Contacts of the strand formed by residues 282 - 286 (chain B) in PDB entry 2VZE
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 CYS 282 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B PRO* 3.2 39.8 + - + +
68B ALA 3.6 9.9 - - - -
70B TRP* 3.9 20.0 - - - -
255B ASP 3.0 15.4 + - - +
256B ILE* 3.3 19.3 - - + -
257B MET* 2.9 25.6 + - - -
276B PRO* 4.2 4.0 - - - +
281B ALA* 1.3 73.6 - - - +
283B THR* 1.3 76.2 + - - +
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Residues in contact with THR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 2.9 18.3 + - - +
69B LEU* 3.8 14.8 - - + +
70B TRP 3.0 25.6 + - - +
120B TRP* 4.5 5.2 - - - +
257B MET* 3.5 9.2 + - - +
259B THR* 5.2 1.2 + - - -
271B CYS 4.8 0.2 + - - -
272B SER* 2.5 39.6 + - - +
276B PRO* 3.7 14.4 - - - +
277B TRP* 3.7 18.2 - - + -
281B ALA 3.8 1.2 + - - -
282B CYS* 1.3 79.0 - - - +
284B PHE* 1.3 61.5 + - - +
285B VAL* 4.7 2.0 - - + -
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Residues in contact with PHE 284 (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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70B TRP* 3.4 40.6 - + + -
72B VAL* 3.9 29.6 - - + -
256B ILE* 3.8 6.5 - - + -
257B MET 2.8 17.0 + - - +
258B TRP* 3.1 33.8 - + + -
259B THR 4.2 4.5 + - - +
272B SER* 5.0 0.9 + - - -
282B CYS 4.1 0.2 + - - -
283B THR* 1.3 75.1 + - - +
285B VAL* 1.3 73.9 + - - +
286B HIS* 4.4 3.1 - - + -
299B THR* 3.7 20.4 - - + -
303B TYR* 3.7 39.0 - + + -
305B ILE* 3.5 27.1 - - + -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.8 22.7 - - + -
70B TRP 2.9 11.7 + - - +
71B TRP* 3.2 25.3 - - + -
72B VAL* 2.9 27.2 + - - +
115B ARG* 3.9 14.6 - - + +
120B TRP* 3.6 44.0 - - + +
258B TRP* 4.5 1.3 - - - +
259B THR 5.8 1.3 - - - +
272B SER* 4.5 4.0 - - - +
283B THR* 4.7 2.2 - - + -
284B PHE* 1.3 82.2 - - - +
286B HIS* 1.3 69.8 + - - +
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Residues in contact with HIS 286 (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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72B VAL* 3.2 22.8 - - + +
73B ASN 3.7 5.4 - - - -
74B GLY* 3.6 35.0 - - - -
115B ARG* 3.5 19.4 + - - +
258B TRP* 3.8 30.1 + + + +
284B PHE* 4.4 1.8 - - + -
285B VAL* 1.3 77.2 - - - +
287B LEU* 1.3 67.2 + - - +
288B LEU* 3.0 33.3 + - + +
289B PRO* 5.1 1.3 - - + -
295B VAL* 3.7 23.4 - - + +
299B THR* 3.3 31.2 + - + -
303B TYR* 5.5 0.6 - + - -
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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