Contacts of the strand formed by residues 162 - 165 (chain C) in PDB entry 3VG9
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 THR 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C PRO* 5.8 1.9 - - - +
161C VAL* 1.3 75.1 + - - +
163C LEU* 1.3 61.2 + - - +
164C THR* 4.1 16.1 + - + -
207C ASN 3.4 1.6 - - - +
208C VAL* 3.2 5.6 - - - +
209C ALA* 2.9 49.1 + - - +
211C PRO* 5.3 5.2 - - - +
216C LYS* 5.2 2.0 + - - +
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C CYS* 4.5 1.8 - - + -
153C VAL* 3.8 15.7 - - + -
161C VAL* 4.0 6.3 + - + -
162C THR* 1.3 76.7 - - - +
164C THR* 1.3 71.0 + - - +
165C TRP* 3.6 21.3 - - + +
174C VAL* 5.9 0.7 - - - +
176C THR* 4.6 18.4 + - + +
188C LEU* 3.7 26.9 - - + -
190C SER* 3.5 37.0 - - - +
206C CYS* 4.1 8.7 - - - -
207C ASN 3.1 9.6 - - - +
208C VAL* 4.0 7.6 - - + -
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Residues in contact with THR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C THR* 4.1 15.0 - - + -
163C LEU* 1.3 82.3 - - - +
165C TRP* 1.3 72.4 + - - +
167C SER* 3.9 6.8 - - - -
168C GLY* 3.7 20.0 - - - +
206C CYS* 3.6 2.6 - - - -
207C ASN* 2.9 50.7 + - - +
216C LYS* 5.6 0.5 + - - -
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Residues in contact with TRP 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 4.8 0.7 - - + -
150C GLY* 3.6 26.7 - - - -
151C CYS* 3.7 13.7 - - + -
163C LEU* 3.6 9.7 - - + +
164C THR* 1.3 82.0 - - - +
166C ASN* 1.3 72.8 + - - +
167C SER 3.1 0.4 - - - -
168C GLY* 2.9 11.0 + - - +
170C LEU* 3.2 35.5 + - + +
174C VAL* 3.6 30.1 - - + +
190C SER* 2.9 41.9 + - - -
192C VAL* 3.6 31.6 - - + +
204C ILE* 3.9 12.6 - - + -
205C THR 3.2 14.1 - - - -
206C CYS* 3.9 12.3 - - + -
221C ILE* 4.0 20.4 - - + -
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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