Contacts of the strand formed by residues 174 - 181 (chain A) 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 ALA 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY 3.4 7.4 + - - +
173A THR* 1.3 78.4 - - - +
175A ILE* 1.3 69.7 + - - +
176A ARG 4.4 0.2 - - - -
237A VAL* 3.5 19.1 - - + -
238A VAL 3.1 14.8 - - - +
239A PRO* 3.5 13.9 - - + -
240A TYR 3.7 3.8 - - - +
278A GLU* 3.0 32.5 + - - +
279A MET 4.6 1.9 + - - +
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 4.1 10.5 - - + -
163A ILE* 3.2 31.4 - - + -
174A ALA* 1.3 77.4 - - - +
176A ARG* 1.3 61.3 + - - +
236A VAL 3.9 0.9 - - - +
237A VAL* 3.4 6.0 - - - +
238A VAL* 2.7 35.8 + - - +
240A TYR* 4.1 33.0 - - + -
252A ILE* 3.7 15.9 - - + -
254A TYR* 3.2 25.8 + - - +
275A ILE* 3.9 11.0 - - + -
276A THR 3.6 8.5 - - - +
277A LEU* 4.2 16.4 - - + -
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 1.3 76.4 - - - +
177A ALA* 1.3 67.0 + - - +
178A MET* 3.9 22.7 - - - +
226A VAL* 3.9 13.5 - - - +
235A SER* 3.0 30.0 + - - +
236A VAL 3.5 4.5 - - - -
237A VAL* 3.3 24.9 - - + +
274A ILE 3.2 2.1 - - - +
275A ILE* 3.1 7.4 - - - +
276A THR* 2.7 55.1 + - - +
278A GLU* 3.0 41.1 + - + +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE 4.2 0.6 + - - -
176A ARG* 1.3 73.6 - - - +
178A MET* 1.3 59.5 + - - +
215A ILE* 3.6 13.9 - - + +
235A SER* 3.6 0.7 - - - -
236A VAL* 3.0 42.1 + - + +
254A TYR* 3.3 41.5 - - + -
273A ILE* 5.0 2.0 - - + -
274A ILE 3.6 3.8 - - - -
275A ILE* 4.1 9.9 - - + -
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 4.1 33.4 - - + -
176A ARG* 3.9 22.6 - - + -
177A ALA* 1.3 73.7 - - - +
179A PRO* 1.3 78.0 - - - +
180A VAL* 4.0 1.5 + - + +
215A ILE* 3.8 3.8 - - - +
233A ARG* 4.3 22.4 - - - -
234A GLN 3.6 15.3 - - - +
235A SER* 3.6 14.6 - - - -
272A LEU 3.8 0.2 - - - +
273A ILE* 4.6 0.8 - - - +
274A ILE* 2.9 43.5 + - + +
276A THR* 4.9 5.4 - - - +
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Residues in contact with PRO 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A MET* 1.3 91.8 - - + +
180A VAL* 1.3 70.2 + - - +
191A VAL* 3.1 45.6 + - + +
214A LEU* 4.3 10.3 - - + -
215A ILE* 3.2 22.0 - - + -
233A ARG* 3.7 3.8 + - - -
234A GLN 3.7 11.2 - - - +
235A SER* 5.1 0.7 - - - -
271A ILE* 4.3 3.4 - - + -
272A LEU 3.2 6.1 - - - +
273A ILE* 3.8 18.8 - - + -
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 3.8 31.2 - - + +
118A ASN* 6.4 0.7 - - + -
178A MET* 4.7 4.5 - - + +
179A PRO* 1.3 77.4 - - - +
181A TYR* 1.3 73.5 + - - +
187A VAL* 4.3 16.2 - - + +
191A VAL* 3.7 6.7 - - - -
233A ARG* 3.2 35.2 - - - +
271A ILE* 4.2 2.0 - - - -
272A LEU* 2.5 47.5 + - + +
274A ILE* 4.9 12.6 - - + -
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Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 1.3 86.6 - - - +
182A LYS* 1.3 65.8 + - - +
183A LYS* 4.1 0.8 - - - +
186A HIS* 3.1 45.8 - - + +
187A VAL* 4.0 13.5 + - - +
189A ASP* 3.4 33.8 + - + -
190A VAL 3.7 10.5 + - - -
191A VAL* 4.1 14.5 - - + +
192A LYS 5.0 1.4 + - - -
265A GLY 4.4 0.2 - - - -
266A MET* 3.0 45.1 + - + +
269A ARG* 3.5 32.1 + - + -
270A PRO 3.6 14.1 - - - +
271A ILE* 3.7 11.7 - - + +
272A LEU* 4.9 1.1 - - - +
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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