Contacts of the strand formed by residues 174 - 181 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L GLY 3.8 2.9 + - - +
173L THR* 1.3 77.8 - - - +
175L ILE* 1.3 64.4 + - - +
176L ARG 4.2 0.2 - - - -
237L VAL* 4.4 11.4 - - + -
238L VAL 3.2 24.7 - - - +
239L PRO* 4.0 3.4 - - + -
240L TYR* 3.8 3.1 - - - +
277L LEU* 3.3 4.2 - - - +
278L GLU* 2.4 49.1 + - + +
279L MET 5.2 1.1 - - - +
280L ARG* 6.1 2.0 - - + -
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Residues in contact with ILE 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127L PHE* 4.9 0.4 - - + -
163L ILE* 3.0 48.0 - - + -
174L ALA* 1.3 77.6 - - - +
176L ARG* 1.3 65.1 + - - +
177L ALA 4.3 0.2 + - - -
236L VAL 4.1 0.5 - - - +
237L VAL* 3.2 3.2 - - - -
238L VAL* 2.9 42.9 + - + +
240L TYR* 4.0 24.7 - - + -
250L THR* 5.1 4.7 - - + -
252L ILE* 3.9 19.5 - - + -
254L TYR* 4.2 9.0 + - - +
275L ILE* 4.1 14.1 - - + -
276L THR 3.3 9.2 - - - +
277L LEU* 3.8 17.0 - - + -
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Residues in contact with ARG 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174L ALA 4.2 0.8 - - - -
175L ILE* 1.3 79.0 - - - +
177L ALA* 1.3 63.4 + - - +
178L MET* 3.9 15.5 - - + +
226L VAL* 3.9 16.2 - - - +
233L ARG* 3.4 25.7 - - - +
235L SER* 3.0 29.9 + - - +
236L VAL 3.5 6.3 - - - +
237L VAL* 3.8 28.1 - - + +
254L TYR* 4.9 0.2 - - - -
274L ILE 3.6 0.5 - - - +
275L ILE* 3.3 4.3 - - - -
276L THR* 2.8 42.7 + - - +
278L GLU* 2.4 46.0 + - - +
282L GLY* 5.7 0.6 - - - -
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Residues in contact with ALA 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L ARG* 1.3 74.3 - - - +
178L MET* 1.3 60.1 + - - +
179L PRO* 4.4 0.3 - - - +
215L ILE* 3.1 31.0 - - + +
235L SER* 3.5 4.5 + - - -
236L VAL 3.0 29.4 + - - +
254L TYR* 3.4 27.8 - - + +
273L ILE* 4.9 1.3 - - + -
274L ILE 3.5 4.9 - - - -
275L ILE* 4.3 12.8 - - + -
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Residues in contact with MET 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L PRO* 3.8 31.0 - - + -
176L ARG* 3.9 12.6 - - + -
177L ALA* 1.3 76.0 - - - +
179L PRO* 1.3 81.0 - - + +
180L VAL* 4.6 1.8 - - + -
215L ILE* 4.6 1.3 - - - +
233L ARG* 3.1 53.8 - - + +
234L GLN 3.7 8.7 - - - +
235L SER* 3.7 10.3 - - - +
272L LEU 3.7 0.5 - - - +
273L ILE* 3.5 6.2 - - - +
274L ILE* 2.8 42.6 + - + +
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Residues in contact with PRO 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L ALA 4.4 0.7 - - - +
178L MET* 1.3 94.1 - - + +
180L VAL* 1.3 68.4 + - - +
191L VAL* 3.3 37.8 + - + +
214L LEU* 3.4 33.0 - - + -
215L ILE* 3.7 18.6 - - + -
233L ARG* 5.4 2.9 - - - +
234L GLN* 3.8 15.9 - - + +
235L SER* 5.2 0.4 - - - -
271L ILE* 4.5 4.7 - - + -
272L LEU 3.7 5.2 - - - +
273L ILE* 4.8 4.0 - - + -
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Residues in contact with VAL 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L ILE* 5.7 0.9 - - + -
116L PRO* 3.8 29.2 - - + +
178L MET* 4.6 4.7 - - + -
179L PRO* 1.3 82.1 - - + +
181L TYR* 1.3 71.9 + - - +
187L VAL* 4.0 24.7 - - + +
189L ASP 5.7 1.1 - - - +
191L VAL* 3.5 5.8 - - - +
271L ILE* 3.2 2.8 - - - +
272L LEU* 2.6 48.9 + - + +
274L ILE* 3.4 32.3 - - + -
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Residues in contact with TYR 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180L VAL* 1.3 87.4 - - - +
182L LYS* 1.3 62.0 + - - +
183L LYS 3.4 2.8 + - - +
186L HIS* 3.7 28.7 - - + +
187L VAL* 3.8 12.2 - - - +
189L ASP* 3.5 21.9 + - + -
190L VAL 3.7 19.1 + - - -
191L VAL* 3.5 31.2 - - + +
192L LYS 4.6 2.3 + - - -
265L GLY 3.7 2.3 + - - -
266L MET* 3.4 24.6 + - + +
269L ARG* 2.9 74.9 + - + -
270L PRO 3.6 4.7 - - - +
271L ILE* 3.5 10.3 - - + -
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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