Contacts of the helix formed by residues 315 - 331 (chain A) in PDB entry 2V3V
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 GLN 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLY 4.7 1.2 - - - +
226A LEU* 3.8 28.2 - - + +
313A ARG* 3.1 10.4 + - - +
314A VAL* 1.3 84.4 - - + +
316A GLY* 1.3 56.2 + - - +
317A VAL 3.4 1.6 - - - -
318A PHE* 3.3 24.8 + - + -
319A ALA* 2.8 28.7 + - - +
597A PRO 2.9 27.5 + - - -
599A LYS* 2.8 48.4 + - + +
600A GLY* 3.9 12.8 + - - +
705A ASP* 3.7 1.3 - - - -
712A GLU* 4.6 0.4 + - - -
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER* 3.7 15.9 - - - -
310A ILE 3.4 19.5 - - - -
311A ASN 4.1 0.4 - - - -
313A ARG* 3.0 18.1 + - - +
315A GLN* 1.3 77.0 - - - +
317A VAL* 1.3 60.9 + - - +
319A ALA* 3.4 2.0 + - - +
320A ASN* 2.8 30.3 + - - -
705A ASP* 3.0 3.9 + - - -
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER* 3.8 16.6 - - - +
146A GLY* 3.9 24.7 - - - +
147A GLY 4.0 0.2 - - - +
150A THR* 4.3 4.7 - - + +
316A GLY* 1.3 74.8 - - - +
318A PHE* 1.3 66.2 + - + +
320A ASN* 3.2 4.9 + - - +
321A ASN* 3.0 40.2 + - - +
596A ARG* 4.7 4.0 - - - +
705A ASP* 3.0 20.4 + - - +
707A VAL* 4.0 19.1 - - + -
708A SER* 3.6 35.4 - - - +
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Residues in contact with PHE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.8 15.3 - - + -
315A GLN* 3.3 34.2 + - + +
317A VAL* 1.3 84.4 - - + +
319A ALA* 1.3 61.4 + - - +
321A ASN* 3.2 9.2 + - - +
322A LEU* 3.0 25.6 + - - +
596A ARG* 3.4 57.0 - - + -
597A PRO* 4.2 18.6 - - + -
599A LYS* 6.6 0.2 - - - -
705A ASP* 5.9 0.2 - - - -
707A VAL* 5.3 10.5 - - + -
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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
----------------------------------------------------------
226A LEU* 3.9 25.4 - - + +
229A MET* 3.5 7.9 - - + +
310A ILE* 3.9 35.2 - - + +
313A ARG* 4.9 3.1 - - - +
315A GLN 2.8 20.7 + - - +
316A GLY* 3.7 4.9 - - - +
318A PHE* 1.3 72.4 - - - +
320A ASN* 1.3 62.9 + - - +
322A LEU* 3.4 1.5 + - - -
323A ILE* 3.4 24.6 + - - +
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Residues in contact with ASN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER 3.7 8.0 + - - +
144A ALA* 3.3 23.9 - - - +
147A GLY* 3.6 15.0 - - - -
306A TRP* 2.9 30.2 + - - -
310A ILE* 3.4 5.9 - - - +
311A ASN* 3.1 22.4 + - - -
316A GLY 2.8 27.5 + - - +
317A VAL 3.4 7.9 - - - +
319A ALA* 1.3 72.5 - - - +
321A ASN* 1.3 67.5 + - - +
323A ILE* 3.2 12.3 + - - +
324A HIS* 3.2 29.1 + - - +
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY* 3.4 7.9 + - - -
150A THR* 3.0 22.8 + - - -
151A SER* 2.9 30.0 + - - +
317A VAL* 3.0 19.7 + - - +
318A PHE* 3.4 9.3 - - - +
320A ASN* 1.3 75.2 - - - +
322A LEU* 1.3 57.5 + - + +
324A HIS* 3.2 2.8 + - - +
325A ASN* 2.9 32.2 + - - +
594A TRP* 3.7 23.5 - - + -
596A ARG* 2.8 36.3 + - + -
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.5 55.9 - - + +
229A MET* 3.9 19.9 - - + +
230A HIS* 3.5 38.1 - - + +
318A PHE 3.0 17.4 + - - +
319A ALA 3.8 6.1 - - - +
320A ASN 3.2 0.2 - - - -
321A ASN* 1.3 72.2 - - - +
323A ILE* 1.3 65.1 + - - +
325A ASN* 3.3 30.5 - - + +
326A LEU* 3.4 14.6 + - - +
594A TRP 3.7 7.6 - - - +
596A ARG* 3.9 12.1 - - + -
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Residues in contact with ILE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 4.9 4.5 - - + -
173A ILE* 4.2 14.8 - - + -
229A MET* 3.4 22.9 - - - -
304A SER* 3.6 22.4 - - - +
306A TRP* 3.5 58.1 - - + -
310A ILE* 4.2 13.2 - - + -
319A ALA 3.4 13.0 + - - +
320A ASN* 3.2 7.0 + - - +
322A LEU* 1.3 76.7 - - - +
324A HIS* 1.3 63.7 + - - +
326A LEU* 3.2 16.7 + - + +
327A HIS* 3.2 13.0 - - + -
340A SER* 3.8 2.9 - - - +
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Residues in contact with HIS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY 3.6 17.6 + - - -
