Contacts of the strand formed by residues 91 - 96 (chain B) in PDB entry 1VDG
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 LEU 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.6 33.0 - - + +
9B TRP* 3.8 30.7 - - - +
10B ALA* 3.9 10.5 - - + +
14B SER* 4.2 13.7 - - - -
24B LEU* 4.1 35.7 - - + -
71B GLY 3.5 0.2 - - - +
72B ARG* 4.6 0.2 - - - -
73B TYR* 2.8 38.5 + - + +
89B ASP 3.7 0.2 + - - -
90B PRO* 1.3 73.4 - - - +
92B GLU* 1.3 67.1 + - - +
93B LEU* 3.4 11.5 + - + -
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Residues in contact with GLU 92 (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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5A LYS* 3.1 33.3 + - - -
89A ASP* 4.0 10.1 - - - +
14B SER* 3.4 21.4 + - - +
71B GLY 3.6 4.3 - - - -
72B ARG* 3.3 16.7 + - + +
90B PRO 4.3 1.8 + - - -
91B LEU* 1.3 78.1 - - - +
93B LEU* 1.3 60.6 + - - +
94B VAL* 3.6 7.6 + - + +
183B TYR* 2.9 39.9 + - + -
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Residues in contact with LEU 93 (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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10B ALA* 5.2 0.7 - - + -
14B SER* 3.7 15.9 - - - +
16B ILE* 4.6 1.6 - - + -
22B VAL* 4.4 12.1 - - + -
24B LEU* 3.7 39.5 - - + -
62B ILE* 4.1 17.5 - - + -
65B ILE* 4.0 22.4 - - + -
69B HIS 3.6 18.6 - - - +
70B ALA* 3.2 8.1 - - - -
71B GLY 2.8 37.2 + - - +
73B TYR* 3.8 12.3 - - + -
91B LEU* 3.4 6.4 + - + -
92B GLU* 1.3 69.8 - - - +
94B VAL* 1.3 65.0 - - - +
183B TYR* 3.4 5.1 - - - +
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Residues in contact with VAL 94 (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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14B SER 2.8 18.1 + - - +
15B VAL* 4.3 6.5 - - + -
16B ILE* 3.1 26.8 + - - +
92B GLU* 4.2 8.7 - - + +
93B LEU* 1.3 79.0 - - - +
95B VAL* 1.3 70.6 + - - +
96B THR* 4.2 3.6 - - + -
182B PRO 4.9 0.2 - - - +
183B TYR* 3.2 27.8 - - + +
185B TRP* 3.1 63.0 - - + +
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Residues in contact with VAL 95 (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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16B ILE 3.3 3.8 - - - +
18B GLN* 3.8 24.5 - - + -
65B ILE* 3.6 26.2 - - + -
66B THR 3.5 23.1 - - - +
67B TRP* 3.4 32.4 - - + -
70B ALA* 4.0 17.3 - - + +
94B VAL* 1.3 77.4 - - - +
96B THR* 1.3 63.5 + - - +
183B TYR 2.9 8.6 + - - +
184B GLU* 3.5 4.3 - - - -
185B TRP 2.9 24.0 + - - +
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Residues in contact with THR 96 (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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15B VAL* 3.6 26.7 - - + -
16B ILE 3.1 8.3 + - - +
17B THR* 3.2 27.9 + - - +
18B GLN* 3.0 29.6 + - - +
67B TRP* 3.7 1.2 - - - -
94B VAL* 4.2 1.1 - - + -
95B VAL* 1.3 76.1 - - - +
97B GLY* 1.3 61.9 + - - +
98B ALA 3.6 1.6 - - - -
175B TYR* 3.5 28.4 + - + +
185B TRP* 3.6 14.8 - - + -
186B SER 3.5 8.3 - - - -
188B PRO* 4.6 5.7 - - - +
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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