Contacts of the strand formed by residues 85 - 92 (chain B) in PDB entry 5V8V
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 GLN 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B THR 3.1 3.5 - - - +
80B ASN* 3.7 1.0 - - - -
81B TYR* 2.9 60.2 + - + +
83B ASP 3.9 0.2 - - - -
84B THR* 1.3 93.6 + - - +
86B TYR* 1.3 61.6 + - - +
87B TYR* 4.1 8.6 - - + -
187B LEU 2.8 27.7 + - - -
189B GLU* 2.9 25.8 + - - +
190B PHE* 3.3 18.4 - - + -
502B 90D 5.4 2.4 + - - +
503B 90D 3.2 32.7 - - + -
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.5 8.9 - - + +
79B THR 3.3 5.6 - - - -
80B ASN* 3.2 23.3 + - + -
83B ASP* 3.7 23.9 + - - -
85B GLN* 1.3 75.3 - - - +
87B TYR* 1.3 60.3 + - - +
102B VAL* 3.5 22.3 - - - +
103B PHE 4.5 1.7 + - - -
228B TYR* 3.4 52.3 + + + +
229B ASN 2.7 29.3 + - - -
239B GLY 3.6 20.6 - - - -
240B GLY* 5.0 0.9 - - - -
383B ALA* 3.9 13.5 - - + -
387B ARG* 3.1 20.4 + - - +
503B 90D 2.7 27.6 + - - +
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.2 8.1 - - - +
79B THR* 2.8 70.0 + - + +
81B TYR* 4.3 7.4 - - + +
85B GLN* 4.1 14.8 - - + -
86B TYR* 1.3 76.9 - - - +
88B GLY* 1.3 58.7 + - - +
100B LYS* 3.7 42.1 + - + +
101B VAL 3.2 22.2 - - - +
102B VAL* 4.0 2.0 - - + +
189B GLU* 3.6 34.1 + - + +
190B PHE* 3.9 21.8 - - + -
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 4.5 0.7 - - - -
77B ILE 3.5 17.9 - - - -
78B LEU* 3.4 10.0 - - - +
87B TYR* 1.3 76.5 - - - +
89B GLU* 1.3 59.8 + - - -
99B PHE 3.5 0.2 - - - +
100B LYS* 3.3 6.8 - - - -
101B VAL* 2.8 38.1 + - - +
103B PHE* 3.9 6.9 - - - -
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Residues in contact with GLU 89 (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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76B VAL* 3.8 19.4 - - + +
77B ILE 4.5 1.0 + - - -
88B GLY* 1.3 73.2 - - - -
90B ILE* 1.3 76.2 + - - +
98B THR* 3.3 30.7 + - + +
99B PHE 3.3 11.9 - - - +
100B LYS* 4.8 6.2 - - + +
164B THR 4.6 1.4 - - - +
166B GLY 5.1 4.2 + - - -
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Residues in contact with ILE 90 (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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88B GLY 4.1 0.2 + - - -
89B GLU* 1.3 82.2 - - - +
91B GLY* 1.3 59.3 + - - +
92B ILE* 4.2 22.2 - - + -
97B GLN 4.0 0.3 - - - +
98B THR* 3.2 4.0 - - - -
99B PHE* 2.8 36.4 + - + +
101B VAL* 3.6 32.5 - - + -
103B PHE* 4.0 14.4 - - + -
110B VAL* 4.9 5.2 - - + -
112B VAL* 4.9 1.1 - - + -
163B ILE* 4.3 11.4 - - + -
164B THR 3.4 15.5 - - - +
165B VAL* 4.1 15.7 - - + -
194B VAL* 3.6 25.4 - - + -
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Residues in contact with GLY 91 (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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90B ILE* 1.3 74.2 - - - +
92B ILE* 1.3 63.7 + - - -
93B GLY 4.3 0.2 + - - -
96B PRO* 4.2 12.3 - - - -
97B GLN 3.6 7.4 - - - -
98B THR* 4.1 8.3 - - - -
162B ILE 3.8 0.5 - - - +
163B ILE* 3.3 3.8 - - - +
164B THR* 2.7 50.0 + - - +
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Residues in contact with ILE 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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90B ILE* 4.2 10.1 - - + -
91B GLY* 1.3 79.0 - - - +
93B GLY* 1.3 62.9 + - - +
97B GLN* 3.0 39.4 + - - +
99B PHE* 4.0 13.7 - - + -
110B VAL* 5.4 1.1 - - + -
112B VAL* 4.0 33.9 - - + -
130B PHE* 3.8 23.8 - - + -
161B ASP* 3.9 14.6 - - + -
162B ILE 3.3 9.6 - - - +
163B ILE* 3.7 30.1 - - + -
174B PHE* 4.0 13.0 - - + -
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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