Contacts of the strand formed by residues 260 - 267 (chain B) in PDB entry 6S6A
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 ALA 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B VAL 3.5 6.3 - - - -
255B ARG* 3.4 41.5 - - + +
259B PHE* 1.3 86.1 - - - +
261B ALA* 1.3 58.6 + - - +
262B PHE* 3.7 13.4 - - + -
275B VAL* 3.9 0.2 - - - -
276B MET* 3.1 34.5 + - + +
278B ASP* 4.8 7.2 - - + -
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Residues in contact with ALA 261 (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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252B MET 4.8 0.2 - - - -
253B GLU* 3.5 3.7 - - - +
254B VAL* 3.1 33.4 + - + +
259B PHE* 3.3 18.4 - - + -
260B ALA* 1.3 70.0 - - - +
262B PHE* 1.3 72.8 + - - +
263B ILE* 5.4 2.7 - - + -
273B MET* 3.6 31.0 - - + -
274B VAL 3.2 10.3 - - - +
275B VAL* 4.2 5.4 - - + +
295D VAL* 4.7 3.8 - - + -
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Residues in contact with PHE 262 (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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252B MET 3.4 7.9 - - - +
253B GLU* 3.8 33.9 - - + -
255B ARG* 4.3 6.7 - - - -
260B ALA* 3.7 20.2 - - + -
261B ALA* 1.3 77.6 - - - +
263B ILE* 1.3 58.8 + - - +
272B VAL* 3.7 1.4 - - - +
273B MET* 2.9 13.3 - - - +
274B VAL* 2.9 43.1 + - + +
276B MET* 4.2 15.0 - - + -
283B SER* 4.1 17.0 - - - -
286B THR* 3.8 26.5 - - + -
287B LEU* 3.9 28.5 - - + -
290B ILE* 4.2 21.5 - - + -
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Residues in contact with ILE 263 (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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206B PHE* 5.7 0.9 - - + -
211B PHE* 4.6 4.5 - - + -
235B ILE* 3.7 34.5 - - + -
249B PHE* 4.3 14.1 - - + -
251B SER* 3.6 3.3 - - - -
252B MET* 2.7 59.0 + - + +
254B VAL* 5.6 2.7 - - + -
261B ALA* 5.4 1.8 - - + -
262B PHE* 1.3 79.1 - - - +
264B ASP* 1.3 67.1 + - - +
271B TYR* 4.0 18.8 - - + -
272B VAL 3.2 10.5 - - - +
273B MET* 3.9 28.3 - - + -
287B LEU* 6.1 0.5 - - - +
295D VAL* 5.2 7.9 - - + -
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Residues in contact with ASP 264 (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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250B GLN* 3.7 11.4 - - - +
251B SER* 3.6 22.0 - - - -
262B PHE* 6.0 0.2 - - + -
263B ILE* 1.3 75.3 - - - +
265B ILE* 1.3 71.6 + - - +
271B TYR* 3.3 8.2 - - - -
272B VAL* 2.9 40.9 + - + +
287B LEU* 4.3 11.8 - - + +
290B ILE* 4.5 10.8 - - + +
291B ARG* 3.5 22.6 + - - -
294B ARG* 3.4 25.2 + - - +
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Residues in contact with ILE 265 (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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208B ARG* 4.0 33.0 - - - +
249B PHE 4.3 4.3 - - - +
250B GLN* 3.6 37.3 + - + +
264B ASP* 1.3 80.2 + - - +
266B PHE* 1.3 64.7 + - - +
267B THR 3.6 17.0 - - - +
270B THR 3.7 8.3 - - - +
271B TYR* 3.7 18.4 - - + +
294B ARG* 3.1 27.2 + - - +
321D ASN* 5.1 4.9 - - - +
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Residues in contact with PHE 266 (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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191B LEU* 5.0 1.1 - - + -
194B PHE* 4.0 20.4 - + - -
205B LEU* 3.7 21.8 - - + -
265B ILE* 1.3 76.2 - - - +
267B THR* 1.3 62.8 + - + +
270B THR* 3.0 19.2 + - - +
272B VAL* 3.6 33.9 - - + +
290B ILE* 3.9 32.3 - - + -
293B ALA* 3.9 8.5 - - + -
294B ARG* 3.1 40.7 - - + +
297B PHE* 3.3 56.3 - + + -
298B GLU* 4.8 0.5 - - - +
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Residues in contact with THR 267 (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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265B ILE* 3.6 12.2 - - - +
266B PHE* 1.3 84.2 - - + +
268B SER* 1.3 68.6 + - - +
269B ASN 2.9 2.9 + - - -
270B THR* 2.8 34.0 + - + +
294B ARG 4.4 1.1 - - - +
297B PHE* 3.8 19.1 - - + -
298B GLU* 3.3 40.6 - - - +
301B GLU* 2.4 34.2 + - - +
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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