Contacts of the helix formed by residues 260 - 268 (chain A) in PDB entry 2VWJ
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 LEU 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.7 13.7 - - + -
208A THR 3.0 16.8 + - - +
209A TYR* 3.8 13.5 - - + -
258A PHE* 3.5 26.6 + - + -
259A ASP* 1.3 76.2 + - - +
261A TYR* 1.3 58.4 + - - +
263A VAL* 3.0 7.2 + - + +
264A ILE* 2.9 46.4 + - + +
319A THR* 3.5 31.9 - - + +
322A LEU* 3.6 24.2 - - + +
323A GLY* 3.7 11.9 - - - +
326A PHE* 4.0 8.5 - - + -
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Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 3.3 37.5 - + + -
210A ASN* 3.8 32.5 - - + +
213A ASN* 5.9 1.1 - - - -
259A ASP* 3.2 8.3 + - - +
260A LEU* 1.3 78.3 - - - +
262A PRO* 1.3 78.3 - - + +
264A ILE* 4.3 1.0 - - + +
265A ARG* 3.0 61.8 + - + +
273A TYR* 3.9 30.6 - + + +
25B C 4.8 10.2 - - - +
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Residues in contact with PRO 262 (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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212A ASP* 5.0 2.7 - - + +
259A ASP* 3.4 33.9 - - + +
261A TYR* 1.3 102.7 - - + +
263A VAL* 1.3 60.4 + - - +
265A ARG* 4.1 4.7 - - + +
266A ARG* 3.2 31.2 + - - +
345A SER 4.3 8.7 - - - +
346A ARG* 4.3 25.1 - - + +
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Residues in contact with VAL 263 (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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258A PHE* 3.8 26.0 - - + -
259A ASP 4.1 5.4 - - - +
260A LEU* 3.0 11.4 + - - +
262A PRO* 1.3 74.5 - - - +
264A ILE* 1.3 65.6 + - - +
266A ARG* 3.4 15.8 + - - +
267A THR* 3.0 27.6 + - - +
326A PHE* 3.5 35.9 - - + -
330A GLU* 3.7 20.9 - - + +
345A SER* 3.5 25.6 - - - +
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Residues in contact with ILE 264 (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 TYR* 4.2 7.0 - - + +
260A LEU* 2.9 54.3 + - + +
261A TYR* 4.3 4.0 - - + +
263A VAL* 1.3 73.6 - - - +
265A ARG* 1.3 59.6 + - - +
267A THR* 4.3 4.7 - - - -
268A ILE* 3.0 45.3 + - + +
273A TYR* 4.4 6.0 - - + -
278A VAL* 3.7 46.4 - - + -
322A LEU* 4.4 4.9 - - + -
326A PHE* 3.7 31.2 - - + -
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Residues in contact with ARG 265 (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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261A TYR* 3.0 55.3 + - + +
262A PRO* 4.2 4.9 - - + +
264A ILE* 1.3 75.0 - - - +
266A ARG* 1.3 64.3 + - - +
268A ILE 3.7 10.4 - - - +
273A TYR* 2.8 59.8 + - + -
6B G 3.7 12.5 - - - +
25B C 2.9 40.5 + - - +
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Residues in contact with ARG 266 (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 PRO* 3.2 17.1 + - - +
263A VAL* 3.7 19.9 + - - +
264A ILE 3.3 0.2 - - - -
265A ARG* 1.3 78.7 - - - +
267A THR* 1.3 64.5 + - - +
268A ILE 5.1 0.3 - - - +
330A GLU* 3.8 17.0 + - - -
333A LEU* 5.0 7.9 - - - +
344A VAL 4.0 1.9 + - - -
345A SER* 2.6 43.6 + - - +
346A ARG 5.1 1.0 - - - -
347A SER 3.0 27.1 + - - +
348A SER* 4.4 8.7 - - - +
349A THR* 5.0 11.8 - - - +
352A LEU* 5.5 5.7 - - - +
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Residues in contact with THR 267 (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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263A VAL* 3.0 21.8 + - - +
264A ILE* 3.2 4.4 + - - -
266A ARG* 1.3 80.4 + - - +
268A ILE* 1.3 76.3 + - + +
282A ILE* 5.6 0.4 - - + -
326A PHE* 4.0 29.0 - - + -
330A GLU* 5.5 1.0 + - - -
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Residues in contact with ILE 268 (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 ILE* 3.0 29.8 + - + +
265A ARG 3.7 6.6 - - - +
266A ARG 5.2 0.7 - - - -
267A THR* 1.3 96.9 - - + +
269A ASN* 1.3 56.2 + - - +
270A LEU* 3.8 25.8 - - + -
273A TYR* 2.6 35.8 + - + -
278A VAL* 5.2 1.3 - - - -
281A ALA* 4.0 19.3 - - + -
282A ILE* 4.0 24.2 - - + -
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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