Contacts of the strand formed by residues 265 - 269 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PRO* 3.7 2.4 - - - +
96D THR* 2.9 32.0 + - - +
98D GLN 4.3 4.3 - - - -
253D MET 3.1 15.5 - - - -
255D GLY 3.7 5.4 - - - -
264D GLY* 1.3 75.4 - - - -
266D PHE* 1.3 74.6 + - - +
302D MET* 3.8 9.8 - - - +
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Residues in contact with PHE 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 4.8 1.3 - - + -
84D VAL* 3.9 20.0 - - + -
88D PHE* 3.8 23.3 - + - -
93D ILE* 4.0 18.4 - - + -
94D VAL 3.4 13.0 - - - +
95D PRO* 3.8 7.2 - - + -
96D THR* 3.4 6.3 + - - -
102D ALA* 3.6 6.5 - - - +
251D CYS* 4.7 1.3 - - - -
252D THR* 3.5 2.1 - - - -
253D MET* 2.7 70.8 + - + +
259D CYS* 4.3 7.4 - - - -
265D GLY* 1.3 80.3 - - - +
267D LEU* 1.3 59.3 - - - +
268D CYS* 3.7 30.7 - - - -
302D MET* 4.0 26.7 - - + -
306D LEU* 4.6 2.5 - - + -
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Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D HIS 4.6 0.2 - - - -
93D ILE* 3.3 3.6 - - - +
94D VAL* 2.7 50.7 + - + +
96D THR* 5.1 2.2 - - + -
102D ALA* 3.9 17.7 - - + +
105D LEU* 4.3 20.0 - - + -
106D LEU* 3.8 35.0 - - + +
109D LEU* 4.9 2.5 - - + -
212D PHE* 6.1 0.2 - - + -
251D CYS 3.4 14.1 - - - +
252D THR* 3.9 5.8 - - + -
266D PHE* 1.3 73.2 - - - +
268D CYS* 1.3 65.8 + - - +
269D MET* 3.6 28.1 - - + +
274D MET* 5.4 0.2 - - + -
278D ALA* 4.2 14.4 - - + -
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Residues in contact with CYS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D VAL* 3.6 31.4 - - - -
90D PHE* 3.5 30.1 - - + -
92D HIS 3.4 12.3 - - - +
93D ILE* 4.2 4.0 - - - -
212D PHE* 4.8 1.9 - - - -
250D GLY* 3.1 4.0 - - - -
251D CYS* 2.8 35.4 + - - +
266D PHE* 3.7 21.5 - - - -
267D LEU* 1.3 80.0 - - - +
269D MET* 1.3 65.5 + - - +
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Residues in contact with MET 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D PHE* 4.3 1.8 - - - +
91D LYS 3.7 1.3 + - - -
92D HIS* 2.9 36.2 + - - +
94D VAL* 4.6 5.6 - - - -
109D LEU* 4.8 0.2 - - + -
212D PHE* 4.9 0.2 - - + -
249D ASP 3.5 12.8 - - - +
250D GLY* 3.9 2.0 - - - -
267D LEU* 3.6 30.5 - - + -
268D CYS* 1.3 78.4 - - - +
270D ASN* 1.3 62.4 + - - +
271D ASP* 3.7 21.8 - - + +
274D MET* 3.4 42.2 - - + +
275D PHE* 3.8 28.5 - - + +
278D ALA* 3.8 15.0 - - + -
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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