Contacts of the strand formed by residues 87 - 92 (chain A) in PDB entry 2VRM
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 ARG 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLU* 1.3 77.7 - - - +
88A LEU* 1.3 66.3 + - - +
89A ILE* 4.2 0.3 + - - +
98A PRO* 3.6 30.4 - - + +
99A PHE* 3.6 12.6 - - - +
100A ARG* 3.5 44.9 - - + +
309A LYS 2.8 28.3 + - - -
310A ASP* 3.0 20.5 + - - +
311A TYR* 3.3 27.0 + - + +
312A CYS* 2.9 24.8 + - - -
313A GLY 4.4 1.0 + - - -
314A THR 4.7 0.7 - - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 3.6 34.8 - - + +
86A GLU 4.0 9.9 - - - +
87A ARG* 1.3 76.6 - - - +
89A ILE* 1.3 61.2 + - - +
98A PRO* 3.2 5.5 - - - +
99A PHE* 2.7 71.4 + - + +
100A ARG* 4.6 0.9 - - - -
101A GLY 3.8 19.1 - - - +
102A PRO* 4.2 9.0 - - + +
312A CYS* 4.1 2.2 - - - -
314A THR* 3.7 33.7 - - + +
316A ILE* 5.2 2.2 - - + -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG 4.7 1.1 - - - +
88A LEU* 1.3 80.3 - - - +
90A HIS* 1.3 63.1 + - - +
91A HIS 4.0 0.4 - - - +
96A SER* 3.6 30.1 - - - +
97A TYR 3.9 3.8 - - - +
98A PRO* 4.6 3.1 - - + -
99A PHE* 3.9 3.6 - - - -
311A TYR* 3.7 38.8 - - + -
314A THR 2.9 13.7 + - - +
315A MET* 3.4 7.2 - - + -
316A ILE* 2.8 35.7 + - - +
371A VAL* 3.7 27.1 - - + +
372A LEU* 3.8 26.9 - - + -
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Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 1.3 73.5 - - - +
91A HIS* 1.3 64.8 + - - +
92A VAL* 4.1 28.7 - - + +
97A TYR* 2.8 51.9 + - + +
99A PHE* 3.8 15.0 - - + -
104A PRO* 3.8 21.9 - - + +
105A PRO 6.0 0.2 + - - -
115A HIS* 6.3 1.8 - + - -
164A LEU* 4.1 27.3 - - + +
316A ILE* 3.3 29.8 - - + +
318A ASP* 4.8 7.6 + - - +
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Residues in contact with HIS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE 3.9 0.8 - - - -
90A HIS* 1.3 71.4 - - - +
92A VAL* 1.3 64.0 + - - +
94A GLY* 3.4 41.1 - - - -
95A LYS* 3.2 9.6 - - - -
96A SER* 2.8 26.2 + - - +
316A ILE 2.8 13.4 + - - +
317A ILE* 4.1 16.2 - - + -
318A ASP* 2.9 33.9 + - - +
367A LEU* 5.5 2.5 - - + +
370A LYS* 4.5 19.0 + - - +
371A VAL* 3.7 41.8 - - + +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A HIS* 3.8 24.9 + - + +
91A HIS* 1.3 75.8 - - - +
93A LYS* 1.3 80.3 + - + +
94A GLY 3.3 1.3 - - - +
95A LYS* 2.9 19.7 + - - +
97A TYR* 3.7 29.2 + - + +
163A GLN* 3.9 20.9 - - - +
318A ASP* 3.9 20.0 - - + +
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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