148A TYR* 3.5 37.8 + + - -
151A SER* 3.4 31.0 - - - +
152A PHE* 3.7 14.3 - + + -
306A TRP* 3.5 19.4 - + - -
320A ASN* 3.2 23.1 + - - +
321A ASN 3.2 5.6 + - - +
323A ILE* 1.3 78.4 - - - +
325A ASN* 1.3 51.7 + - - +
327A HIS* 3.1 6.6 + - - +
328A LEU* 2.9 41.9 + - + +
340A SER* 2.8 33.3 + - - -
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Residues in contact with ASN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A HIS* 4.5 4.4 + - - -
233A ALA* 5.9 0.4 - - + -
266A TYR* 3.8 18.5 + - - +
321A ASN* 2.9 18.7 + - - +
322A LEU* 3.3 27.4 - - + +
324A HIS* 1.3 74.7 - - - +
326A LEU* 1.3 57.6 + - + +
328A LEU* 3.9 0.3 - - - +
329A ILE* 2.8 35.4 + - - +
592A VAL 4.1 3.3 - - - +
593A ILE* 3.3 26.7 - - + +
594A TRP* 2.9 43.7 + - - +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 4.2 13.9 - - + -
229A MET* 3.8 25.8 - - + +
232A MET* 3.8 30.7 - - + -
233A ALA* 3.8 22.4 - - + +
236A ILE* 4.2 13.2 - - + -
296A PHE* 3.4 28.2 - - + -
322A LEU 3.6 13.9 - - - +
323A ILE* 3.2 11.8 + - - +
325A ASN* 1.3 78.1 - - + +
327A HIS* 1.3 53.6 + - - +
329A ILE* 3.7 4.2 - - + +
330A THR* 2.6 39.9 + - - +
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Residues in contact with HIS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 3.3 18.2 - + - -
302A THR 3.4 14.8 - - - -
304A SER* 2.9 32.1 + - - -
323A ILE* 3.2 23.3 - - + -
324A HIS* 3.1 7.6 + - - +
326A LEU* 1.3 78.0 - - - +
328A LEU* 1.3 54.6 + - - +
330A THR* 3.6 4.5 - - - -
331A GLY* 2.8 29.6 + - - -
332A GLN* 2.7 35.8 + - - +
333A ILE* 4.3 12.2 - - + +
339A THR 3.1 25.1 + - - -
340A SER* 3.7 21.3 - - - -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 4.8 1.1 - - - +
152A PHE* 4.0 21.8 - - + -
246A PHE* 3.4 34.3 - - + -
247A TRP* 3.9 3.1 - - - +
251A VAL* 3.9 11.5 - - + +
324A HIS* 2.9 25.4 + - + +
325A ASN 3.9 0.2 - - - +
327A HIS* 1.3 76.3 - - + +
329A ILE* 1.3 64.4 + - - +
330A THR 3.3 0.5 + - - -
331A GLY 3.4 7.1 + - - -
333A ILE* 4.4 9.9 - - + -
583A PHE* 4.9 0.9 - - + -
591A ALA* 3.6 33.4 - - + -
592A VAL 3.5 30.1 - - - +
593A ILE* 3.8 18.6 - - + -
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Residues in contact with ILE 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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233A ALA* 5.1 4.7 - - + -
236A ILE* 4.2 14.6 - - + -
237A ILE* 3.9 20.0 - - + -
242A ASP* 3.4 10.4 - - + +
243A ASN* 3.0 22.2 + - - +
247A TRP* 3.5 32.5 - - + +
253A PHE* 4.0 3.4 - - + -
263A PHE* 4.0 9.6 - - + -
266A TYR* 3.8 23.1 - - + +
325A ASN 2.8 22.9 + - - +
326A LEU* 3.7 11.4 - - - +
328A LEU* 1.3 73.2 - - - +
330A THR* 1.3 67.4 + - + +
593A ILE* 3.8 20.3 - - + +
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Residues in contact with THR 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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236A ILE* 3.7 41.7 - - + -
241A LEU 4.4 4.5 - - - +
242A ASP* 4.7 0.9 - - - +
243A ASN* 2.8 29.8 + - - +
296A PHE* 3.7 4.6 - - + -
297A ALA* 4.2 12.8 - - + -
326A LEU 2.6 23.9 + - - +
327A HIS* 3.3 4.5 + - - -
329A ILE* 1.3 75.0 - - + +
331A GLY* 1.3 61.3 + - - +
332A GLN* 3.2 28.8 + - - +
335A ARG* 5.5 0.9 + - - -
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Residues in contact with GLY 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASN* 3.8 7.7 + - - +
246A PHE* 3.5 35.0 - - - -
327A HIS 2.8 9.3 + - - -
328A LEU 3.4 4.9 + - - -
329A ILE 3.5 0.2 - - - -
330A THR* 1.3 80.0 - - - +
332A GLN* 1.3 55.1 + - - +
333A ILE* 2.9 19.2 + - - +
335A ARG* 3.8 13.8 + - - -
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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
------------------------------------------------------------
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