Contacts of the strand formed by residues 274 - 281 (chain B) in PDB entry 2Q41
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 VAL 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B SER* 3.9 11.9 - - - +
238B LEU 5.0 0.7 - - - +
239B TRP* 3.8 19.5 - - + -
264B TRP* 4.0 20.4 - - + -
265B THR 3.4 14.8 - - - +
266B SER* 4.3 8.3 - - - -
267B VAL 4.3 1.1 - - - +
270B TYR* 4.0 5.3 + - - +
271B PRO* 3.2 17.5 + - - +
272B SER* 3.0 26.3 + - - +
273B GLY* 1.3 84.5 - - - +
275B ILE* 1.3 65.4 + - - +
266C SER* 3.6 26.2 - - - +
273C GLY 4.9 3.4 - - - +
274C VAL* 5.4 0.4 - - + -
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Residues in contact with ILE 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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106B TYR* 4.0 12.3 - - + -
234B GLN* 3.7 34.1 - - + +
236B GLU* 3.5 26.0 - - - +
237B SER* 4.6 1.3 - - - +
264B TRP* 3.3 4.3 - - - -
265B THR* 2.9 34.6 + - + +
267B VAL* 3.8 22.4 - - + -
270B TYR* 3.7 32.5 - - + -
271B PRO* 6.2 1.8 - - + -
274B VAL* 1.3 78.8 - - - +
276B GLY* 1.3 64.7 + - - +
277B PHE* 4.2 6.5 - - + -
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Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLN* 3.6 4.2 - - - +
235B ALA* 2.7 26.9 + - - -
236B GLU 2.6 20.9 + - - -
262B TYR* 3.7 12.3 - - - -
263B ALA 3.1 10.8 - - - -
264B TRP* 4.0 2.0 - - - -
275B ILE* 1.3 76.0 - - - +
277B PHE* 1.3 70.8 + - - -
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Residues in contact with PHE 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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106B TYR* 3.3 45.1 - + - -
109B MSE 3.9 11.0 - - + -
110B ILE* 3.5 25.8 - - + -
113B LEU* 3.6 31.0 - - + -
232B CYS* 3.9 15.5 - - - -
233B THR 3.0 11.0 - - - +
234B GLN* 4.0 4.5 - - - -
235B ALA* 4.0 5.7 - - - +
262B TYR* 3.4 8.8 - - - -
263B ALA* 2.6 41.4 + - + +
265B THR* 3.7 26.7 - - + -
275B ILE* 4.2 5.4 - - + -
276B GLY* 1.3 82.1 - - - -
278B MSE 1.3 59.8 + - - +
279B LEU* 3.7 3.6 - - + +
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Residues in contact with MSE 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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231B VAL 3.4 1.4 - - - +
232B CYS* 3.1 7.4 - - - -
233B THR* 2.5 47.8 + - + +
235B ALA* 3.5 14.8 - - + -
245B ILE* 5.1 0.7 - - - +
248B ILE* 3.3 25.6 - - + -
249B VAL* 3.5 34.5 - - + -
252B CYS* 3.5 22.7 - - + -
260B VAL* 3.4 32.5 - - + -
261B ASN 3.9 12.1 - - - +
262B TYR* 4.1 10.5 - - - -
277B PHE* 1.3 72.5 - - - +
279B LEU* 1.3 60.5 + - - +
280B CYS* 4.0 7.5 + - - -
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Residues in contact with LEU 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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113B LEU* 3.4 42.2 - - + -
114B PRO* 4.0 4.9 - - + -
231B VAL 3.5 2.5 - - - +
232B CYS* 3.8 24.0 - - + -
260B VAL* 3.1 1.4 - - - -
261B ASN* 2.5 44.6 + - + -
262B TYR 4.8 0.2 - - - -
263B ALA* 4.0 9.4 - - + +
277B PHE* 3.7 14.6 - - + +
278B MSE 1.3 78.1 - - - +
280B CYS* 1.3 60.4 + - - +
289B PHE* 3.6 46.5 - - + -
319B PHE* 4.2 9.2 - - + -
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Residues in contact with CYS 280 (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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230B VAL* 3.0 8.5 - - - +
231B VAL* 2.9 48.9 + - + +
252B CYS* 3.6 38.4 - - - -
256B PHE* 3.6 22.4 - - + -
259B SER 2.9 9.4 - - - +
260B VAL* 3.8 10.3 - - - -
278B MSE 4.1 8.1 - - - -
279B LEU* 1.3 79.1 - - - +
281B SER* 1.3 61.0 + - - +
289B PHE* 3.6 2.6 - - - -
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Residues in contact with SER 281 (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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228B GLY 4.5 0.2 - - - -
229B GLY 3.0 11.0 - - - -
230B VAL* 3.9 1.1 - - - -
256B PHE* 4.0 6.6 - - - +
258B GLY* 2.9 24.1 + - - -
259B SER* 2.5 46.0 + - - +
280B CYS* 1.3 76.7 - - - +
282B THR* 1.3 62.8 + - - +
285B PRO 5.2 1.1 + - - -
287B VAL* 3.5 39.0 + - - +
289B PHE* 4.2 0.4 - - - -
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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