Contacts of the strand formed by residues 271 - 278 (chain K) in PDB entry 3VD1
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 ILE 271 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K PRO* 4.0 17.7 - - + -
180K VAL 3.2 20.4 - - - +
181K TYR* 3.8 14.6 - - + -
182K LYS* 3.9 2.5 - - - +
191K VAL* 4.5 3.6 - - + -
214K LEU* 4.8 4.5 - - + -
260K SER* 5.3 2.6 - - - -
266K MET* 3.5 34.1 - - + -
269K ARG 3.5 13.0 - - - +
270K PRO* 1.3 73.4 - - - +
272K LEU* 1.3 68.7 + - - +
273K ILE* 4.1 17.7 - - + -
291K GLU* 3.6 5.6 - - - +
292K GLY* 2.9 40.6 + - - +
293K ARG* 4.9 0.7 - - - +
294K ILE* 5.4 5.4 - - + -
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Residues in contact with LEU 272 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K ASN* 3.8 30.1 - - + +
179K PRO* 3.7 2.3 - - - +
180K VAL* 3.0 59.5 + - + +
181K TYR 4.1 0.7 - - - +
182K LYS* 4.1 29.8 - - + +
271K ILE* 1.3 77.6 - - - +
273K ILE* 1.3 61.7 + - - +
274K ILE* 3.9 10.5 + - + -
289K SER* 4.1 8.5 - - - +
290K PHE 3.4 13.5 - - - +
291K GLU* 3.9 11.0 - - + +
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Residues in contact with ILE 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K LEU* 5.8 0.2 - - + -
161K ILE* 5.8 0.2 - - + -
177K ALA* 5.0 7.9 - - + -
178K MET 4.0 5.6 - - - +
179K PRO* 4.1 23.3 - - + -
214K LEU* 5.4 1.1 - - + -
215K ILE* 4.5 4.9 - - + -
254K TYR* 6.5 0.2 - - + -
256K PHE* 4.1 31.2 - - + -
271K ILE* 4.1 14.1 - - + -
272K LEU* 1.3 73.5 - - - +
274K ILE* 1.3 64.3 + - - +
275K ILE* 4.0 14.1 - - + -
289K SER* 3.1 4.5 - - - -
290K PHE* 2.5 76.9 + - + +
292K GLY* 4.2 12.6 - - - -
294K ILE* 6.0 1.3 - - + -
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Residues in contact with ILE 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K PRO* 5.2 3.8 - - + -
117K SER 3.5 28.0 - - - +
118K ASN* 3.9 6.3 - - + -
176K ARG* 3.3 5.9 - - - +
177K ALA* 3.5 0.7 - - - -
178K MET* 3.0 46.9 + - + +
180K VAL* 4.2 15.9 - - + -
272K LEU* 3.9 16.4 - - + -
273K ILE* 1.3 74.0 - - - +
275K ILE* 1.3 64.8 + - - +
276K THR* 3.8 17.4 + - - +
287K ARG* 4.5 12.3 - - + +
288K ARG 4.0 1.8 - - - -
289K SER* 3.3 24.5 - - - -
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Residues in contact with ILE 275 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K PHE* 4.0 17.9 - - + -
129K VAL* 4.6 13.2 - - + -
161K ILE* 4.6 5.4 - - + -
163K ILE* 5.1 12.1 - - + -
175K ILE* 3.7 21.3 - - + -
176K ARG 3.3 1.6 - - - -
177K ALA* 4.1 15.9 - - + -
254K TYR* 4.3 16.6 - - + +
273K ILE* 4.1 10.5 - - + -
274K ILE* 1.3 74.0 - - - +
276K THR* 1.3 73.8 + - - +
287K ARG* 3.5 1.8 - - - +
288K ARG* 2.8 42.2 + - + +
290K PHE* 3.7 27.1 - - + -
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Residues in contact with THR 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K PHE* 4.3 1.8 - - - -
175K ILE* 3.2 6.1 - - - -
176K ARG* 2.8 45.9 + - - -
274K ILE* 3.8 15.9 + - - +
275K ILE* 1.3 85.8 + - - +
277K LEU* 1.3 65.5 + - - +
278K GLU* 3.3 21.8 - - + +
283K GLN* 5.3 5.6 - - + +
284K VAL* 6.3 1.3 - - - -
285K LEU 6.0 0.4 - - - +
286K GLY 3.3 17.3 - - - +
287K ARG* 4.1 18.1 + - + +
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Residues in contact with LEU 277 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K HIS* 5.6 3.6 - - + -
127K PHE* 3.3 42.2 - - + -
163K ILE* 4.8 1.6 - - + -
165K VAL* 5.0 7.9 - - + -
168K PRO* 4.7 9.0 - - + -
173K THR* 4.0 20.4 - - - +
174K ALA 3.4 9.9 - - - +
175K ILE* 4.3 15.7 - - + +
240K TYR* 4.4 20.0 - - + -
276K THR* 1.3 71.2 - - - +
278K GLU* 1.3 63.7 + - - +
285K LEU* 3.4 25.7 + - + -
286K GLY* 2.9 37.1 + - - +
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Residues in contact with GLU 278 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K THR* 2.9 8.6 - - - -
174K ALA* 2.5 52.8 + - - +
176K ARG* 2.9 47.8 + - - +
237K VAL* 4.6 5.8 - - - +
276K THR* 3.3 23.7 - - + +
277K LEU* 1.3 77.1 - - - +
279K MET* 1.3 69.3 - - - +
283K GLN* 3.3 46.7 + - + +
284K VAL 4.0 3.6 - - - +
285K LEU* 4.4 3.6 - - - +
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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