Contacts of the strand formed by residues 194 - 200 (chain C) in PDB entry 2VIG
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 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C TYR* 3.2 29.8 - - + +
139C TRP* 3.6 18.4 - - + -
143C PHE* 3.4 14.2 - - + -
150C GLY* 3.3 4.0 - - - -
151C CYS* 3.0 27.4 + - - -
192C ALA* 3.5 2.3 - - - +
193C SER* 1.3 81.8 - - - +
195C ALA* 1.3 60.3 + - - +
215C VAL 3.3 8.1 - - - -
217C MET* 3.8 6.1 - - - +
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Residues in contact with ALA 195 (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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123C TYR* 4.5 3.4 - - - -
151C CYS* 3.4 26.9 - - - +
153C ALA* 5.0 1.1 - - + -
194C ALA* 1.3 75.7 - - - +
196C VAL* 1.3 63.5 + - - +
197C VAL* 3.6 20.9 + - + +
213C PHE 3.2 3.5 - - - +
214C LEU* 3.7 2.1 - - - -
215C VAL* 2.9 35.9 + - + +
217C MET* 3.9 9.4 - - + -
241C LEU* 4.3 7.4 - - + -
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Residues in contact with VAL 196 (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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122C LEU 4.3 7.0 - - - +
123C TYR* 3.8 34.3 - - + +
126C PRO* 4.3 10.5 - - + -
127C ILE* 4.3 4.0 - - + -
151C CYS 3.1 7.6 + - - +
152C PHE* 3.7 3.6 - - + -
153C ALA* 2.9 27.2 + - - +
195C ALA* 1.3 72.2 - - - +
197C VAL* 1.3 59.3 + - - +
198C PHE* 3.9 27.4 - - + -
212C ALA* 4.4 5.4 - - + -
213C PHE 3.4 7.6 - - - +
214C LEU* 4.0 17.9 - - + -
254C LEU* 4.2 20.2 - - + -
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Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ALA* 3.7 12.3 - - + +
168C THR* 5.2 3.6 - - + -
179C LEU* 4.5 12.1 - - + -
183C LYS* 4.2 11.2 - - + -
195C ALA* 3.6 21.1 - - + +
196C VAL* 1.3 78.0 - - - +
198C PHE* 1.3 70.6 + - - +
199C ALA* 5.1 1.1 - - + +
212C ALA* 3.4 2.3 - - - -
213C PHE* 2.8 42.7 + - + +
215C VAL* 3.5 30.5 - - + -
241C LEU* 5.0 0.2 - - + -
243C PHE* 4.0 30.1 - - + -
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Residues in contact with PHE 198 (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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126C PRO* 5.8 0.2 - - + -
152C PHE* 3.3 40.2 - + - -
153C ALA 3.1 19.0 + - - +
154C LEU* 3.7 28.5 - - + -
166C ALA* 4.6 2.0 - - - +
168C THR* 4.6 0.5 - - - -
183C LYS* 2.6 34.0 + - - +
196C VAL* 3.9 20.9 - - + -
197C VAL* 1.3 73.4 - - - +
199C ALA* 1.3 58.2 + - - +
210C ILE* 4.0 9.2 - - + -
211C SER 3.3 8.3 - - - +
212C ALA* 3.7 22.4 - - + -
260C GLY 3.4 29.6 - - - -
263C ILE* 3.9 8.1 - - + -
264C ALA* 3.6 19.1 - - + -
267C THR* 5.5 0.2 - - - -
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Residues in contact with ALA 199 (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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166C ALA* 5.2 1.1 - - - -
168C THR* 3.5 20.4 - - + +
169C THR 4.0 3.1 - - - +
170C ALA* 3.7 17.5 - - + +
179C LEU* 4.7 6.5 - - + -
197C VAL* 3.9 1.8 + - + +
198C PHE* 1.3 75.0 - - - +
200C SER* 1.3 62.9 + - - +
201C THR* 3.4 1.0 + - - -
210C ILE* 3.4 4.6 - - - +
211C SER* 2.9 31.8 + - - +
213C PHE* 3.7 23.6 - - + -
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Residues in contact with SER 200 (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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166C ALA* 3.6 22.2 + - - +
168C THR 2.7 17.5 + - - -
169C THR* 3.4 15.0 - - - +
170C ALA 3.0 21.3 + - - +
199C ALA* 1.3 69.2 - - - +
201C THR* 1.3 61.3 + - - +
202C ASP 3.7 16.3 + - - -
209C SER* 3.4 13.4 + - - -
210C ILE* 4.4 8.6 - - - +
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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
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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