Contacts of the helix formed by residues 310 - 327 (chain A) in PDB entry 2WSK
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 HIS 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PHE* 4.0 13.5 - + - -
28A ALA* 5.3 3.7 - - + +
55A ASP* 5.7 2.0 - - - -
286A SER* 3.9 30.5 + - - +
307A ASN* 3.3 30.4 + - - +
309A SER* 1.3 78.1 - - - +
311A PRO* 1.3 67.8 - - + +
312A ALA* 3.0 42.7 + - + +
313A VAL* 2.8 16.1 + - + +
314A VAL* 2.7 33.9 + - - +
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Residues in contact with PRO 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A SER 3.4 7.7 - - - +
310A HIS* 1.3 95.5 - - + +
312A ALA* 1.3 59.0 + - - +
314A VAL* 3.7 9.2 - - + +
315A ASP* 3.0 35.7 + - - +
352A PRO* 6.0 0.7 - - + -
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.8 0.3 - - - +
26A PHE* 3.2 54.5 - - + +
287A TYR* 5.6 0.6 - - - -
310A HIS* 3.0 12.0 + - + +
311A PRO* 1.3 77.2 - - - +
313A VAL* 1.3 59.6 + - - +
315A ASP* 3.5 9.2 + - - +
316A TYR* 3.0 26.7 + - - +
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Residues in contact with VAL 313 (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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26A PHE* 5.5 0.7 - - + -
286A SER* 3.8 15.5 - - - +
287A TYR* 4.0 25.1 - - + +
306A LEU* 4.5 13.9 - - + -
307A ASN 3.2 34.8 - - - +
308A LEU* 3.9 17.0 - - + -
310A HIS* 2.8 20.5 + - + +
312A ALA* 1.3 76.6 - - + +
314A VAL* 1.3 53.4 - - - +
316A TYR* 3.2 8.7 + - + +
317A ALA* 2.7 34.5 + - - +
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU 3.3 25.6 - - - +
309A SER 4.0 0.4 - - - -
310A HIS 2.7 23.6 + - - +
311A PRO* 3.7 9.9 - - + +
313A VAL* 1.3 70.5 - - - +
315A ASP* 1.3 67.7 + - - +
317A ALA* 3.9 5.6 - - - +
318A SER* 2.8 30.1 + - - +
352A PRO* 3.7 27.6 - - + +
353A LEU* 4.0 9.0 - - + +
356A ALA* 3.6 31.2 - - + -
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Residues in contact with ASP 315 (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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12A LEU* 4.8 7.0 - - + -
311A PRO 3.0 23.8 + - - +
312A ALA* 3.6 8.3 - - - +
314A VAL* 1.3 79.6 - - - +
316A TYR* 1.3 53.2 + - - +
318A SER* 3.1 7.0 + - - -
319A ALA* 2.8 39.1 + - - +
322A ARG* 4.8 0.7 + - - +
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Residues in contact with TYR 316 (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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12A LEU* 4.2 13.2 - - + +
95A PRO* 3.3 39.5 + - + +
96A CYS* 3.9 19.7 - - - -
226A MET* 3.7 39.6 + - + +
227A PHE* 3.8 15.5 - + - -
264A LEU* 6.0 0.7 - - + -
279A LEU* 4.9 6.6 - - + +
287A TYR* 4.4 27.8 - + + +
306A LEU* 4.6 11.0 - - + -
312A ALA 3.0 12.3 + - - +
313A VAL* 3.3 18.2 - - + +
315A ASP* 1.3 79.6 - - - +
317A ALA* 1.3 70.2 + - + +
319A ALA* 3.3 2.3 + - - +
320A CYS* 3.0 22.8 + - + +
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Residues in contact with ALA 317 (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 LEU* 4.5 20.8 - - + +
306A LEU* 6.3 0.4 - - + -
308A LEU* 4.4 20.2 - - + -
313A VAL 2.7 20.4 + - - +
314A VAL* 3.9 5.2 - - - +
316A TYR* 1.3 82.0 - - + +
318A SER* 1.3 58.2 + - - +
320A CYS* 2.8 24.2 + - - +
321A LEU* 3.0 18.1 + - - +
353A LEU* 4.6 9.9 - - + -
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Residues in contact with SER 318 (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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314A VAL* 2.8 27.3 + - - +
315A ASP* 3.1 11.3 + - - -
317A ALA* 1.3 73.2 - - - +
319A ALA* 1.3 59.4 + - - +
321A LEU* 3.5 6.0 + - - -
322A ARG* 3.0 39.1 + - - +
353A LEU* 4.7 7.9 - - - +
356A ALA* 4.7 19.0 - - - +
357A ILE* 5.3 0.7 - - - -
360A CYS* 6.0 1.1 - - - -
363A LEU* 3.7 21.3 - - - +
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Residues in contact with ALA 319 (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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12A LEU* 4.4 15.7 - - + -
227A PHE* 3.9 12.2 - - + -
315A ASP 2.8 24.8 + - - +
316A TYR 3.6 5.6 - - - +
318A SER* 1.3 74.4 + - - +
320A CYS* 1.3 57.5 + - - +
322A ARG* 3.3 24.9 + - - +
