Contacts of the helix formed by residues 285 - 297 (chain A) in PDB entry 2V62
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 CYS 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A LEU* 3.9 14.8 - - - -
244A LEU* 3.7 21.8 - - - -
245A CYS* 3.8 17.9 - - - -
275A VAL* 3.7 26.2 - - + +
276A LEU* 4.0 8.5 + - - +
279A ALA* 3.5 23.6 - - + +
283A SER 3.7 0.2 + - - -
284A SER* 1.3 69.6 + - - +
286A CYS* 1.3 54.6 + - - +
287A GLU* 3.3 2.9 - - - -
288A ILE* 3.8 12.6 - - + +
289A ALA* 2.7 36.4 + - - +
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Residues in contact with CYS 286 (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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276A LEU* 3.6 21.3 - - + +
284A SER* 3.2 24.9 + - - +
285A CYS* 1.3 78.6 - - - +
287A GLU* 1.3 63.2 + - - +
289A ALA* 3.5 1.7 + - - +
290A GLN* 3.1 28.8 + - - +
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Residues in contact with GLU 287 (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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140A LYS* 2.8 38.3 + - - -
144A LEU* 3.9 26.9 - - + +
284A SER* 4.0 2.0 + - - +
285A CYS 4.5 0.2 - - - -
286A CYS* 1.3 79.2 + - - +
288A ILE* 1.3 61.0 + - + +
290A GLN* 3.4 1.3 + - - -
291A PHE* 2.9 29.9 + - - +
312A ILE* 3.3 32.7 - - - +
313A LEU* 4.2 3.8 - - + +
315A PRO* 3.9 26.3 - - + +
316A HIS* 5.3 4.3 - - - -
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Residues in contact with ILE 288 (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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143A VAL* 4.4 4.9 - - + -
144A LEU* 4.4 15.5 - - + -
237A GLY 3.9 22.0 - - - +
240A MET* 3.8 40.6 - - + +
241A LEU* 4.1 12.3 - - + +
244A LEU* 3.7 31.0 - - + -
275A VAL* 4.3 11.2 - - + -
284A SER 5.2 0.2 - - - +
285A CYS* 3.3 15.7 + - + +
287A GLU* 1.3 76.6 - - + +
289A ALA* 1.3 57.4 + - - +
291A PHE* 3.3 7.0 + - - +
292A LEU* 3.0 35.6 + - + +
313A LEU* 4.9 0.7 - - + -
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Residues in contact with ALA 289 (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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271A LEU* 4.2 3.2 - - - +
272A PRO* 3.9 16.8 - - + +
275A VAL* 3.7 18.9 - - + +
276A LEU* 3.7 27.8 - - + -
285A CYS 2.7 22.4 + - - +
286A CYS 3.7 2.2 - - - +
288A ILE* 1.3 73.1 - - - +
290A GLN* 1.3 57.2 + - - +
292A LEU* 3.3 3.5 + - - +
293A VAL* 2.9 33.1 + - - +
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Residues in contact with GLN 290 (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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272A PRO* 5.4 0.8 - - - +
286A CYS 3.1 17.5 + - - +
287A GLU* 4.8 0.4 - - - -
289A ALA* 1.3 72.4 - - - +
291A PHE* 1.3 64.2 + - - +
293A VAL* 3.4 23.8 + - - +
294A CYS* 3.0 26.8 + - - +
312A ILE* 3.8 33.0 - - + +
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Residues in contact with PHE 291 (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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151A LEU* 3.9 24.9 - - + -
233A VAL* 3.2 43.7 - - + -
236A LEU* 4.1 13.2 - - + -
237A GLY* 3.6 19.3 - - - -
240A MET* 3.8 19.7 - - + -
287A GLU 2.9 19.0 + - - +
288A ILE* 3.5 8.5 - - - +
290A GLN* 1.3 75.3 - - - +
292A LEU* 1.3 64.1 + - + +
294A CYS* 3.3 5.5 + - - +
295A ALA* 2.9 24.1 + - + +
309A LEU* 3.6 28.7 - - + +
312A ILE* 3.6 10.4 - - + +
313A LEU* 4.0 20.4 - - + -
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Residues in contact with LEU 292 (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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234A GLU* 4.0 21.3 - - + +
237A GLY* 3.9 31.2 - - - +
238A TYR* 4.6 5.8 - - + +
241A LEU* 5.0 2.5 - - + -
267A LEU* 4.3 14.1 - - + -
268A LEU* 4.1 14.7 - - + +
271A LEU* 3.6 15.8 - - + +
275A VAL* 3.9 26.0 - - + -
288A ILE* 3.0 28.6 + - + +
289A ALA 3.9 2.9 - - - +
291A PHE* 1.3 75.9 - - + +
293A VAL* 1.3 58.4 + - - +
295A ALA* 3.7 7.9 - - + +
296A HIS* 2.8 32.4 + - - +
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Residues in contact with VAL 293 (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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271A LEU* 3.8 28.3 - - + -
272A PRO* 4.2 16.6 - - + -
289A ALA 2.9 21.8 + - - +
290A GLN* 3.4 28.5 + - - +
292A LEU* 1.3 75.8 - - - +
294A CYS* 1.3 62.1 + - - +
296A HIS* 3.4 3.4 + - - +
297A SER* 3.2 21.3 + - - -
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Residues in contact with CYS 294 (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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290A GLN* 3.0 17.0 + - - +
291A PHE 3.4 8.5 - - - +
293A VAL* 1.3 75.1 - - - +
295A ALA* 1.3 65.4 + - - +
297A SER* 2.7 26.7 + - - -
298A LEU* 3.8 9.9 + - - +
305A ASN* 5.2 7.9 - - - -
308A ALA* 5.1 10.1 - - - -
309A LEU* 3.6 27.6 - - + -
312A ILE* 4.2 14.4 - - + -
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Residues in contact with ALA 295 (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 ARG* 4.7 6.3 - - - +
233A VAL* 3.7 26.9 - - + -
234A GLU* 4.4 13.5 - - + +
291A PHE* 2.9 17.6 + - + +
292A LEU* 3.7 17.5 - - + +
294A CYS* 1.3 75.4 - - - +
296A HIS* 1.3 61.5 + - - +
298A LEU* 3.2 31.4 + - - +
309A LEU* 4.8 1.0 - - - +
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Residues in contact with HIS 296 (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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268A LEU* 3.4 51.0 - - + +
269A ASP* 4.0 11.5 + - - -
271A LEU* 4.4 7.0 - - + -
292A LEU 2.8 19.1 + - - +
293A VAL* 3.9 4.3 - - - +
295A ALA* 1.3 77.6 - - - +
297A SER* 1.3 59.0 + - - +
298A LEU 3.2 2.0 + - - +
280B PRO* 3.5 37.0 - - + +
281B SER* 3.9 8.1 + - - +
282B GLY* 3.4 31.9 - - - -
283B SER* 4.9 1.8 + - - -
1331B EDO 3.9 0.9 + - - -
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Residues in contact with SER 297 (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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293A VAL* 3.2 11.4 + - - -
294A CYS* 2.7 25.8 + - - -
296A HIS* 1.3 76.2 - - - +
298A LEU* 1.3 65.2 + - - +
299A ALA 3.5 0.7 + - - -
302A GLU* 3.7 6.1 + - - +
247B LYS* 4.7 7.9 + - - -
1331B EDO 3.3 28.7 + - - -
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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