Contacts of the strand formed by residues 265 - 269 (chain B) 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 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PRO* 3.7 1.2 - - - +
96B THR* 2.8 34.2 + - - +
98B GLN 4.3 4.5 - - - -
253B MET 3.1 15.5 - - - -
255B GLY 3.6 5.6 - - - -
264B GLY* 1.3 73.9 - - - -
266B PHE* 1.3 69.3 + - - +
294B LEU* 4.1 0.2 - - - +
302B MET* 3.6 14.0 - - - +
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 4.8 0.2 - - + -
84B VAL* 3.9 21.3 - - + -
88B PHE* 3.8 21.8 - + - -
93B ILE* 4.1 16.8 - - + -
94B VAL 3.3 13.0 - - - +
95B PRO* 3.9 7.4 - - + -
96B THR* 3.3 5.8 + - - -
102B ALA* 3.6 8.6 - - - +
251B CYS* 4.7 0.7 - - - -
252B THR* 3.7 0.2 - - - -
253B MET* 2.9 63.2 + - + -
259B CYS* 4.3 12.6 - - - -
265B GLY* 1.3 79.5 - - - +
267B LEU* 1.3 61.2 + - - +
268B CYS* 3.4 32.5 - - - -
302B MET* 3.7 22.2 - - + -
306B LEU* 4.5 4.5 - - + -
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.3 2.9 - - - -
94B VAL* 2.7 48.0 + - + +
96B THR* 4.9 2.9 - - + -
102B ALA* 3.7 13.7 - - + +
105B LEU* 4.4 16.6 - - + -
106B LEU* 3.7 25.4 - - + +
109B LEU* 4.8 2.5 - - + -
251B CYS 3.5 14.8 - - - +
252B THR* 3.7 20.4 - - + -
266B PHE* 1.3 76.4 - - - +
268B CYS* 1.3 64.1 + - - +
269B MET* 3.5 31.5 - - + +
274B MET* 5.6 0.2 - - + -
278B ALA* 4.2 13.7 - - + -
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Residues in contact with CYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 3.7 19.3 - - - -
88B PHE* 4.6 0.2 - - - -
90B PHE* 3.4 29.4 - - + -
92B HIS 3.4 11.7 - - - +
93B ILE* 4.3 3.4 - - - -
212B PHE* 4.8 1.7 - - - -
250B GLY* 3.2 3.2 - - - -
251B CYS* 3.0 34.2 + - - +
266B PHE* 3.4 36.6 - - - -
267B LEU* 1.3 80.5 - - - +
269B MET* 1.3 70.2 + - - +
274B MET* 5.5 0.2 - - - +
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Residues in contact with MET 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 4.3 2.1 - - - +
91B LYS 3.7 1.8 + - - -
92B HIS* 3.0 31.5 + - - +
94B VAL* 4.9 4.5 - - - -
109B LEU* 5.0 0.2 - - + -
212B PHE* 4.7 0.4 - - + -
249B ASP 3.4 14.8 - - - +
250B GLY* 3.8 2.4 - - - -
267B LEU* 3.5 29.8 - - + -
268B CYS* 1.3 83.0 - - - +
270B ASN* 1.3 65.3 + - - +
271B ASP 3.7 20.2 - - - +
274B MET* 3.3 46.0 - - + +
275B PHE* 3.9 25.6 - - + +
278B ALA* 3.8 17.9 - - + -
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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
------------------------------------------------------------
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