Contacts of the strand formed by residues 256 - 263 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C THR* 3.0 28.9 + - - -
206C TYR 3.6 6.4 + - - +
207C ARG* 3.4 25.8 - - - +
254C ASP* 3.4 11.3 + - + +
255C GLU* 1.3 77.5 - - - +
257C PHE* 1.3 66.3 + - - +
291C ARG* 3.8 4.0 - - - -
292C ALA* 3.1 33.0 + - + +
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Residues in contact with PHE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C TRP* 3.8 28.9 - + + -
205C THR* 3.3 5.8 - - - -
206C TYR* 2.7 40.0 + - - -
208C GLY 3.1 29.2 - - - -
210C LEU* 3.7 28.5 - - + -
252C VAL* 4.5 4.7 - - + -
254C ASP* 3.3 26.7 - - + -
256C ASP* 1.3 81.2 + - - +
258C VAL* 1.3 63.4 + - - +
259C LEU 3.9 8.3 - - - +
260C VAL* 4.3 3.4 - - + -
289C TYR* 3.7 45.3 - + + -
290C VAL 3.5 9.4 - - - +
291C ARG* 4.5 2.0 - - - -
292C ALA 3.6 4.0 - - - +
329C LEU* 5.3 0.4 - - + -
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLY* 3.3 2.0 - - - -
173C PHE* 2.8 28.9 + - + -
203C LEU* 4.7 16.8 - - + -
204C ARG 4.3 11.0 - - - +
205C THR* 4.2 14.8 - - + -
206C TYR* 3.1 15.1 - - - -
257C PHE* 1.3 76.0 - - - +
259C LEU* 1.3 74.8 + - + +
290C VAL* 2.8 33.1 + - + +
291C ARG 4.0 17.0 - - - +
292C ALA* 4.0 2.7 - - - +
293C GLY 5.0 1.1 - - - +
294C VAL* 4.5 7.2 - - + +
299C LEU* 4.4 16.2 - - + -
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C TRP* 3.4 10.3 - - - +
172C GLY* 4.4 0.2 - - - -
173C PHE* 4.1 13.0 - - + +
174C ILE* 4.0 35.9 - - + +
257C PHE* 3.6 3.6 - - - +
258C VAL* 1.3 97.0 - - + +
260C VAL* 1.3 74.8 + - - +
261C LEU* 4.1 8.1 - - + +
288C PHE* 4.5 8.7 - - + +
289C TYR* 3.2 8.6 - - - +
290C VAL* 3.1 50.0 + - + +
299C LEU* 4.9 1.6 - - + -
1001C UUL 4.2 26.0 - - + -
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Residues in contact with VAL 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LEU* 3.8 4.1 - - + +
170C ALA* 3.4 5.7 - - - +
171C TRP* 2.9 54.8 + - + +
174C ILE* 5.4 0.3 - - - +
210C LEU* 4.3 16.4 - - + -
257C PHE* 4.3 9.2 - - + -
259C LEU* 1.3 80.6 - - - +
261C LEU* 1.3 65.3 + - - +
262C ALA 4.9 1.1 - - - +
287C LEU* 4.0 18.2 - - + -
288C PHE 3.5 9.9 - - - +
289C TYR* 4.2 9.4 - - + -
327C PHE* 5.8 2.9 - - + -
329C LEU* 3.6 31.4 - - + -
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Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C SER* 4.0 15.9 - - - -
169C LEU 3.5 7.6 - - - +
170C ALA* 4.5 10.3 - - + -
174C ILE* 4.0 11.2 - - + -
259C LEU* 4.1 12.1 - - + -
260C VAL* 1.3 75.5 - - - +
262C ALA* 1.3 71.7 + - - +
263C LEU* 3.7 15.8 + - + -
268C LEU* 4.0 23.1 - - + -
286C HIS 3.7 1.2 - - - +
287C LEU* 3.4 3.8 - - - -
288C PHE* 2.8 55.2 + - + +
1001C UUL 3.9 26.9 - - + -
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C LEU* 4.8 1.2 - - + +
168C SER* 3.2 6.4 - - - -
169C LEU* 2.9 39.8 + - + +
260C VAL* 4.2 1.8 - - + +
261C LEU* 1.3 72.1 - - - +
263C LEU* 1.3 57.8 + - - +
264C LEU* 4.8 2.3 - - - +
285C MET* 3.0 34.8 - - + -
286C HIS 3.3 5.8 - - - +
287C LEU* 4.1 13.0 - - + +
327C PHE* 3.9 16.6 - - + -
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C LEU* 3.3 23.8 - - + +
168C SER* 4.1 10.3 - - - -
261C LEU* 3.7 17.4 + - + -
262C ALA* 1.3 74.5 - - - +
264C LEU* 1.3 63.0 + - - +
265C HIS 3.2 26.9 - - - +
267C HIS 4.0 17.9 - - - +
268C LEU* 4.4 15.3 - - + -
274C ALA* 4.0 27.6 - - + -
275C ALA* 4.3 8.7 - - + -
285C MET 3.8 0.2 - - - -
286C HIS* 2.8 49.4 + - + +
288C PHE* 4.5 4.3 - - + -
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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