Contacts of the strand formed by residues 250 - 254 (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 GLY 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.4 16.0 - - - -
212C PHE* 3.5 14.8 - - - -
213C TYR 3.2 15.9 + - - -
248C ALA* 3.4 10.8 - - - +
249C ASP* 1.3 82.3 - - - +
251C CYS* 1.3 65.1 - - - +
268C CYS 3.0 15.7 - - - -
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Residues in contact with CYS 251 (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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88C PHE* 4.2 12.1 - - - -
90C PHE* 3.7 19.5 - - + -
106C LEU* 5.5 0.4 - - - -
212C PHE* 4.0 5.8 - - - -
213C TYR* 3.2 25.6 - - + +
215C ALA* 4.6 2.5 - - + -
245C PHE* 4.1 15.3 - - + -
250C GLY* 1.3 75.5 - - - +
252C THR* 1.3 72.7 + - - +
253C MET* 4.7 3.4 - - - -
266C PHE* 4.7 0.2 - - - -
267C LEU* 3.5 7.1 - - - +
268C CYS* 2.9 47.6 + - - +
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Residues in contact with THR 252 (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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99C GLY* 4.6 2.2 - - - -
102C ALA* 3.8 32.5 - - - +
103C GLU* 3.9 24.0 + - + +
106C LEU* 3.9 23.6 - - + -
213C TYR 3.0 10.6 + - - +
214C ASP* 3.6 16.0 + - - +
215C ALA* 3.2 22.2 + - - +
216C THR* 4.3 1.3 + - - -
251C CYS* 1.3 77.7 - - - +
253C MET* 1.3 61.7 + - - +
266C PHE 3.6 4.9 - - - -
267C LEU* 4.0 5.2 - - + -
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Residues in contact with MET 253 (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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88C PHE* 4.1 17.3 - - + -
99C GLY* 3.7 10.7 - - - -
102C ALA* 4.7 0.4 - - - +
215C ALA* 3.2 36.6 - - - +
216C THR* 3.9 11.2 - - - +
218C CYS* 4.2 7.2 - - - -
251C CYS* 4.7 4.3 - - - -
252C THR* 1.3 75.3 - - - +
254C SER* 1.3 70.7 + - - +
255C GLY 4.3 0.2 - - - +
258C ASP* 4.5 8.1 - - + -
259C CYS* 3.4 26.5 - - - -
265C GLY* 3.1 4.7 - - - -
266C PHE* 2.8 74.6 + - + +
306C LEU* 4.9 1.8 - - + -
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Residues in contact with SER 254 (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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99C GLY* 4.0 2.0 - - - -
216C THR* 3.4 33.7 - - - +
253C MET* 1.3 80.5 - - - +
255C GLY* 1.3 62.1 + - - +
256C LYS* 3.1 10.7 + - - +
257C LYS* 3.1 30.2 + - - +
258C ASP 4.2 1.6 + - - -
264C GLY 4.1 1.6 - - - -
1000C PLP 2.5 35.1 + - - -
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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