Contacts of the helix formed by residues 84 - 92 (chain A) in PDB entry 2VR2
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 HIS 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ASP* 3.1 8.3 + - - +
83A PHE* 1.3 77.9 - - - +
85A GLN* 1.3 69.1 + - - +
87A THR* 2.8 16.6 + - - -
88A LYS* 2.9 46.0 + - + +
124A LYS* 3.5 38.5 - - + +
126A CYS* 3.6 20.3 - - - -
455A VAL 5.9 0.6 + - - -
456A THR* 5.1 1.2 - - - -
457A ALA* 3.6 22.8 + - + +
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Residues in contact with GLN 85 (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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80A ILE 5.4 0.4 - - - +
81A ASP* 4.1 6.7 - - - +
82A ASP* 3.0 16.2 + - - +
84A HIS* 1.3 85.8 + - - +
86A GLY* 1.3 56.3 + - - +
88A LYS* 3.5 36.3 - - - +
89A ALA* 2.8 31.2 + - - +
420A HIS* 2.8 27.0 + - - +
421A GLN 5.1 0.2 - - - -
422A ALA* 4.1 23.8 - - + +
1496A CL 3.9 11.5 - - - +
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Residues in contact with GLY 86 (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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70A MET* 3.8 24.3 - - - +
81A ASP* 4.1 12.6 + - - -
82A ASP 2.7 24.0 + - - -
85A GLN* 1.3 75.5 - - - +
87A THR* 1.3 54.7 + - - +
89A ALA* 3.6 1.9 + - - +
90A ALA* 3.0 24.4 + - - +
352A VAL* 3.7 11.8 - - - +
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Residues in contact with THR 87 (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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83A PHE* 2.6 28.5 + - - +
84A HIS 2.8 11.3 + - - -
86A GLY* 1.3 74.4 - - - +
88A LYS* 1.3 65.5 + - - +
89A ALA 3.2 0.4 - - - -
90A ALA* 3.2 8.2 + - - +
91A LEU* 2.9 28.4 + - - +
98A ILE* 3.8 26.2 - - + -
125A VAL* 4.1 12.8 - - + -
126A CYS* 3.0 25.1 + - - +
127A CYS* 3.7 23.3 - - - -
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Residues in contact with LYS 88 (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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84A HIS* 2.9 42.2 + - + +
85A GLN* 3.5 34.3 - - - +
87A THR* 1.3 77.9 + - - +
89A ALA* 1.3 59.9 + - - +
91A LEU* 3.4 3.5 + - - +
92A SER 3.2 10.0 + - - -
126A CYS* 4.4 13.8 - - - +
453A PHE* 3.2 60.4 - - + +
455A VAL* 5.3 4.3 - - + +
1496A CL 3.1 24.8 - - - +
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Residues in contact with ALA 89 (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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85A GLN 2.8 17.7 + - - +
86A GLY* 3.7 6.7 - - - +
88A LYS* 1.3 75.4 - - - +
90A ALA* 1.3 63.8 + - - +
92A SER* 2.6 23.9 + - - -
352A VAL* 4.3 3.6 - - + -
353A GLU* 3.3 19.2 - - + +
420A HIS* 3.5 27.1 + - - +
421A GLN* 3.8 21.1 - - + +
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Residues in contact with ALA 90 (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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86A GLY 3.0 16.5 + - - +
87A THR* 3.2 13.9 + - - +
89A ALA* 1.3 75.5 - - - +
91A LEU* 1.3 59.6 + - - +
93A GLY* 3.1 9.9 + - - -
94A GLY 3.2 0.2 + - - -
95A THR* 2.9 44.0 + - + +
98A ILE* 4.3 7.6 - - + -
127A CYS* 4.7 2.5 - - - -
352A VAL* 3.8 28.4 - - + +
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Residues in contact with LEU 91 (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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87A THR 2.9 19.9 + - - +
88A LYS* 3.7 6.1 - - - +
90A ALA* 1.3 71.8 - - - +
92A SER* 1.3 60.7 + - - +
93A GLY 3.0 6.2 + - - -
94A GLY 3.4 3.6 + - - -
95A THR 3.6 13.5 - - - +
96A THR* 4.0 3.8 - - + -
126A CYS* 3.8 33.9 - - + +
127A CYS* 3.8 17.5 - - + -
440A THR* 2.9 42.3 + - + -
442A SER* 3.9 9.4 - - - -
447A VAL* 3.8 35.0 - - + -
448A TYR* 4.0 7.0 - - + +
453A PHE* 4.9 2.9 - - + -
455A VAL* 4.3 8.1 - - + -
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Residues in contact with SER 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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88A LYS 3.2 11.7 + - - -
89A ALA* 2.6 23.6 + - - -
91A LEU* 1.3 75.1 - - - +
93A GLY* 1.3 55.6 + - - +
94A GLY 3.7 0.2 - - - -
353A GLU* 3.2 21.1 - - - +
412A ARG* 5.2 3.5 + - - -
420A HIS* 3.3 20.1 + - - -
437A PRO* 3.7 14.2 - - - +
448A TYR* 3.6 36.2 + - - -
453A PHE* 3.7 6.5 - - - -
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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