Contacts of the strand formed by residues 191 - 196 (chain A) in PDB entry 3V4V
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 SER 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A PHE* 3.9 12.5 - - - -
182A ALA* 2.9 33.1 + - - -
185A SER* 3.3 19.1 - - - -
190A GLY* 1.3 76.2 - - - -
192A LEU* 1.3 86.5 + - - +
193A PHE* 4.9 1.7 - - - -
204A ALA* 4.3 0.9 - - - +
205A PHE* 2.9 29.6 + - - -
218A LEU* 2.9 14.5 + - - +
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Residues in contact with LEU 192 (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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179A VAL* 4.6 1.1 - - + -
180A MET 3.4 7.2 - - - +
191A SER* 1.3 91.1 + - - +
193A PHE* 1.3 66.1 + - - +
204A ALA* 3.2 27.9 - - - +
205A PHE* 3.3 7.6 + - + +
218A LEU* 4.9 3.1 - - + -
219A GLY* 3.5 25.1 - - - +
222A VAL* 3.5 18.6 - - + -
235A VAL* 3.7 22.0 - - + -
236A VAL 3.7 24.0 - - - +
237A GLY* 4.0 2.9 - - - -
251A PHE* 3.9 26.2 - - + -
258A LEU* 4.1 15.8 - - + +
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Residues in contact with PHE 193 (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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149A PRO* 3.7 31.2 - - + -
150A CYS* 3.5 31.9 - - - -
162A PHE* 4.1 32.3 - + - -
167A ALA* 4.6 4.0 - - + -
178A ILE 3.3 3.3 - - - +
179A VAL* 3.4 3.6 - - - +
180A MET* 2.9 54.7 + - + +
182A ALA* 3.6 22.9 - - + -
185A SER* 4.5 3.4 - - - -
191A SER* 4.9 0.7 - - - -
192A LEU* 1.3 76.8 - - - +
194A VAL* 1.3 64.0 + - - +
195A TYR 3.9 0.9 - - - -
202A TYR* 5.0 9.4 - - + -
203A LYS 3.4 4.5 - - - -
204A ALA* 3.6 24.9 - - + -
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Residues in contact with VAL 194 (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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177A LEU* 3.8 21.2 - - + +
178A ILE 3.2 4.0 - - - -
179A VAL* 3.8 23.8 - - + -
192A LEU* 5.6 0.2 - - + -
193A PHE* 1.3 78.3 - - - +
195A TYR* 1.3 63.5 + - - +
196A ASN* 3.1 6.4 + - - +
201A LYS 3.6 1.4 - - - +
202A TYR* 4.7 0.7 - - - -
203A LYS* 2.8 47.1 + - + +
235A VAL* 3.8 23.6 - - + -
253A ILE* 4.4 6.3 - - + -
258A LEU* 3.6 28.0 - - + -
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Residues in contact with TYR 195 (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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145A LYS* 2.8 32.2 + - + +
147A ILE* 4.5 14.4 - - + -
177A LEU* 3.5 1.5 - - - -
178A ILE* 3.0 56.2 + - + -
180A MET* 4.1 6.1 - - + +
193A PHE 3.9 1.4 - - - -
194A VAL* 1.3 69.2 - - - +
196A ASN* 1.3 70.6 + - - +
197A ILE* 3.2 22.2 + - + -
200A ASN* 3.0 41.9 - - - +
201A LYS 3.8 5.2 - - - -
202A TYR* 3.4 47.7 - + + -
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Residues in contact with ASN 196 (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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176A ASP* 3.6 21.9 + - - +
177A LEU* 4.7 13.0 - - + +
194A VAL 3.1 4.9 + - - +
195A TYR* 1.3 72.2 - - - +
197A ILE* 1.3 64.3 + - - +
198A THR* 3.2 18.1 + - - -
199A THR* 2.7 49.6 + - - +
200A ASN* 3.6 4.5 + - - -
201A LYS* 3.0 16.5 + - + +
203A LYS* 4.5 20.2 - - - +
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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