323A TYR* 2.9 27.5 + - - +
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Residues in contact with CYS 320 (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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226A MET* 3.4 42.8 - - + -
227A PHE* 3.4 20.8 - - + -
262A ILE* 4.5 13.5 - - - -
264A LEU* 4.7 6.7 - - + -
316A TYR* 3.0 14.3 + - + +
317A ALA* 2.8 13.8 + - - +
319A ALA* 1.3 74.1 - - - +
321A LEU* 1.3 65.4 + - - +
323A TYR* 3.2 9.7 + - - +
324A TRP* 3.0 30.2 + - - -
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Residues in contact with LEU 321 (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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262A ILE* 3.8 24.0 - - + -
264A LEU* 4.2 12.3 - - + -
317A ALA 3.0 15.1 + - - +
318A SER* 3.8 7.9 - - - +
319A ALA 3.4 0.2 - - - -
320A CYS* 1.3 77.9 - - - +
322A ARG* 1.3 61.5 + - - +
324A TRP* 3.5 1.0 + - - -
325A VAL* 3.3 26.7 + - - +
333A PHE* 3.4 24.9 - - + -
335A PHE* 3.7 31.2 - - + -
353A LEU* 5.0 2.0 - - + -
357A ILE* 3.8 30.3 - - + -
363A LEU* 3.5 24.5 - - + -
368A LEU* 5.8 1.3 - - + -
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Residues in contact with ARG 322 (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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315A ASP* 4.8 0.8 + - - +
318A SER* 3.0 41.8 + - - +
319A ALA* 3.3 28.0 + - - +
321A LEU* 1.3 74.9 - - - +
323A TYR* 1.3 59.7 + - - +
325A VAL* 3.2 3.0 + - - -
326A GLU* 2.8 65.4 + - + +
360A CYS* 3.7 24.2 - - - -
362A VAL* 4.3 16.4 - - + -
363A LEU* 3.6 7.4 - - + +
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Residues in contact with TYR 323 (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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98A ARG* 3.7 35.1 + - + +
227A PHE* 3.3 48.2 + + + -
241A LEU* 3.3 25.9 - - + +
319A ALA 2.9 14.7 + - - +
320A CYS 3.3 8.3 - - - +
322A ARG* 1.3 77.2 - - - +
324A TRP* 1.3 84.3 + + - +
326A GLU* 5.0 2.2 - - - -
327A THR* 2.8 70.4 + - + +
328A CYS* 6.2 0.7 - - + -
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Residues in contact with TRP 324 (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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201A VAL* 4.7 4.0 - - + -
202A ALA* 4.5 9.8 - - + +
226A MET 3.0 28.7 + - - -
227A PHE 4.1 9.4 - - - -
228A ALA 3.9 10.8 - - - -
229A LEU* 3.9 44.4 - - + -
241A LEU* 5.0 3.8 - - + -
244A PHE* 4.9 0.9 - + - -
260A LEU* 3.9 23.8 - - + -
262A ILE* 4.8 7.3 - - + +
320A CYS* 3.0 32.8 + - - -
321A LEU* 3.5 0.9 + - - +
322A ARG 3.3 0.4 - - - -
323A TYR* 1.3 92.0 - + - +
325A VAL* 1.3 56.7 + - - +
328A CYS* 2.9 50.1 - - + +
329A HIS 3.1 5.9 + - - -
330A VAL* 3.3 11.4 + - + +
333A PHE* 3.7 28.0 - + + -
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Residues in contact with VAL 325 (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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321A LEU 3.3 15.0 + - - +
322A ARG 3.2 7.2 + - - +
324A TRP* 1.3 78.8 - - - +
326A GLU* 1.3 60.2 + - - +
329A HIS* 2.8 30.2 + - - +
330A VAL* 4.1 15.3 - - + +
333A PHE* 3.7 20.9 - - + -
362A VAL* 3.5 26.0 - - + -
363A LEU* 4.1 8.7 - - + -
365A GLN* 4.5 4.7 - - - +
366A VAL* 3.9 26.7 - - + -
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Residues in contact with GLU 326 (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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138A TRP* 4.5 2.3 + - - -
322A ARG* 2.8 49.1 + - - +
323A TYR* 4.4 2.4 - - - +
325A VAL* 1.3 74.7 - - + +
327A THR* 1.3 59.5 + - - +
329A HIS* 3.3 20.1 + - - -
362A VAL* 3.6 30.3 - - + +
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Residues in contact with THR 327 (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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134A ASP* 3.4 14.1 + - + +
138A TRP* 3.3 10.9 + - - +
241A LEU* 4.2 8.1 - - + -
245A ARG* 3.1 38.4 + - - +
323A TYR* 2.8 60.7 + - + +
326A GLU* 1.3 76.7 - - - +
328A CYS* 1.3 57.0 + - + +
329A HIS 3.7 0.2 - - - -
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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