Contacts of the strand formed by residues 169 - 173 (chain A) in PDB entry 2V3V
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 CYS 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA* 3.8 6.4 - - - +
168A THR* 1.3 75.9 - - - +
170A PHE* 1.3 77.1 + - - +
171A PHE* 4.2 2.2 - - - -
199A LYS* 3.2 14.1 - - + +
201A ILE* 4.7 6.1 - - - -
295A ALA* 3.7 33.2 - - - -
296A PHE* 3.9 9.4 - - - -
299A SER* 3.2 21.1 - - - +
301A ALA 3.2 3.3 + - - +
302A THR* 3.5 17.9 - - - +
303A MET 3.1 24.3 + - - -
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 3.3 47.3 - - + -
167A ALA* 3.5 20.9 - - + -
169A CYS* 1.3 80.8 - - - +
171A PHE* 1.3 58.7 + - - +
172A ILE* 3.8 19.3 - - + -
188A ILE* 4.1 22.2 - - + -
191A ARG* 3.7 20.6 - - + -
198A VAL* 3.8 20.9 - - + -
199A LYS 2.9 7.4 + - - +
200A ILE* 3.6 14.4 - - + -
201A ILE* 3.0 27.4 + - - +
303A MET* 3.3 12.6 - - + -
305A LEU* 3.6 21.1 - - + -
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A CYS* 4.2 2.6 - - - -
170A PHE* 1.3 71.7 - - - +
172A ILE* 1.3 59.4 + - - +
173A ILE* 3.8 37.2 + - + +
201A ILE* 3.8 29.4 - - + -
203A ALA* 4.4 12.1 - - + -
228A PHE* 4.8 5.8 - + - -
229A MET* 4.2 17.3 - - + -
232A MET* 3.8 31.0 - - + -
292A ALA* 4.8 0.9 - - + -
296A PHE* 3.9 23.8 - + + -
302A THR* 4.8 1.5 - - + +
303A MET 2.9 9.4 + - - +
304A SER* 3.3 27.6 - - - +
305A LEU 3.1 24.1 + - - +
323A ILE* 4.9 3.1 - - + -
326A LEU* 4.2 9.4 - - + -
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Residues in contact with ILE 172 (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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170A PHE* 3.9 19.1 - - + -
171A PHE* 1.3 73.6 - - - +
173A ILE* 1.3 61.5 + - - +
175A SER* 3.9 21.3 - - - +
177A THR* 3.5 22.9 - - - +
185A PHE* 5.8 0.9 - - + -
188A ILE* 4.2 25.1 - - + -
200A ILE* 3.9 24.7 - - + -
201A ILE 2.8 13.7 + - - +
202A VAL* 3.2 13.7 - - + +
203A ALA* 2.8 25.2 + - - -
210A THR* 4.6 9.0 - - + -
213A ILE* 5.7 1.6 - - + -
305A LEU* 3.3 20.9 - - + +
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.8 32.1 - - + +
172A ILE* 1.3 74.8 - - - +
174A GLY* 1.3 67.9 + - - +
175A SER 3.3 1.1 - - - -
203A ALA* 3.3 14.8 - - + +
220A PHE* 3.9 19.1 - - + -
225A ASP* 3.9 15.9 - - + -
228A PHE* 5.7 0.4 - - + -
229A MET* 4.0 17.3 - - + -
304A SER* 5.8 0.2 - - - -
305A LEU 3.1 7.8 + - - +
306A TRP* 3.0 43.3 - - + +
310A ILE* 3.7 13.0 - - + +
323A ILE* 4.2 12.1 - - + -
812A MGD 3.5 12.6 - - - +
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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
------------------------------------------------------------
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