Contacts of the strand formed by residues 256 - 263 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205F THR* 2.9 28.7 + - - +
206F TYR 3.2 14.7 - - - +
207F ARG* 4.1 17.4 + - - +
254F ASP* 3.5 8.9 - - - +
255F GLU* 1.3 92.6 - - - +
257F PHE* 1.3 71.5 + - - +
291F ARG* 4.3 0.2 - - - -
292F ALA* 3.9 25.1 + - + +
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Residues in contact with PHE 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F TRP* 4.1 26.0 - + + -
205F THR* 3.7 5.3 - - - -
206F TYR* 3.0 38.2 + - - +
208F GLY* 3.4 19.5 - - - -
210F LEU* 3.9 27.6 - - + -
252F VAL* 4.2 5.6 - - + -
254F ASP* 3.3 40.4 - - + -
255F GLU 4.4 0.2 - - - -
256F ASP* 1.3 79.0 - - - +
258F VAL* 1.3 59.0 + - - +
259F LEU 4.1 6.7 - - - +
260F VAL* 4.0 13.9 - - + -
289F TYR* 3.6 40.8 - + + -
290F VAL 3.7 10.3 - - - +
291F ARG* 4.7 1.6 - - - +
292F ALA 4.8 0.4 - - - +
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Residues in contact with VAL 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE* 2.8 34.2 + - + +
203F LEU* 4.7 7.6 - - + -
204F ARG 4.6 11.9 - - - +
205F THR* 4.4 4.9 - - + +
206F TYR* 3.3 11.8 - - - -
257F PHE* 1.3 73.4 - - - +
259F LEU* 1.3 76.2 + - + +
290F VAL* 3.0 17.2 + - + +
291F ARG 3.5 26.0 - - - +
292F ALA* 4.4 5.8 - - - +
293F GLY 5.2 0.4 - - - +
294F VAL* 4.2 7.2 - - + -
299F LEU* 3.8 25.4 - - + -
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Residues in contact with LEU 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F TRP* 3.4 12.6 - - - +
172F GLY* 4.6 0.4 - - - -
173F PHE* 4.3 4.5 - - + +
174F ILE* 3.5 32.3 - - + -
257F PHE* 3.4 2.7 - - - +
258F VAL* 1.3 92.0 - - + +
260F VAL* 1.3 64.0 + - - +
261F LEU* 4.4 17.3 - - + +
288F PHE* 5.3 2.2 - - + -
289F TYR* 3.3 10.5 - - - +
290F VAL* 3.0 58.0 + - + +
299F LEU* 4.7 2.2 - - + -
319F LEU* 5.6 0.2 - - + -
1001F UUL 4.2 36.3 - - + -
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Residues in contact with VAL 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F LEU 3.7 2.2 - - - +
170F ALA* 3.5 4.0 - - - +
171F TRP* 3.1 58.8 + - + +
210F LEU* 4.4 15.9 - - + -
257F PHE* 4.0 21.5 - - + -
259F LEU* 1.3 77.9 - - - +
261F LEU* 1.3 63.0 + - - +
262F ALA* 5.0 1.8 - - + +
287F LEU* 4.1 20.0 - - + -
288F PHE 3.9 4.3 - - - +
289F TYR* 4.2 4.3 - - + -
327F PHE* 6.3 2.2 - - + -
329F LEU* 3.9 24.5 - - + -
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Residues in contact with LEU 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F SER* 4.1 16.8 - - - -
169F LEU 3.7 0.9 - - - +
170F ALA* 4.1 18.6 - - + -
174F ILE* 5.3 4.5 - - + -
259F LEU* 4.3 12.3 - - + -
260F VAL* 1.3 74.4 - - - +
262F ALA* 1.3 71.3 + - - +
263F LEU* 3.7 16.1 + - + -
268F LEU* 3.6 38.4 - - + -
274F ALA* 5.0 0.4 - - + -
286F HIS 3.8 0.3 - - - +
287F LEU* 3.5 3.9 - - - -
288F PHE* 2.9 56.6 + - + +
1001F UUL 4.1 17.3 - - + -
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Residues in contact with ALA 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F SER* 3.1 9.0 - - - -
169F LEU* 3.0 40.1 + - + +
260F VAL* 4.2 1.6 - - + +
261F LEU* 1.3 72.1 - - - +
263F LEU* 1.3 58.8 + - - +
285F MET* 3.3 24.7 - - + -
286F HIS 3.4 6.5 - - - +
287F LEU* 4.3 11.7 - - + +
324F VAL* 6.3 0.2 - - + -
327F PHE* 4.1 22.4 - - + -
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Residues in contact with LEU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F LEU* 3.4 22.7 - - + +
168F SER* 4.0 12.1 - - - -
261F LEU* 3.7 16.8 + - + +
262F ALA* 1.3 74.1 - - - +
264F LEU* 1.3 63.3 + - - +
265F HIS 3.2 26.2 - - - +
266F SER 4.2 4.3 - - - +
267F HIS 4.0 18.2 - - - +
268F LEU* 4.6 12.1 - - + -
274F ALA* 4.2 25.1 - - + -
275F ALA* 4.5 1.6 - - + -
285F MET* 3.7 1.8 - - - +
286F HIS* 2.8 45.6 + - + +
288F PHE* 4.4 13.0 - - + -
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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