Contacts of the strand formed by residues 271 - 278 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B PRO* 4.9 3.4 - - + -
180B VAL 3.1 11.7 - - - +
181B TYR* 3.9 18.2 - - + +
182B LYS* 4.3 2.0 - - - +
191B VAL* 4.3 6.3 - - + -
214B LEU* 4.0 19.7 - - + -
256B PHE* 5.8 0.4 - - + -
260B SER* 5.0 2.7 - - - +
266B MET* 3.6 32.1 - - - -
269B ARG 3.6 9.9 - - - +
270B PRO* 1.3 80.0 - - - +
272B LEU* 1.3 64.1 + - - +
273B ILE* 4.6 17.3 - - + -
291B GLU* 3.4 6.6 - - - +
292B GLY* 3.1 39.2 + - - +
294B ILE* 4.7 9.6 - - + -
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASN* 4.0 30.1 - - + +
149B LYS* 4.1 12.3 - - + +
178B MET 3.9 0.3 - - - +
179B PRO* 3.6 2.6 - - - +
180B VAL* 2.6 43.7 + - + +
181B TYR 5.6 0.9 - - - +
182B LYS* 3.4 44.8 - - + +
271B ILE* 1.3 74.9 - - - +
273B ILE* 1.3 64.4 + - - +
274B ILE* 4.2 2.6 + - + +
289B SER* 4.0 22.9 - - - -
290B PHE 3.7 9.6 - - - +
291B GLU* 3.7 22.9 - - + +
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 4.6 2.7 - - + -
177B ALA* 4.9 4.0 - - + -
178B MET 3.4 13.2 - - - +
179B PRO* 5.1 1.1 - - + -
215B ILE* 3.8 19.3 - - + -
256B PHE* 3.3 36.1 - - + -
271B ILE* 4.6 15.3 - - + -
272B LEU* 1.3 79.1 - - - +
274B ILE* 1.3 65.6 + - - +
275B ILE* 4.1 6.8 + - + -
288B ARG 3.7 0.3 - - - +
289B SER* 3.6 21.8 - - - -
290B PHE* 3.1 49.2 + - + +
292B GLY* 4.7 11.4 - - - +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 4.4 12.6 - - + +
117B SER 4.5 1.8 - - - +
118B ASN* 3.7 30.3 - - + +
176B ARG* 3.4 4.3 - - - +
177B ALA* 3.4 0.6 - - - -
178B MET* 2.9 47.5 + - + +
180B VAL* 3.8 26.9 - - + -
272B LEU* 4.7 3.8 - - + +
273B ILE* 1.3 74.3 - - - +
275B ILE* 1.3 61.1 + - - +
276B THR* 3.8 6.0 + - + +
287B ARG* 3.5 26.9 - - - -
288B ARG 3.3 7.4 - - - +
289B SER* 3.3 24.9 - - - +
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE* 3.7 14.5 - - + -
129B VAL* 3.6 13.5 - - + -
161B ILE* 3.0 37.9 - - + -
163B ILE* 4.1 12.8 - - + -
175B ILE* 3.4 29.2 - - + -
176B ARG 2.9 7.9 - - - +
177B ALA* 4.8 5.8 - - + -
252B ILE* 5.4 0.2 - - + -
254B TYR* 4.5 7.9 - - + +
273B ILE* 4.8 8.7 - - + +
274B ILE* 1.3 75.3 - - - +
276B THR* 1.3 59.4 + - - +
287B ARG* 3.4 19.2 - - - -
288B ARG* 3.5 11.6 + - + +
290B PHE* 3.5 23.8 - - + -
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Residues in contact with THR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ALA 3.7 0.5 - - - +
175B ILE* 3.3 3.4 - - - -
176B ARG* 2.6 55.1 + - - +
178B MET* 6.1 4.3 - - + -
274B ILE* 3.8 8.3 + - + +
275B ILE* 1.3 75.9 - - - +
277B LEU* 1.3 60.4 + - - +
278B GLU* 2.7 31.7 + - - +
284B VAL* 4.7 2.9 - - + -
286B GLY 3.8 6.7 - - - -
287B ARG* 3.4 43.3 - - + +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B HIS* 5.0 13.5 - - + +
127B PHE* 3.4 50.5 - - + -
165B VAL* 4.9 11.4 - - + -
173B THR* 5.1 7.2 - - + -
174B ALA 3.1 9.9 - - - +
175B ILE* 4.2 13.9 - - + +
240B TYR* 5.6 4.3 - - + -
276B THR* 1.3 74.2 - - - +
278B GLU* 1.3 62.8 + - - +
284B VAL* 3.9 1.2 - - - -
285B LEU* 3.2 36.9 + - + +
286B GLY* 3.3 34.2 + - - +
287B ARG 3.8 0.4 - - - +
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B THR* 2.9 18.0 + - - +
174B ALA* 2.7 32.3 + - + +
176B ARG* 2.8 34.3 + - - -
276B THR* 2.7 31.9 + - - +
277B LEU* 1.3 82.5 - - - +
279B MET* 1.3 67.6 + - - +
282B GLY* 4.4 10.8 - - - -
283B GLN 3.7 10.8 - - - +
284B VAL* 4.3 17.8 - - - +
285B LEU* 3.4 10.5 - - - -
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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