Contacts of the strand formed by residues 211 - 214 (chain C) in PDB entry 1C7G
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 ILE 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C ILE* 3.6 18.6 - - + +
180C LEU* 4.9 7.6 - - + -
197C MET 5.6 0.2 - - - +
200C VAL* 3.9 10.3 - - + +
201C HIS* 3.6 28.5 - - + +
204C ALA* 3.5 31.0 - - + -
209C ILE 4.4 1.3 - - - +
210C LYS* 1.3 79.8 - - - +
212C PHE* 1.3 62.8 + - - +
213C TYR* 3.5 31.2 - - + -
247C TYR 3.9 14.4 - - - +
248C ALA* 3.6 1.1 - - - -
249C ASP* 2.7 47.5 + - - +
250C GLY 3.6 0.2 + - - -
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Residues in contact with PHE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 3.8 39.3 - - + -
110C ALA* 4.4 9.6 - - + -
177C TYR* 3.6 31.2 - + + -
178C ILE 3.0 17.0 + - - +
179C CYS* 3.4 8.0 - - - -
180C LEU 3.4 10.4 + - - -
210C LYS* 3.7 30.3 - - + -
211C ILE* 1.3 72.4 - - - +
213C TYR* 1.3 66.5 + - - +
249C ASP* 3.9 9.2 - - + -
250C GLY* 3.5 36.1 - - - +
251C CYS 4.0 2.5 - - - +
268C CYS 4.6 2.9 - - - -
269C MET* 4.7 0.9 - - + -
274C MET* 3.7 32.3 - - + -
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Residues in contact with TYR 213 (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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106C LEU* 6.0 0.2 - - - +
179C CYS* 5.3 0.7 - - - -
180C LEU* 3.1 27.5 - - + +
182C VAL* 4.5 13.2 - - + -
197C MET* 3.5 34.8 + - + +
211C ILE* 3.5 24.2 - - + -
212C PHE* 1.3 77.9 - - - +
214C ASP* 1.3 60.4 - - - +
215C ALA* 3.3 6.0 + - + +
244C MET* 3.1 35.4 + - + -
245C PHE* 3.9 19.7 - + + -
247C TYR* 3.5 16.4 + - - +
248C ALA* 3.5 17.5 - - + -
250C GLY 3.2 6.7 + - - -
251C CYS* 3.2 13.4 - - + +
252C THR* 3.0 27.7 + - - +
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Residues in contact with ASP 214 (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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103C GLU* 4.4 2.0 - - - -
123C PHE* 4.6 0.7 - - - +
126C THR* 3.6 14.0 + - - +
179C CYS* 4.3 15.2 - - - -
180C LEU 2.9 7.4 + - - +
181C ALA* 3.5 17.5 - - + +
182C VAL 3.2 21.8 + - - +
212C PHE 4.0 0.2 + - - -
213C TYR* 1.3 72.5 - - - +
215C ALA* 1.3 54.6 + - - +
216C THR* 3.1 29.5 + - - +
252C THR* 3.6 14.4 + - - +
1000C PLP 2.7 36.3 + - - +
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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