Contacts of the strand formed by residues 263 - 268 (chain A) in PDB entry 6BHG
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 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LYS* 5.8 1.0 - - - +
258A LEU* 5.4 0.5 - - - +
261A GLY 3.4 1.2 + - - -
262A SER* 1.3 73.5 - - - +
264A VAL* 1.3 60.9 + - - +
278A ALA* 3.7 7.8 - - - +
279A GLY 3.0 25.6 + - - +
280A ILE* 3.6 13.1 - - - +
298A ASP* 2.8 44.1 + - - -
312A PRO* 4.1 1.7 - - - +
313A ILE* 3.2 40.9 + - + +
316A PRO* 3.8 30.3 - - + +
320A THR* 3.2 23.1 + - - +
323A ASP* 2.8 42.6 + - - +
324A ILE* 3.5 13.5 - - - +
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 4.1 26.2 - - + -
262A SER 4.1 1.3 - - - +
263A ARG* 1.3 80.7 - - - +
265A VAL* 1.3 67.5 + - - +
266A ALA* 4.8 0.4 - - + -
278A ALA* 3.3 3.8 - - - -
279A GLY 2.8 44.9 + - - +
281A VAL* 3.8 23.8 - - + -
295A ILE* 4.0 30.1 - - + -
310A LEU* 4.3 6.5 - - + -
311A TYR 3.4 13.5 - - - +
312A PRO* 4.5 2.0 - - + -
313A ILE* 3.7 7.1 - - - +
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 4.4 9.6 - - + -
213A TRP* 3.4 55.6 - - + +
248A ALA* 3.9 6.3 - - + -
264A VAL* 1.3 76.3 - - - +
266A ALA* 1.3 63.3 + - - +
276A LEU* 3.7 28.5 - - + -
277A TYR 3.5 10.1 - - - +
278A ALA* 4.6 0.4 - - - -
310A LEU* 3.2 4.2 - - - +
311A TYR* 2.8 44.1 + - + +
313A ILE* 3.9 6.5 - - + -
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Residues in contact with ALA 266 (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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264A VAL* 4.2 1.8 - - + -
265A VAL* 1.3 75.6 - - - +
267A LYS* 1.3 66.8 + - - +
268A TYR 3.3 1.2 + - - -
276A LEU* 3.5 7.3 - - - -
277A TYR 2.9 31.4 + - - +
295A ILE* 4.1 20.2 - - + -
297A PHE* 3.7 23.6 - - + -
305A VAL* 4.4 3.6 - - + -
309A GLU 3.3 11.2 - - - +
310A LEU* 4.1 9.9 - - + -
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Residues in contact with LYS 267 (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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266A ALA* 1.3 72.2 - - - +
268A TYR* 1.3 59.2 + - - +
269A LYS* 3.8 17.1 + - - +
274A VAL* 4.1 20.6 - - + -
275A TRP 3.5 5.8 - - - -
276A LEU* 3.7 17.0 - - + -
297A PHE* 3.7 9.8 - - - -
303A SER* 4.6 1.7 + - - -
305A VAL* 3.7 13.7 - - - +
308A SER 4.5 4.8 + - - -
309A GLU* 2.9 53.6 + - + +
311A TYR* 4.5 15.0 - - - -
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Residues in contact with TYR 268 (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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266A ALA 3.3 0.2 + - - -
267A LYS* 1.3 71.1 - - - +
269A LYS* 1.3 63.5 + - - +
270A ASP* 4.1 18.4 + - + -
274A VAL* 3.4 4.0 - - - +
275A TRP* 2.8 49.1 + + + +
277A TYR* 3.8 23.6 - + + -
297A PHE* 3.7 33.7 - + + -
299A ASP* 2.6 40.8 + - - -
301A TYR* 3.4 38.9 - + + +
11B THR* 4.9 2.9 - - - +
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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