Contacts of the strand formed by residues 256 - 263 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205E THR* 2.7 35.2 + - - -
206E TYR 3.5 10.9 + - - -
207E ARG* 3.8 27.5 + - - +
254E ASP* 3.7 9.1 - - - +
255E GLU* 1.3 80.6 - - - +
257E PHE* 1.3 66.4 + - - +
291E ARG* 4.2 1.2 - - - -
292E ALA* 3.3 29.3 + - + +
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Residues in contact with PHE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TRP* 3.8 26.7 - + + -
205E THR* 3.2 6.5 - - - -
206E TYR* 2.6 43.4 + - - +
208E GLY 3.6 22.0 - - - -
209E ARG 4.8 0.2 - - - -
210E LEU* 3.8 24.5 - - + -
252E VAL* 3.8 13.5 - - + -
254E ASP* 3.6 28.0 - - + -
255E GLU* 4.0 2.5 - - - -
256E ASP* 1.3 79.7 + - - +
258E VAL* 1.3 61.5 + - - +
259E LEU 4.3 5.4 - - - +
260E VAL* 4.1 13.2 - - + -
289E TYR* 3.6 38.4 - + + -
290E VAL 3.6 11.0 - - - +
291E ARG* 4.6 1.6 - - + -
292E ALA 4.2 1.1 - - - +
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Residues in contact with VAL 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E GLY* 4.7 0.2 - - - -
173E PHE* 2.8 45.4 + - + +
203E LEU* 4.3 17.9 - - + -
204E ARG 4.4 3.1 - - - +
205E THR* 4.6 5.8 - - + -
206E TYR* 3.3 13.0 - - - -
257E PHE* 1.3 74.6 - - - +
259E LEU* 1.3 52.2 + - + +
290E VAL* 2.8 30.2 + - + +
291E ARG 3.2 27.1 - - - +
292E ALA* 4.2 5.2 - - - +
293E GLY 5.3 0.2 - - - +
294E VAL* 4.0 7.4 - - + -
299E LEU* 4.3 21.1 - - + -
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Residues in contact with LEU 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TRP* 3.3 12.6 - - - +
172E GLY* 4.5 0.4 - - - -
173E PHE* 4.0 15.7 - - + +
174E ILE* 3.8 33.0 - - + -
257E PHE* 3.7 2.4 - - - +
258E VAL* 1.3 82.1 - - + +
260E VAL* 1.3 75.4 + - - +
261E LEU* 4.3 6.1 - - + +
288E PHE* 4.4 5.4 - - + +
289E TYR* 3.3 7.8 - - - +
290E VAL* 2.9 56.5 + - + +
299E LEU* 5.0 1.1 - - + -
1001E UUL 3.8 34.5 - - + -
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Residues in contact with VAL 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E LEU* 3.9 4.2 - - + +
170E ALA* 3.5 4.0 - - - +
171E TRP* 2.9 60.6 + - + +
174E ILE* 5.1 1.1 - - - +
210E LEU* 4.2 22.0 - - + -
257E PHE* 4.1 15.0 - - + -
259E LEU* 1.3 80.1 - - - +
261E LEU* 1.3 64.6 + - - +
262E ALA 4.3 0.7 - - - +
287E LEU* 4.0 17.0 - - + -
288E PHE 3.5 8.3 - - - +
289E TYR* 3.9 11.0 - - + -
327E PHE* 6.2 2.7 - - + -
329E LEU* 4.2 16.6 - - + -
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Residues in contact with LEU 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E SER* 4.1 6.5 - - - -
169E LEU 3.7 6.5 - - - +
170E ALA* 4.0 16.2 - - + -
174E ILE* 4.2 11.2 - - + -
259E LEU* 4.4 2.5 - - + -
260E VAL* 1.3 75.1 - - - +
262E ALA* 1.3 75.7 + - - +
263E LEU* 4.2 9.6 - - + -
268E LEU* 3.7 47.1 - - + -
274E ALA* 5.0 0.2 - - + -
286E HIS 3.6 1.4 - - - +
287E LEU* 3.3 8.5 - - - +
288E PHE* 2.7 60.3 + - + +
1001E UUL 3.9 16.2 - - + -
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Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E SER* 3.1 9.2 - - - -
169E LEU* 3.0 44.7 + - + +
260E VAL* 4.3 1.0 - - + +
261E LEU* 1.3 73.2 - - - +
263E LEU* 1.3 60.1 + - - +
285E MET* 3.4 27.1 - - + -
286E HIS 3.4 4.7 - - - -
287E LEU* 4.4 8.0 - - + +
327E PHE* 4.1 21.8 - - + -
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Residues in contact with LEU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E LEU* 3.5 19.7 - - + +
168E SER* 4.2 11.7 - - - -
261E LEU* 4.2 11.4 - - + -
262E ALA* 1.3 74.8 - - - +
264E LEU* 1.3 63.4 + - - +
265E HIS 3.2 26.1 + - - +
266E SER 4.5 0.4 - - - +
267E HIS 3.9 15.7 - - - +
268E LEU* 4.4 17.7 - - + +
274E ALA* 3.8 28.9 - - + -
275E ALA* 4.1 11.4 - - + -
285E MET* 3.8 1.9 - - - +
286E HIS* 2.7 48.5 + - + +
288E PHE* 4.4 7.0 - - + -
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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