Contacts of the helix formed by residues 265 - 282 (chain A) in PDB entry 2WJP
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 GLY 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A SER* 1.3 78.9 + - - +
266A GLN* 1.3 67.1 + - - -
267A HIS* 3.3 9.2 - - - -
268A ASN 3.0 12.4 + - - -
269A TYR* 3.1 25.9 + - - -
1444A AZI 6.3 2.5 - - - -
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Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 3.6 38.1 - - + +
239A LEU* 4.2 15.3 - - + -
241A HIS* 4.5 12.5 + - - +
265A GLY* 1.3 71.2 - - - -
267A HIS* 1.3 58.1 + - - +
269A TYR* 3.0 13.8 + - - +
270A THR* 2.9 27.0 + - + +
331A ASN* 5.8 3.8 - - - +
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Residues in contact with HIS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 4.6 12.3 - - - +
264A SER 5.0 4.5 - - - -
265A GLY* 4.7 4.8 - - - -
266A GLN* 1.3 79.4 + - - +
268A ASN* 1.3 82.6 + - - +
270A THR* 3.2 11.3 + - - +
271A ASN* 2.9 40.2 + - - +
303A PHE* 6.5 1.1 - - + -
328A ALA* 4.1 39.9 + - + +
329A ALA* 5.7 1.1 - - - -
1444A AZI 5.5 7.0 - - - -
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Residues in contact with ASN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 4.3 5.4 + - - +
261A MET* 4.2 3.2 - - - +
263A LEU* 3.9 43.6 - - + +
264A SER 3.0 28.3 + - - +
265A GLY 3.0 2.7 + - - +
267A HIS* 1.3 94.1 + - - +
269A TYR* 1.3 61.1 + - + +
271A ASN* 3.3 19.2 + - - +
272A ALA* 2.9 27.4 + - - +
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.9 22.0 - - + -
246A THR* 4.3 19.7 - - + -
248A LEU* 4.0 4.2 - - + +
258A VAL* 3.5 44.9 + - + +
261A MET* 4.1 10.3 - - + -
263A LEU 3.7 19.3 + - - -
264A SER* 3.5 21.3 - - - -
265A GLY* 3.1 28.0 + - - -
266A GLN* 3.0 11.7 + - - +
268A ASN* 1.3 81.0 - - + +
270A THR* 1.3 58.0 + - - +
272A ALA* 3.2 7.9 + - - +
273A LEU* 3.0 30.2 + - - +
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Residues in contact with THR 270 (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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213A ASP* 5.5 0.2 - - - +
230A PHE* 3.8 22.9 - - + -
231A GLY* 4.3 14.6 - - - +
232A VAL* 3.8 29.2 - - + -
239A LEU* 4.3 9.9 - - + -
266A GLN* 2.9 17.7 + - + +
267A HIS* 3.2 16.8 + - - +
269A TYR* 1.3 72.7 - - - +
271A ASN* 1.3 61.8 + - - +
273A LEU* 3.2 8.8 + - + +
274A ALA* 2.9 28.6 + - - +
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Residues in contact with ASN 271 (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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113A ASN 5.1 0.5 - - - +
114A GLY* 4.0 20.9 - - - -
117A THR* 4.0 20.9 + - + +
118A VAL* 3.6 28.1 - - + +
121A LEU* 4.4 3.1 - - + -
177A LEU* 4.5 6.1 - - - +
178A ASN* 5.6 1.9 + - - -
230A PHE* 5.9 0.4 - - - -
267A HIS* 2.9 34.6 + - - +
268A ASN* 3.5 22.8 + - - +
269A TYR 3.3 0.2 - - - -
270A THR* 1.3 78.1 + - - +
272A ALA* 1.3 56.7 + - - +
274A ALA* 3.3 2.4 + - - -
275A ALA* 2.9 30.3 + - - +
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Residues in contact with ALA 272 (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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121A LEU* 4.1 6.2 - - + +
248A LEU* 4.1 11.2 - - + -
261A MET* 3.8 21.5 - - + -
268A ASN 2.9 14.0 + - - +
269A TYR* 3.4 9.9 - - - +
271A ASN* 1.3 74.7 - - - +
273A LEU* 1.3 65.5 + - - +
275A ALA* 3.4 1.6 + - - +
276A LEU* 2.9 24.9 + - - +
293A LEU* 3.6 30.1 - - + +
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Residues in contact with LEU 273 (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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230A PHE* 4.0 12.1 - - + -
231A GLY 3.4 28.0 - - - +
237A TYR* 3.7 17.3 - - + +
238A HIS* 3.6 34.3 - - - +
239A LEU* 3.7 15.9 - - + -
248A LEU* 3.9 26.2 - - + -
249A ARG 4.2 3.8 - - - +
250A VAL* 5.9 0.2 - - + -
269A TYR 3.0 17.3 + - - +
270A THR* 3.2 13.2 + - - +
272A ALA* 1.3 77.7 - - - +
274A ALA* 1.3 57.5 + - - +
276A LEU* 3.3 8.0 + - + +
277A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 274 (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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118A VAL* 4.5 3.6 - - + -
