Contacts of the strand formed by residues 256 - 264 (chain A) in PDB entry 3VNG
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 PHE 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.5 40.2 - + - -
14A PHE* 3.5 38.2 - + + -
15A ARG* 5.0 3.8 - - + -
250A GLY 3.7 1.8 - - - -
251A TYR* 3.9 20.6 - + - -
255A THR* 1.3 87.8 - - - +
257A LEU* 1.3 64.8 + - - +
258A ASP* 3.6 1.0 + - - -
279A GLY* 3.3 9.5 - - - -
280A ARG 3.8 7.9 - - - +
281A SER* 3.4 28.7 - - - -
301A FUU 3.7 39.9 - + - -
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Residues in contact with LEU 257 (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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231A HIS* 4.2 13.7 - - + +
232A ARG 3.5 24.9 - - - +
233A ARG* 3.8 30.1 - - + +
249A GLY* 3.2 30.5 - - - +
250A GLY 3.0 10.5 + - - +
252A ASP* 4.0 19.5 - - + +
255A THR* 4.2 20.4 - - + +
256A PHE* 1.3 73.1 - - - +
258A ASP* 1.4 60.1 + - - +
259A SER* 4.1 10.1 - - - +
276A MET* 4.4 0.5 - - - +
279A GLY* 3.5 0.4 - - - -
280A ARG 3.0 18.4 + - - -
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Residues in contact with ASP 258 (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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256A PHE 3.6 1.8 + - - -
257A LEU* 1.4 72.5 - - - +
259A SER* 1.4 71.6 + - - +
275A ARG* 2.6 48.8 + - - -
276A MET* 2.6 48.6 + - - +
278A SER* 3.7 7.4 - - - +
279A GLY* 3.5 23.6 + - - +
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Residues in contact with SER 259 (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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231A HIS* 3.6 11.5 - - - -
233A ARG* 3.1 31.5 + - - -
249A GLY 3.1 23.9 + - - -
257A LEU* 3.5 10.3 - - - -
258A ASP* 1.4 85.6 + - - +
260A VAL* 1.3 59.9 + - - +
261A GLU* 3.8 2.3 - - - +
272A GLU* 2.9 31.6 + - - +
274A THR 4.2 2.9 - - - -
275A ARG* 4.6 1.8 - - - +
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Residues in contact with VAL 260 (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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24A TYR* 5.5 2.7 - - + -
31A TRP* 4.4 4.5 - - + -
246A TYR* 4.5 11.4 - - + -
247A VAL 3.3 12.3 - - - +
248A LEU* 4.0 21.5 - - + -
258A ASP 3.8 2.2 - - - +
259A SER* 1.3 79.4 + - - +
261A GLU* 1.4 63.7 + - - +
272A GLU* 3.4 4.4 - - - +
273A VAL* 3.0 33.2 + - + -
274A THR* 2.9 38.4 + - + +
276A MET* 3.8 29.6 - - + +
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Residues in contact with GLU 261 (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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229A MET* 3.7 14.4 - - - +
230A LYS* 2.9 31.6 + - - +
231A HIS* 3.1 22.1 + - + +
233A ARG* 2.8 26.6 + - - +
245A ILE 3.7 0.5 - - - +
246A TYR* 3.4 4.3 - - - +
247A VAL* 3.0 44.0 + - + +
259A SER* 3.8 6.9 - - - +
260A VAL* 1.4 79.1 - - - +
262A CYS* 1.3 60.5 + - - +
270A TRP* 3.7 18.6 - - + +
271A SER 3.3 10.6 + - - +
272A GLU* 4.3 9.6 - - + -
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Residues in contact with CYS 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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244A ARG* 3.6 33.7 - - - -
245A ILE 3.1 5.4 - - - -
246A TYR* 3.7 29.2 - - + -
261A GLU* 1.3 75.1 - - - +
263A TYR* 1.3 62.3 + - - +
264A ASP* 3.9 0.7 + - - +
269A THR 3.7 0.9 - - - +
270A TRP* 3.3 6.1 - - - -
271A SER* 2.6 36.6 + - - +
273A VAL* 3.5 29.4 - - + -
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Residues in contact with TYR 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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194A LEU* 4.5 0.4 - - + -
199A TYR* 3.6 29.4 - + - -
215A ARG* 4.2 6.9 + - - -
226A VAL* 3.8 14.6 - - + +
227A ALA* 4.3 3.6 - - + -
244A ARG* 3.3 13.2 - - - +
245A ILE* 2.7 43.5 + - + -
262A CYS* 1.3 72.3 - - - +
264A ASP* 1.3 58.1 + - - +
265A PRO* 3.4 29.7 + - + +
268A ASP* 2.5 53.5 + - - +
269A THR 3.6 10.3 - - - -
270A TRP* 3.3 51.2 - + + -
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Residues in contact with ASP 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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244A ARG* 3.0 38.9 + - - +
262A CYS 3.9 1.4 + - - +
263A TYR* 1.3 73.6 - - - +
265A PRO* 1.3 61.7 - - - +
266A ASP* 2.9 25.5 + - - +
267A THR* 3.4 25.0 + - - +
268A ASP* 2.8 30.7 + - - -
269A THR* 2.9 16.0 + - - +
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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