Contacts of the helix formed by residues 316 - 332 (chain A) in PDB entry 2WVL
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 ASP 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A LYS 4.0 2.6 + - - +
315A GLY* 1.3 71.9 - - - -
317A GLU* 1.3 62.3 + - + +
318A HIS 3.0 4.0 - - - -
319A ILE* 2.8 36.4 + - - +
320A ARG* 3.9 2.4 + - - +
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Residues in contact with GLU 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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315A GLY* 4.8 0.2 - - - -
316A ASP* 1.3 78.4 - - + +
318A HIS* 1.3 64.3 + - + +
320A ARG* 3.9 35.6 + - - +
321A ASP* 3.0 36.7 + - - +
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Residues in contact with HIS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TYR* 3.4 30.3 + - + +
313A ASN* 3.5 19.7 + - - -
315A GLY* 3.3 33.2 - - - +
316A ASP 3.0 0.6 + - - +
317A GLU* 1.3 77.6 - - + +
319A ILE* 1.3 61.8 + - + +
321A ASP* 3.4 5.3 + - - +
322A MET* 2.9 41.0 + - + +
400A GDD 4.6 4.7 - - - +
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Residues in contact with ILE 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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217A ARG* 4.4 14.8 - - - +
218A TYR* 3.9 32.8 - - + +
221A VAL* 3.7 29.9 - - + +
315A GLY 4.3 10.5 - - - +
316A ASP* 2.8 24.7 + - - +
318A HIS* 1.3 79.0 - - + +
320A ARG* 1.3 71.0 + - - +
322A MET* 3.1 19.9 + - + +
323A LEU* 3.3 11.3 + - - +
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Residues in contact with ARG 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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316A ASP* 3.9 3.3 + - - +
317A GLU* 3.9 29.9 - - + +
318A HIS 3.6 0.2 - - - -
319A ILE* 1.3 81.3 - - - +
321A ASP* 1.3 83.0 + - - +
323A LEU* 3.1 12.0 + - - +
324A LEU* 3.0 32.5 + - - +
351A ALA* 6.2 2.0 - - + -
352A GLY* 3.1 41.0 + - - +
353A ALA* 4.9 1.8 - - - +
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Residues in contact with ASP 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TYR* 4.3 17.2 - - + -
317A GLU* 3.0 32.1 + - - +
318A HIS* 3.4 6.2 + - - +
319A ILE 3.2 0.6 - - - -
320A ARG* 1.3 94.2 + - - +
322A MET* 1.3 66.3 + - - +
324A LEU* 2.9 13.0 + - - +
325A ALA* 2.8 26.0 + - - +
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Residues in contact with MET 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A TYR* 3.8 28.3 - - + -
221A VAL* 5.1 4.9 - - + -
225A ASN* 3.8 5.5 + - - +
248A ASN* 4.1 25.0 - - - +
268A TYR* 3.7 42.0 - - + +
318A HIS* 2.9 31.8 + - + +
319A ILE* 3.3 21.1 - - + +
321A ASP* 1.3 77.0 - - - +
323A LEU* 1.3 65.7 + - - +
325A ALA* 3.4 2.8 + - - +
326A CYS* 3.2 18.5 + - - +
400A GDD 4.7 17.0 - - - +
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Residues in contact with LEU 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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220A ARG* 4.8 7.2 - - - +
221A VAL* 4.3 16.9 - - + +
224A ARG* 3.8 31.6 - - + -
225A ASN* 3.4 23.5 - - - +
319A ILE 3.3 5.0 + - - +
320A ARG* 3.1 13.8 + - - +
322A MET* 1.3 78.5 - - - +
324A LEU* 1.3 65.9 + - - +
326A CYS* 3.0 15.2 + - - +
327A LEU* 3.1 28.4 + - + +
347A GLU* 4.4 13.5 - - - +
348A LEU* 4.8 9.6 - - + -
351A ALA* 4.8 16.4 - - + -
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Residues in contact with LEU 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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320A ARG* 3.0 26.6 + - - +
321A ASP* 2.9 19.8 + - - +
323A LEU* 1.3 73.0 - - - +
325A ALA* 1.3 57.6 + - - +
327A LEU* 3.3 3.1 + - - +
328A ALA* 3.0 27.9 + - + +
348A LEU* 3.7 21.2 - - + +
352A GLY 3.7 20.9 - - - +
353A ALA* 3.9 14.8 - - + -
360A PRO* 4.6 19.3 - - + -
361A PRO* 5.0 9.9 - - + -
