Contacts of the helix formed by residues 265 - 276 (chain B) in PDB entry 2W9Z
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 GLU 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B ALA* 5.6 3.5 - - - +
118B LYS* 3.4 21.8 + - - -
263B GLU 5.0 1.3 - - - +
264B MET* 1.3 76.8 - - - +
266B GLU* 1.3 83.2 + - + +
267B SER* 4.2 4.7 - - - +
268B GLY* 3.5 1.8 + - - -
269B ALA* 3.1 20.3 + - - +
294B TYR* 3.1 35.7 + - + -
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Residues in contact with GLU 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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265B GLU* 1.3 88.1 - - + +
267B SER* 1.3 67.1 + - - +
269B ALA* 3.3 9.9 + - - +
270B GLN* 3.5 18.7 + - - +
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Residues in contact with SER 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 GLU* 4.2 2.2 - - - +
266B GLU* 1.3 78.2 - - - +
268B GLY* 1.3 55.8 + - - +
269B ALA 2.9 4.9 - - - -
270B GLN* 2.6 36.7 + - - +
271B LEU 2.8 12.3 + - - -
292B HIS* 3.7 14.3 - - - -
293B SER* 3.8 17.5 - - - -
294B TYR* 3.8 22.0 - - - -
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Residues in contact with GLY 268 (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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204B PHE* 3.2 18.2 - - - -
264B MET* 2.8 23.4 - - - +
265B GLU 3.5 4.8 + - - -
266B GLU 3.3 1.6 - - - -
267B SER* 1.3 73.8 - - - +
269B ALA* 1.3 54.1 + - - +
271B LEU* 4.7 0.4 - - - -
272B LEU 3.3 5.7 + - - -
294B TYR* 3.1 47.6 - - - -
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Residues in contact with ALA 269 (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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257B VAL* 3.7 30.8 - - + +
258B GLN* 5.2 5.6 - - + +
264B MET* 3.0 20.3 - - + +
265B GLU 3.1 11.2 + - - +
266B GLU* 3.5 10.5 - - - +
267B SER 2.9 0.4 - - - -
268B GLY* 1.3 77.4 - - - +
270B GLN* 1.3 63.4 + - + +
271B LEU 3.3 0.4 - - - -
272B LEU* 3.7 2.9 + - - +
273B LEU* 3.4 25.6 + - - +
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Residues in contact with GLN 270 (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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266B GLU* 3.7 17.0 + - - +
267B SER* 2.6 23.6 + - - +
269B ALA* 1.3 72.7 - - + +
271B LEU* 1.3 60.0 + - - +
273B LEU* 3.5 13.3 - - + +
274B GLU* 3.4 26.9 + - - +
292B HIS* 4.6 8.6 + - + +
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Residues in contact with LEU 271 (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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204B PHE* 4.4 5.4 - - + -
267B SER 2.8 9.3 + - - +
268B GLY* 4.1 4.9 - - - +
270B GLN* 1.3 73.8 - - - +
272B LEU* 1.3 63.4 + - - +
273B LEU 3.0 4.5 - - - -
274B GLU* 3.0 23.0 + - - +
275B MET* 3.0 51.1 + - + +
284B ILE* 3.6 23.3 - - + -
289B ALA* 4.3 1.8 - - + -
292B HIS* 3.1 31.1 - - + +
294B TYR* 4.3 9.4 - - + -
295B LEU* 3.4 36.1 - - + -
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Residues in contact with LEU 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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201B GLY* 2.9 43.1 - - - +
204B PHE* 3.6 14.1 - - + -
205B ALA* 3.3 27.6 - - + -
213B LEU* 4.7 4.7 - - + -
257B VAL* 5.1 5.2 - - + -
261B VAL* 5.0 5.6 - - + -
264B MET* 3.7 23.3 - - + -
268B GLY 3.3 16.2 + - - +
269B ALA 3.9 5.6 - - - +
270B GLN 3.5 0.4 - - - -
271B LEU* 1.3 78.1 - - - +
273B LEU* 1.3 58.5 + - + +
275B MET* 3.6 3.0 + - - -
276B LEU* 2.9 36.1 + - + +
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Residues in contact with LEU 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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229B LEU* 5.4 9.6 - - + -
230B ILE* 3.9 26.9 - - + +
255B ARG 5.8 3.1 - - - +
257B VAL* 4.4 21.8 - - + +
269B ALA 3.4 13.8 + - - +
270B GLN* 3.5 15.7 - - + +
271B LEU 3.0 0.4 - - - -
272B LEU* 1.3 77.2 - - + +
274B GLU* 1.3 60.5 + - + +
275B MET 3.1 1.6 - - - -
276B LEU* 2.8 32.1 + - + +
277B THR* 3.1 5.2 + - - -
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Residues in contact with GLU 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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270B GLN* 3.4 9.6 + - - +
271B LEU* 3.0 35.2 + - - +
273B LEU* 1.3 78.5 - - + +
275B MET* 1.3 60.3 + - - +
277B THR* 3.4 16.1 + - - -
282B LYS 5.6 2.7 - - - +
283B ARG* 3.6 3.6 - - - +
284B ILE* 3.2 46.2 + - + +
292B HIS* 4.0 15.1 + - - -
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Residues in contact with MET 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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121B MET* 4.2 15.7 - - + -
125B LEU* 4.5 7.0 - - + -
197B MET* 3.8 9.6 - - + +
198B TRP* 3.5 19.4 - - - -
200B VAL* 4.1 12.6 - - + +
201B GLY* 3.8 31.4 - - - -
204B PHE* 4.2 13.2 - - + -
271B LEU* 3.0 47.4 + - + +
272B LEU 3.7 7.4 - - - +
274B GLU* 1.3 75.8 - - - +
276B LEU* 1.3 66.3 + - - +
277B THR 3.4 1.5 + - - -
283B ARG* 3.7 8.9 - - - -
284B ILE* 3.7 17.3 - - + -
289B ALA* 4.1 14.8 - - + -
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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
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198B TRP* 3.1 53.7 - - + +
201B GLY* 3.9 9.2 - - - -
202B CYS* 4.0 10.3 - - - +
213B LEU* 4.8 6.1 - - + -
214B PHE* 3.7 31.0 - - + -
229B LEU* 4.7 9.4 - - + -
230B ILE* 3.0 31.8 - - + +
272B LEU* 2.9 30.1 + - + +
273B LEU* 2.8 11.3 + - + +
275B MET* 1.3 86.4 - - - +
277B THR* 1.3 55.2 + - - +
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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