Contacts of the strand formed by residues 271 - 279 (chain B) in PDB entry 6VSB
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 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU* 3.8 5.4 - - - -
55B PHE 2.8 27.0 + - - +
57B PRO* 3.2 20.7 - - + +
269B TYR* 4.4 8.5 + - + +
270B LEU* 1.3 80.3 - - - +
272B PRO* 1.3 70.4 - - + +
273B ARG* 2.8 46.9 + - + +
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Residues in contact with PRO 272 (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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52B GLN* 3.9 21.5 + - + +
53B ASP 3.5 9.0 - - - +
54B LEU* 3.7 20.2 - - + -
270B LEU 4.9 0.2 - - - +
271B GLN* 1.3 84.4 - - + +
273B ARG* 1.3 58.8 + - - +
274B THR 4.2 0.2 + - - -
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Residues in contact with ARG 273 (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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52B GLN* 4.1 3.4 - - - -
53B ASP 2.8 23.0 + - - +
55B PHE* 3.4 14.4 - - + +
57B PRO* 3.5 38.2 - - - +
271B GLN* 2.8 50.1 + - + +
272B PRO* 1.3 75.1 - - - +
274B THR* 1.3 63.7 + - - +
275B PHE* 3.4 16.9 + - + -
290B ASP* 3.2 21.2 + - - +
292B ALA* 3.4 36.6 + - + +
293B LEU* 4.6 1.8 - - - +
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Residues in contact with THR 274 (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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50B SER* 4.9 9.0 - - - +
51B THR 3.2 21.8 - - - +
52B GLN* 3.3 28.7 + - + +
272B PRO 4.2 0.8 + - - -
273B ARG* 1.3 71.3 - - - +
275B PHE* 1.3 70.1 + - - +
291B CYS* 3.0 44.4 + - - +
301B CYS* 5.5 0.7 - - + -
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Residues in contact with PHE 275 (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 GLY 5.9 0.2 - - - -
36B VAL* 4.6 3.8 - - + -
50B SER* 3.2 2.5 - - - -
51B THR* 2.9 33.3 + - + +
55B PHE* 4.0 32.9 - + + -
56B LEU 3.9 15.5 - - - -
58B PHE* 3.4 32.5 - + - -
273B ARG* 3.4 26.5 + - + -
274B THR* 1.3 84.3 - - - +
276B LEU* 1.3 61.0 + - - +
277B LEU* 3.7 18.5 + - + -
288B ALA* 4.4 9.9 - - + -
289B VAL 3.2 12.8 - - - +
290B ASP* 3.3 36.8 - - - -
291B CYS* 3.9 4.5 - - - -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.9 22.7 - - + +
49B HIS 3.5 13.2 - - - +
50B SER* 3.6 23.1 - - - +
275B PHE* 1.3 70.0 - - - +
277B LEU* 1.3 61.1 + - - +
278B LYS 3.6 0.5 + - - -
288B ALA* 3.3 4.9 - - - -
289B VAL* 3.1 41.8 + - + -
291B CYS* 4.1 0.8 - - - -
300B LYS 3.9 16.2 - - - +
301B CYS* 4.1 11.0 - - - -
304B LYS* 3.9 11.9 - - + -
305B SER 3.8 29.6 - - - +
306B PHE* 3.7 19.6 - - + -
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Residues in contact with LEU 277 (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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36B VAL* 3.7 28.9 - - + -
37B TYR 4.4 1.6 - - - +
39B PRO* 3.6 37.5 - - + -
47B VAL 4.0 0.2 - - - +
48B LEU* 3.6 4.5 - - - -
49B HIS* 2.7 38.4 + - + +
51B THR* 4.1 12.6 - - + -
55B PHE* 4.7 6.3 - - + -
275B PHE* 4.1 24.0 - - + +
276B LEU* 1.3 71.6 - - - +
278B LYS* 1.3 61.0 + - - +
279B TYR* 3.7 24.0 + - + +
285B ILE* 4.1 13.9 - - + -
287B ASP 4.1 1.6 - - - -
288B ALA* 4.2 6.5 - - + -
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Residues in contact with LYS 278 (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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48B LEU* 3.5 20.2 - - + -
276B LEU 3.6 0.6 + - - -
277B LEU* 1.3 70.1 - - - +
279B TYR* 1.3 65.6 + - - +
280B ASN* 5.2 2.7 - - - +
285B ILE* 3.2 6.3 - - - -
286B THR* 3.0 35.0 + - - +
287B ASP* 3.2 41.0 + - + +
306B PHE* 3.6 33.2 - - + +
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Residues in contact with TYR 279 (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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38B TYR* 4.2 8.8 - + - -
39B PRO* 3.8 25.6 - - - +
40B ASP 5.4 2.1 + - - -
42B VAL 5.0 9.7 + - - -
44B ARG* 3.5 72.4 + - + +
45B SER 4.4 0.4 - - - +
46B SER* 3.0 26.9 + - - -
47B VAL 3.4 16.5 + - - +
48B LEU* 5.7 0.2 - - - +
49B HIS* 4.2 6.7 - + + -
277B LEU* 4.0 25.5 - - + +
278B LYS* 1.3 77.3 - - - +
280B ASN* 1.3 60.2 + - - +
283B GLY 3.5 22.9 - - - -
284B THR 3.2 4.0 - - - +
285B ILE* 3.6 25.0 - - + +
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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