177A LEU* 3.5 31.6 - - + -
209A VAL* 4.6 3.5 - - + +
230A PHE* 3.7 24.6 - - + -
270A THR 2.9 16.0 + - - +
271A ASN* 3.7 5.2 - - - +
272A ALA 3.3 0.2 - - - -
273A LEU* 1.3 75.2 - - - +
275A ALA* 1.3 62.7 + - - +
277A ALA* 3.2 5.0 + - - +
278A LEU* 3.0 31.6 + - + +
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 4.0 7.1 - - + +
121A LEU* 3.8 20.0 - - + -
122A VAL* 3.7 27.0 - - + +
125A MET* 3.7 19.3 - - + -
271A ASN 2.9 18.4 + - - +
272A ALA 3.7 3.1 - - - +
274A ALA* 1.3 76.5 - - - +
276A LEU* 1.3 56.7 + - - +
278A LEU 3.4 1.0 + - - -
279A ALA* 2.9 29.5 + - - +
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Residues in contact with LEU 276 (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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125A MET* 3.8 9.1 - - + +
237A TYR* 4.0 7.0 - - + -
248A LEU* 5.4 3.6 - - + -
250A VAL* 4.0 26.5 - - + -
255A VAL* 4.0 17.7 - - + -
272A ALA 2.9 17.8 + - - +
273A LEU* 3.7 7.6 - - + +
275A ALA* 1.3 72.9 - - - +
277A ALA* 1.3 61.0 + - - +
279A ALA* 3.8 1.9 - - - +
280A ASP* 2.8 43.9 + - - +
286A ARG* 3.8 21.5 - - - -
289A SER* 3.8 29.2 - - - -
290A LEU* 4.2 13.0 - - + -
293A LEU* 4.8 5.6 - - + -
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Residues in contact with ALA 277 (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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209A VAL* 3.9 27.3 - - + +
228A VAL* 4.3 4.2 - - + +
230A PHE* 5.5 1.6 - - + -
237A TYR* 3.6 36.7 + - + -
273A LEU 2.9 17.2 + - - +
274A ALA* 3.6 5.2 - - - +
276A LEU* 1.3 76.0 - - - +
278A LEU* 1.3 63.1 + - - +
280A ASP* 3.7 1.7 - - - +
281A ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 278 (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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107A VAL* 4.0 13.5 - - + +
108A ALA 4.8 0.2 - - - +
109A ILE* 3.7 29.6 - - + -
118A VAL* 3.8 15.7 - - + -
122A VAL* 4.2 7.2 - - + -
173A ALA* 3.8 38.0 - - + +
174A ALA* 4.1 10.3 - - - +
175A THR* 3.8 13.2 - - + -
209A VAL* 3.8 18.4 - - + -
274A ALA 3.0 21.8 + - - +
275A ALA 3.7 3.4 - - - +
277A ALA* 1.3 76.9 - - - +
279A ALA* 1.3 56.7 + - - +
281A ALA* 3.2 3.3 + - - +
282A ALA* 2.9 29.4 + - - +
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Residues in contact with ALA 279 (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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122A VAL* 4.8 5.7 - - + +
125A MET* 3.6 22.4 - - + -
275A ALA 2.9 17.8 + - - +
276A LEU* 3.8 3.8 - - - +
278A LEU* 1.3 72.9 - - - +
280A ASP* 1.3 67.5 + - - +
282A ALA* 3.1 9.7 + - - +
284A LEU* 3.0 43.2 + - + +
289A SER* 3.7 16.2 - - - +
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Residues in contact with ASP 280 (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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237A TYR* 2.5 33.7 + - - +
276A LEU* 2.8 25.9 + - - +
277A ALA 3.7 1.6 - - - +
279A ALA* 1.3 74.3 - - - +
281A ALA* 1.3 57.8 + - - +
283A GLY* 3.0 18.9 + - - -
284A LEU 4.4 7.7 - - - +
286A ARG* 2.9 51.8 + - - +
289A SER* 5.3 0.5 + - - -
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Residues in contact with ALA 281 (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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172A VAL* 4.0 12.2 - - - +
173A ALA* 3.7 20.9 - - + -
206A LYS* 5.7 2.1 - - - +
207A VAL* 3.9 32.4 - - + +
209A VAL* 5.3 0.4 - - + -
228A VAL* 6.2 0.2 - - + -
277A ALA 3.0 18.3 + - - +
278A LEU* 3.6 4.3 - - - +
280A ASP* 1.3 76.0 - - - +
282A ALA* 1.3 60.5 + - - +
283A GLY* 3.1 1.3 + - - -
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.9 24.0 - - + -
122A VAL* 6.0 0.2 - - + -
153A LEU* 4.5 13.5 - - + +
172A VAL* 4.1 18.7 - - + +
173A ALA* 4.8 0.2 - - - +
278A LEU 2.9 16.2 + - - +
279A ALA* 3.1 8.7 + - - +
281A ALA* 1.3 76.2 - - - +
283A GLY* 1.3 60.8 + - - +
284A LEU* 3.4 11.1 + - + +
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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