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TYR* 3.8 11.4 - - + +
269A ALA* 3.5 31.4 - - + +
321A ASP 2.8 17.8 + - - +
322A MET 3.7 4.3 - - - +
324A LEU* 1.3 71.5 - - - +
326A CYS* 1.3 65.7 + - - +
328A ALA* 3.3 8.3 + - - +
329A THR* 3.2 28.4 + - - +
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Residues in contact with CYS 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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225A ASN* 3.4 52.7 - - - +
228A ALA* 5.2 0.2 - - - -
229A LEU* 3.7 26.7 - - - -
247A ALA* 4.4 1.6 - - - -
272A PRO* 3.9 24.0 - - + +
322A MET 3.2 3.2 + - - +
323A LEU 3.0 3.4 + - - +
325A ALA* 1.3 78.8 - - - +
327A LEU* 1.3 63.1 + - + +
329A THR* 2.7 23.5 + - - -
330A VAL* 3.4 9.2 + - - +
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Residues in contact with LEU 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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224A ARG* 4.8 6.3 - - + +
225A ASN* 3.5 26.0 - - - +
228A ALA* 4.0 17.0 - - + -
323A LEU* 3.1 22.3 + - + +
326A CYS* 1.3 77.7 - - + +
328A ALA* 1.3 55.1 + - - +
330A VAL* 3.4 4.8 + - - +
331A TYR* 2.8 35.9 + - - +
344A VAL* 3.5 47.5 - - + +
347A GLU* 3.7 21.3 - - + -
348A LEU* 3.7 29.4 - - + -
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Residues in contact with ALA 328 (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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324A LEU* 3.0 17.3 + - + +
325A ALA* 3.4 14.6 - - - +
327A LEU* 1.3 76.7 - - - +
329A THR* 1.3 57.0 + - - +
331A TYR* 3.2 7.7 + - - +
332A HIS* 3.0 34.5 + - - +
348A LEU* 5.0 0.6 - - - +
360A PRO* 4.4 15.3 - - + -
361A PRO 3.8 22.4 - - - +
363A PRO* 4.5 9.2 - - + -
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Residues in contact with THR 329 (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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269A ALA* 3.6 32.1 - - + +
272A PRO* 3.9 9.9 - - + +
273A GLN* 3.5 32.4 + - - +
276A VAL* 4.1 11.5 - - - +
325A ALA 3.2 14.3 + - - +
326A CYS* 2.7 23.2 + - - -
328A ALA* 1.3 75.4 - - - +
330A VAL* 1.3 63.6 + - - +
332A HIS* 3.9 1.4 - - - -
333A SER* 3.4 21.3 + - - -
363A PRO* 3.7 14.4 - - + -
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Residues in contact with VAL 330 (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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228A ALA* 3.7 35.2 - - + +
229A LEU* 4.2 15.9 - - + -
232A LEU* 4.1 13.9 - - + -
276A VAL* 4.5 7.9 - - + -
326A CYS 3.4 13.0 + - - +
327A LEU* 3.4 9.1 + - - +
328A ALA 3.2 0.2 - - - -
329A THR* 1.3 82.0 + - - +
331A TYR* 1.3 68.4 + - - +
332A HIS 3.0 2.7 + - - -
333A SER* 3.0 19.0 + - - -
336A ALA* 3.5 7.8 - - - +
340A VAL* 3.9 23.3 - - + -
344A VAL* 4.2 10.3 - - + -
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Residues in contact with TYR 331 (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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327A LEU 2.8 22.0 + - - +
328A ALA 3.6 4.7 - - - +
330A VAL* 1.3 76.5 - - - +
332A HIS* 1.3 85.3 + + - +
333A SER 3.7 1.4 + - - +
336A ALA* 4.0 1.9 - - - +
341A ARG* 3.0 85.7 + - + +
344A VAL* 4.0 12.6 - - + -
345A LEU* 3.6 27.3 - - + +
359A GLU* 3.3 33.3 + - - -
360A PRO* 3.9 19.7 - - + -
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Residues in contact with HIS 332 (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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328A ALA 3.0 19.5 + - - +
329A THR 3.9 3.4 - - - +
330A VAL 3.1 0.2 - - - -
331A TYR* 1.3 99.2 - + - +
333A SER* 1.3 64.5 + - - +
334A LYS* 3.6 8.7 + - - +
359A GLU* 4.7 6.5 + - + -
360A PRO 2.9 30.2 + - - -
361A PRO 4.2 0.4 + - - -
362A PRO* 3.5 35.9 - - + +
363A PRO* 4.4 10.8 - - + -
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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