -
83J ILE* 4.6 6.5 - - + -
84J ARG* 3.5 54.1 - - + -
87J LEU* 3.6 16.7 - - + +
89J HIS* 4.8 9.0 - - + -
94J GLY 3.0 18.8 + - - +
95J ARG* 3.9 8.1 - - + +
97J ALA* 1.3 75.5 - - - +
99J GLU* 1.3 70.7 + - + +
101J VAL* 3.1 25.7 + - + +
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Residues in contact with GLU 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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28140 A 2.9 20.6 + - - -
28150 G 3.1 36.5 + - - +
6J PHE* 4.6 8.7 - - - -
80J LYS* 5.4 2.8 + - - +
95J ARG* 2.8 56.8 + - - +
96J GLU* 3.1 6.6 + - - +
98J PHE* 1.3 84.0 - - + +
100J SER* 1.3 56.5 + - - +
101J VAL 3.2 6.3 + - - +
102J ARG* 4.7 5.4 + - - +
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Residues in contact with SER 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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6J PHE* 3.7 13.3 - - - -
30J ALA* 4.4 1.9 + - - +
33J GLY 5.3 1.7 + - - -
34J GLU 3.7 12.9 + - - +
35J THR* 3.4 17.7 - - - -
36J VAL 3.1 22.5 + - - -
96J GLU 2.9 13.4 + - - -
97J ALA* 2.7 23.7 + - - -
99J GLU* 1.3 77.1 - - - +
101J VAL* 1.3 58.1 + - - +
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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