Contacts of the strand formed by residues 256 - 263 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D THR* 4.7 9.9 + - - +
206D TYR 3.5 3.6 - - - +
207D ARG* 3.0 31.6 + - - +
254D ASP* 3.7 4.1 - - + +
255D GLU* 1.3 78.5 - - - +
257D PHE* 1.3 64.0 + - - +
291D ARG* 3.7 7.1 - - - +
292D ALA* 2.8 39.1 + - + +
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Residues in contact with PHE 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D TRP* 3.7 29.6 - + + -
205D THR* 3.4 8.4 - - - -
206D TYR* 2.9 38.8 + - - +
208D GLY 3.2 28.7 - - - -
209D ARG 5.1 0.2 - - - -
210D LEU* 4.0 24.9 - - + -
252D VAL* 4.1 4.3 - - + -
254D ASP* 3.3 31.4 - - - -
255D GLU* 3.9 2.9 - - - -
256D ASP* 1.3 77.0 - - - +
258D VAL* 1.3 63.3 + - - +
259D LEU 4.0 9.9 - - - +
260D VAL* 4.3 3.1 - - + -
289D TYR* 3.6 41.7 - + + -
290D VAL 3.3 11.9 - - - +
291D ARG* 4.5 1.3 - - - -
292D ALA 4.1 1.3 - - - +
329D LEU* 5.3 0.2 - - + -
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLY* 3.6 0.2 - - - -
173D PHE* 2.7 43.1 + - + +
203D LEU* 5.4 6.1 - - + -
204D ARG 4.8 7.4 - - - +
205D THR* 4.9 6.1 - - + -
206D TYR* 3.2 14.6 - - - -
257D PHE* 1.3 75.7 - - - +
259D LEU* 1.3 74.3 + - + +
290D VAL* 2.8 29.8 + - + +
291D ARG 4.2 4.3 - - - +
292D ALA* 4.4 6.7 - - - -
293D GLY 5.3 0.2 - - - +
294D VAL* 3.7 16.8 - - + -
299D LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D TRP* 3.4 11.2 - - - +
172D GLY* 4.5 0.4 - - - -
173D PHE* 4.1 12.3 - - + +
174D ILE* 3.6 37.5 - - + +
257D PHE* 3.6 3.8 - - - +
258D VAL* 1.3 96.8 - - + +
260D VAL* 1.3 68.6 + - - +
261D LEU* 4.7 5.2 - - + +
288D PHE* 4.7 5.8 - - + +
289D TYR* 3.1 13.2 - - - +
290D VAL* 2.9 50.1 + - + +
299D LEU* 5.2 0.4 - - + -
1001D UUL 4.0 32.3 - - + -
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Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LEU* 3.9 3.6 - - + +
170D ALA* 3.4 3.3 - - - +
171D TRP* 2.8 62.7 + - + +
174D ILE* 5.2 0.3 - - - +
210D LEU* 4.3 15.5 - - + -
257D PHE* 4.3 10.3 - - + -
259D LEU* 1.3 79.1 - - - +
261D LEU* 1.3 66.2 + - - +
262D ALA* 5.0 1.1 - - + +
287D LEU* 4.1 17.9 - - + -
288D PHE 3.5 7.6 - - - +
289D TYR* 4.1 9.6 - - + -
327D PHE* 5.7 3.6 - - + -
329D LEU* 3.9 29.8 - - + -
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Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D SER* 4.1 8.5 - - - -
169D LEU 3.5 6.7 - - - +
170D ALA* 4.2 11.9 - - + -
174D ILE* 4.2 13.0 - - + -
259D LEU* 4.3 1.5 - - + -
260D VAL* 1.3 76.5 - - - +
262D ALA* 1.3 72.7 + - - +
263D LEU* 4.0 14.4 - - + -
268D LEU* 3.6 46.2 - - + -
274D ALA* 5.0 0.4 - - + -
286D HIS 3.7 0.9 - - - +
287D LEU* 3.3 6.1 - - - -
288D PHE* 2.7 68.2 + - + +
1001D UUL 4.2 11.2 - - + -
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Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D LEU* 4.7 0.7 - - + -
168D SER* 3.2 7.3 - - - -
169D LEU* 2.8 44.0 + - + +
260D VAL* 4.3 1.6 - - + +
261D LEU* 1.3 73.5 - - - +
263D LEU* 1.3 58.5 + - - +
285D MET* 3.1 24.0 - - + -
286D HIS 3.4 5.6 - - - -
287D LEU* 4.1 13.0 - - + +
327D PHE* 4.2 22.2 - - + -
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Residues in contact with LEU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D LEU* 3.6 17.7 - - + +
168D SER* 4.3 7.2 - - - -
261D LEU* 4.0 17.9 - - + -
262D ALA* 1.3 74.8 - - - +
264D LEU* 1.3 67.1 + - - +
265D HIS 3.1 27.6 - - - +
266D SER 4.4 2.0 - - - +
267D HIS 3.9 16.8 - - - +
268D LEU* 4.5 7.6 - - + -
274D ALA* 3.7 30.1 - - + -
275D ALA* 4.3 4.5 - - + -
285D MET* 3.3 1.5 - - - +
286D HIS* 2.6 50.8 + - + +
288D PHE* 4.1 14.8 - - + -
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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
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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