Contacts of the strand formed by residues 174 - 181 (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 ALA 174 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K GLY 3.6 4.9 + - - +
173K THR* 1.3 75.2 - - - +
175K ILE* 1.3 63.7 + - - +
237K VAL* 3.3 27.1 - - + -
238K VAL 3.4 11.2 - - - +
239K PRO* 4.3 2.7 - - + -
240K TYR* 3.9 2.2 - - - +
276K THR 4.1 0.4 - - - -
277K LEU* 3.4 6.8 - - - +
278K GLU* 2.5 43.7 + - + +
279K MET 4.9 3.4 - - - +
280K ARG* 5.9 0.7 - - - -
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Residues in contact with ILE 175 (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* 5.1 1.1 - - + -
163K ILE* 4.3 21.8 - - + -
174K ALA* 1.3 78.3 - - - +
176K ARG* 1.3 64.7 + - - +
236K VAL 3.6 1.7 - - - +
237K VAL* 3.2 3.2 - - - -
238K VAL* 2.6 42.9 + - + +
239K PRO 5.7 0.2 - - - +
240K TYR* 4.3 26.2 - - + -
250K THR* 5.4 3.1 - - + -
252K ILE* 3.4 28.3 - - + -
254K TYR* 4.0 15.3 + - - +
275K ILE* 3.7 27.4 - - + -
276K THR 3.2 6.1 - - - +
277K LEU* 4.3 14.6 - - + +
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Residues in contact with ARG 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175K ILE* 1.3 77.7 - - - +
177K ALA* 1.3 66.2 + - - +
178K MET* 4.3 19.2 - - + +
226K VAL* 3.5 24.5 - - - +
235K SER* 3.2 37.3 + - - -
236K VAL 3.5 6.3 - - - +
237K VAL* 4.1 20.2 - - + +
274K ILE 3.3 2.2 - - - +
275K ILE* 3.3 6.1 - - - -
276K THR* 2.8 38.3 + - - +
278K GLU* 2.9 39.7 + - - +
283K GLN* 4.5 15.0 + - - +
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Residues in contact with ALA 177 (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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176K ARG* 1.3 77.9 - - - +
178K MET* 1.3 56.7 + - - +
215K ILE* 2.7 39.2 - - + +
235K SER* 3.5 1.2 - - - -
236K VAL* 3.1 25.0 + - + +
254K TYR* 3.4 31.6 - - + +
273K ILE* 5.0 3.1 - - + -
274K ILE 3.5 5.4 - - - -
275K ILE* 4.1 10.3 - - + -
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Residues in contact with MET 178 (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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113K GLU 6.0 1.3 - - - +
116K PRO* 4.1 25.6 - - + -
176K ARG* 4.1 20.3 - - + +
177K ALA* 1.3 73.6 - - - +
179K PRO* 1.3 75.1 - - - +
215K ILE* 4.8 1.3 - - - -
233K ARG* 4.0 39.3 - - + -
234K GLN 3.5 6.7 - - - +
235K SER* 3.4 24.5 - - - +
273K ILE* 4.0 1.5 - - - -
274K ILE* 3.0 39.0 + - + +
283K GLN* 6.2 1.1 - - - +
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Residues in contact with PRO 179 (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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177K ALA 4.4 2.5 - - - +
178K MET* 1.3 98.6 - - - +
180K VAL* 1.3 65.5 + - - +
191K VAL* 3.5 37.9 - - + +
214K LEU* 4.2 15.5 - - + -
215K ILE* 4.4 13.5 - - + +
233K ARG* 4.2 4.7 + - - -
234K GLN* 3.6 14.9 - - + +
271K ILE* 4.0 14.6 - - + -
272K LEU 3.7 7.0 - - - +
273K ILE* 4.1 13.2 - - + -
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Residues in contact with VAL 180 (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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116K PRO* 3.4 34.1 - - + +
118K ASN* 5.9 0.9 - - + -
179K PRO* 1.3 81.9 - - - +
181K TYR* 1.3 66.2 + - - +
187K VAL* 4.0 10.3 - - + +
191K VAL* 3.3 13.6 - - - +
233K ARG* 3.4 22.4 - - - +
271K ILE* 3.2 2.4 - - - +
272K LEU* 3.0 48.3 + - + +
274K ILE* 4.2 15.9 - - + -
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Residues in contact with TYR 181 (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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180K VAL* 1.3 81.9 - - - +
182K LYS* 1.3 65.2 + - - +
183K LYS 4.4 0.2 - - - -
186K HIS* 3.5 29.2 - - + -
187K VAL* 3.8 14.5 - - - +
189K ASP* 2.7 51.4 - - + -
190K VAL 4.2 2.0 + - - -
191K VAL* 3.7 20.1 - - + -
192K LYS 4.8 1.7 + - - -
265K GLY 3.2 12.0 + - - -
266K MET* 3.5 14.6 - - + +
269K ARG* 3.0 49.9 + - + -
270K PRO 4.1 2.7 - - - -
271K ILE* 3.8 23.8 - - + -
272K LEU* 4.1 2.8 - - - +
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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