Contacts of the strand formed by residues 256 - 263 (chain A) in PDB entry 3VZC
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A THR* 4.6 11.1 + - - +
206A TYR 3.4 2.6 - - - +
207A ARG* 3.1 32.2 + - - +
254A ASP* 3.5 7.0 - - + +
255A GLU* 1.3 82.2 + - - +
257A PHE* 1.3 66.7 + - - +
291A ARG* 3.8 4.9 - - - +
292A ALA* 2.9 38.1 + - + +
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Residues in contact with PHE 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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171A TRP* 3.9 27.4 - + + -
205A THR* 3.2 5.9 - - - -
206A TYR* 2.6 42.6 + - - +
208A GLY 3.5 26.5 - - - -
210A LEU* 3.9 25.8 - - + -
252A VAL* 4.2 4.7 - - + -
254A ASP* 3.3 25.1 - - - -
255A GLU* 4.0 1.8 - - - -
256A ASP* 1.3 80.6 - - - +
258A VAL* 1.3 63.8 + - - +
259A LEU 4.0 8.5 - - - +
260A VAL* 3.9 12.3 - - + -
289A TYR* 3.3 41.1 - + + -
290A VAL 3.4 12.1 - - - +
291A ARG* 4.7 0.9 - - - -
292A ALA 3.9 1.3 - - - +
329A LEU* 5.4 0.4 - - + -
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Residues in contact with VAL 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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173A PHE* 2.8 34.5 + - + +
203A LEU* 4.5 14.1 - - + -
204A ARG 4.4 8.7 - - - +
205A THR* 4.7 9.0 - - + -
206A TYR* 3.1 14.4 - - - -
257A PHE* 1.3 77.0 - - - +
259A LEU* 1.3 65.4 + - + +
290A VAL* 2.8 30.6 + - + -
291A ARG 3.8 17.9 - - - +
292A ALA* 4.1 7.6 - - - -
293A GLY 4.9 0.7 - - - +
294A VAL* 3.9 15.3 - - + -
299A LEU* 4.1 20.6 - - + -
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Residues in contact with LEU 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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171A TRP* 3.3 13.0 - - - +
172A GLY* 4.5 0.2 - - - -
173A PHE* 4.0 12.8 - - + +
174A ILE* 3.9 26.9 - - + +
257A PHE* 3.6 3.2 - - - +
258A VAL* 1.3 91.9 - - + +
260A VAL* 1.3 75.5 + - - +
261A LEU* 4.1 14.8 - - + +
288A PHE* 4.3 8.3 - - + +
289A TYR* 3.2 6.4 - - - +
290A VAL* 2.8 54.7 + - + +
299A LEU* 4.8 0.7 - - + -
1001A UUL 4.0 31.9 - - + -
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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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169A LEU* 4.6 3.3 - - + +
170A ALA* 3.4 3.1 - - - +
171A TRP* 2.9 53.1 + - + +
174A ILE* 5.5 0.5 - - - +
210A LEU* 4.3 17.3 - - + -
257A PHE* 3.9 17.5 - - + -
259A LEU* 1.3 81.4 - - - +
261A LEU* 1.3 66.6 + - - +
262A ALA 5.2 0.4 - - - +
287A LEU* 4.0 18.4 - - + -
288A PHE 3.4 9.2 - - - +
289A TYR* 3.8 12.1 - - + -
327A PHE* 6.0 2.0 - - + -
329A LEU* 4.0 24.0 - - + -
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Residues in contact with LEU 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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168A SER* 4.1 8.3 - - - -
169A LEU 3.6 7.2 - - - +
170A ALA* 4.2 10.3 - - + -
174A ILE* 4.0 7.0 - - + -
259A LEU* 4.1 9.9 - - + -
260A VAL* 1.3 76.4 - - - +
262A ALA* 1.3 73.7 + - - +
263A LEU* 4.0 14.1 + - + -
268A LEU* 3.9 43.7 - - + -
274A ALA* 5.1 1.1 - - + -
286A HIS 3.8 0.9 - - - +
287A LEU* 3.4 6.8 - - - +
288A PHE* 2.7 60.0 + - + +
1001A UUL 4.0 17.3 - - + -
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Residues in contact with ALA 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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168A SER* 3.0 9.0 - - - -
169A LEU* 2.8 44.6 + - + +
260A VAL* 4.3 0.8 - - + +
261A LEU* 1.3 73.4 - - - +
263A LEU* 1.3 57.8 + - - +
285A MET* 3.7 27.4 - - + -
286A HIS 3.4 5.4 - - - +
287A LEU* 4.2 12.1 - - + +
327A PHE* 4.2 19.7 - - + -
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Residues in contact with LEU 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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167A LEU* 3.5 19.1 - - + +
168A SER* 4.1 12.6 - - - -
261A LEU* 4.2 14.6 - - + -
262A ALA* 1.3 75.2 - - - +
264A LEU* 1.3 61.1 + - - +
265A HIS 3.0 27.8 - - - +
266A SER 4.4 2.5 - - - +
267A HIS 3.9 18.4 - - - +
268A LEU* 4.5 10.1 - - + +
274A ALA* 4.0 26.7 - - + -
275A ALA* 4.1 11.7 - - + -
285A MET* 4.0 1.2 - - - +
286A HIS* 2.8 49.2 + - + +
288A PHE* 4.3 7.9 - - + -
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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