Contacts of the strand formed by residues 91 - 97 (chain B) in PDB entry 1VLM
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 PHE 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ARG* 3.3 43.1 - - + -
39B GLY 3.5 27.6 - - - -
40B VAL* 3.5 26.9 - - + -
57B ILE* 4.3 11.7 - - + -
86B LEU* 3.9 31.2 - - + -
89B GLU 3.7 0.2 - - - -
90B SER* 1.3 106.3 - - - +
92B ASP* 1.3 63.0 + - - +
93B PHE 3.9 9.2 - - - +
116B ILE* 3.1 24.0 + - + +
117B LEU* 3.5 5.3 - - + -
118B LYS* 2.9 30.9 + - - +
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Residues in contact with ASP 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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35B PRO* 5.0 0.2 - - - +
36B GLU 4.0 13.5 - - - +
37B GLY* 3.2 9.1 - - - -
38B ARG* 2.8 34.8 + - - +
91B PHE* 1.3 73.5 - - - +
93B PHE* 1.3 62.5 + - + +
117B LEU* 3.8 0.9 - - - -
118B LYS* 3.3 34.0 + - - +
121B GLY* 3.2 9.6 - - - -
122B TYR* 3.0 25.1 + - - -
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Residues in contact with PHE 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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34B LEU* 3.6 37.9 - - + -
35B PRO* 3.5 42.0 - - + -
36B GLU 4.1 5.6 - - - -
37B GLY 3.5 22.4 - - - -
38B ARG 3.2 4.4 + - - +
39B GLY* 3.0 43.2 - - - -
40B VAL 3.1 4.2 + - - -
55B ILE* 4.0 23.8 - - + -
91B PHE* 3.9 5.7 - - - +
92B ASP* 1.3 84.2 - - - +
94B ALA* 1.3 69.2 + - - +
95B LEU* 5.0 1.1 - - + -
117B LEU* 3.5 5.8 - - - -
122B TYR 3.1 13.9 - - - +
124B ILE* 4.1 8.3 - - + -
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Residues in contact with ALA 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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40B VAL* 3.3 22.4 - - + +
42B ILE* 4.2 14.4 - - + -
93B PHE* 1.3 77.6 - - - +
95B LEU* 1.3 56.2 + - - +
113B ALA* 4.9 2.7 - - + -
116B ILE* 4.3 10.8 - - + -
117B LEU* 4.3 5.6 - - + -
122B TYR 2.9 7.8 + - - +
123B LEU* 3.3 17.5 - - + +
124B ILE* 2.8 34.0 + - - +
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Residues in contact with LEU 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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30B VAL* 3.8 11.2 - - + -
34B LEU* 4.7 5.8 - - + -
40B VAL 3.0 10.8 + - - +
41B GLU* 3.5 23.5 - - + +
42B ILE* 2.8 31.7 + - - +
49B PHE* 4.3 2.2 - - + -
53B LEU* 3.7 20.2 - - + -
55B ILE* 3.5 31.2 - - + -
93B PHE* 5.0 1.3 - - + -
94B ALA* 1.3 74.5 - - - +
96B MSE 1.3 64.6 + - - +
97B VAL* 3.5 30.1 - - + -
124B ILE* 3.3 28.9 - - + +
125B VAL* 5.4 0.2 - - - -
126B GLY 5.5 0.2 - - - +
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Residues in contact with MSE 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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42B ILE* 3.7 37.5 - - + +
95B LEU* 1.3 76.6 - - - +
97B VAL* 1.3 63.0 + - - +
98B THR 4.0 0.2 + - - -
99B THR* 4.0 20.0 - - + -
100B ILE* 3.8 29.4 - - - +
109B ALA* 3.8 18.4 - - + +
110B LEU* 4.5 5.8 - - + -
113B ALA* 3.4 33.2 - - + -
123B LEU* 4.0 15.9 - - + -
124B ILE 2.8 12.2 + - - +
125B VAL* 3.3 14.8 - - + +
126B GLY 2.9 24.8 + - - +
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Residues in contact with VAL 97 (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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26B GLU* 5.1 0.7 - - - +
30B VAL* 4.0 15.5 - - + -
41B GLU* 4.5 8.3 + - - +
43B GLY 4.8 4.0 - - - +
49B PHE* 3.7 43.9 - - + -
95B LEU* 3.5 36.0 - - + +
96B MSE 1.3 71.9 - - - +
98B THR* 1.3 80.4 + - - +
99B THR* 3.1 9.0 + - - -
126B GLY 3.7 4.7 - - - +
199B PHE* 3.9 22.4 - - + -
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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