Contacts of the helix formed by residues 263 - 279 (chain V) in PDB entry 2GLJ
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 263 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V ASN* 5.4 0.9 - - - -
108V SER* 3.6 16.6 + - - -
262V TYR* 1.3 84.5 - - - +
264V GLN* 1.3 65.2 + - - +
265V ASP* 2.6 11.7 + - - +
267V ARG* 3.0 40.7 - - - +
445V GLU* 3.3 6.9 + - - -
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Residues in contact with GLN 264 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V ASN* 5.1 3.0 + - - -
37V ASN* 4.9 8.9 - - - +
259V VAL* 2.7 35.4 - - - +
260V MET 3.9 0.3 - - - -
261V GLY* 3.0 31.3 + - - +
262V TYR 3.2 3.2 + - - +
263V GLY* 1.3 75.7 - - - +
265V ASP* 1.3 57.6 + - - +
266V ASP 2.8 10.7 + - - -
267V ARG* 4.9 0.2 - - - -
268V ILE* 3.2 42.6 + - - +
343V VAL* 3.8 0.2 - - - +
437V LEU* 3.6 10.1 - - + +
445V GLU* 2.8 30.3 + - + +
446V ILE 4.4 0.2 - - - -
447V SER* 2.8 31.2 + - - -
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Residues in contact with ASP 265 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105V HIS* 3.2 5.4 + - - -
107V ASP 4.3 0.9 - - - +
108V SER* 3.5 16.7 + - - +
109V PRO* 5.1 2.0 - - + -
263V GLY 2.6 11.2 + - - +
264V GLN* 1.3 68.8 - - - +
266V ASP* 1.3 58.3 + - - +
267V ARG* 2.7 14.4 + - - +
296V GLU* 3.0 13.6 - - - +
342V ASP* 3.2 0.2 - - - +
343V VAL* 3.4 14.3 - - + +
437V LEU* 3.7 1.5 - - - +
440V MSE 3.0 18.5 - - - +
441V HIS* 3.0 8.9 + - + -
445V GLU* 3.0 21.9 + - - +
6043V MN 2.7 19.9 + - - -
6044V MN 2.5 25.0 + - - -
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Residues in contact with ASP 266 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104V ALA* 3.2 4.6 - - - +
105V HIS* 2.4 69.0 + - + +
264V GLN 2.8 5.0 + - - -
265V ASP* 1.3 71.9 + - - +
267V ARG* 1.3 48.8 + - - +
268V ILE 2.8 6.1 - - - +
269V CYS* 2.7 10.0 + - - +
270V ALA* 2.6 34.0 + - - +
341V SER 2.7 25.6 - - - +
342V ASP* 2.9 18.3 - - - +
343V VAL* 3.3 15.4 - - - +
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Residues in contact with ARG 267 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V ASN* 4.9 3.1 + - - +
36V SER* 5.7 4.3 - - - +
37V ASN* 4.6 15.2 - - + +
40V THR* 3.6 12.0 + - - -
41V GLU* 3.3 42.4 + - - +
42V ARG* 4.9 0.2 - - - +
43V GLU* 4.3 5.9 - - - +
45V VAL* 4.1 23.7 - - + +
105V HIS 4.2 3.5 + - - -
106V ILE* 2.8 29.9 + - - +
107V ASP* 3.9 1.4 - - - +
108V SER* 3.7 29.5 + - - +
110V ARG* 6.0 1.2 - - - +
262V TYR* 4.0 5.3 + - - -
263V GLY* 3.0 35.5 + - - +
264V GLN* 4.9 0.4 - - - -
265V ASP 2.7 10.2 + - - +
266V ASP* 1.3 73.2 - - - +
268V ILE* 1.3 55.3 + - - +
270V ALA* 3.7 10.1 - - + +
271V TYR* 3.1 26.3 + - - +
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Residues in contact with ILE 268 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V ASN* 3.9 23.6 - - - +
264V GLN* 3.2 46.6 + - - +
266V ASP 2.8 0.4 - - - +
267V ARG* 1.3 78.0 - - - +
269V CYS* 1.3 67.7 + - - +
271V TYR* 3.4 2.4 + - - +
272V THR* 3.1 24.7 + - + +
343V VAL* 3.6 21.8 - - + -
435V VAL* 3.9 23.6 - - + -
437V LEU* 4.7 0.7 - - + -
447V SER* 3.8 10.3 - - - +
452V ILE* 3.7 35.2 - - + -
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Residues in contact with CYS 269 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104V ALA* 4.4 0.9 - - + -
266V ASP* 2.7 25.8 + - - +
268V ILE* 1.3 81.2 - - - +
270V ALA* 1.3 55.5 + - - +
271V TYR 3.0 2.0 - - - -
272V THR* 3.0 7.9 + - - -
273V SER* 2.6 42.1 + - - -
341V SER* 3.4 18.8 - - - +
342V ASP 3.9 3.4 - - - -
343V VAL* 4.0 7.6 - - - -
434V GLY* 3.4 32.5 - - - -
435V VAL* 3.8 11.9 - - - -
459V TYR* 3.8 6.6 - - - +
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Residues in contact with ALA 270 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45V VAL* 5.9 2.7 - - + -
49V ILE* 4.8 1.2 - - - +
104V ALA* 3.8 12.5 - - + +
105V HIS 4.4 1.1 - - - +
106V ILE* 4.0 17.3 - - + -
266V ASP 2.6 19.2 + - - +
267V ARG* 3.7 13.5 - - + +
269V CYS* 1.3 74.2 - - - +
271V TYR* 1.3 56.8 + - - +
273V SER* 2.8 16.1 + - - -
274V PHE* 3.3 15.1 + - - +
291V LEU* 3.9 26.6 - - + +
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Residues in contact with TYR 271 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29V ASP* 4.6 4.9 - - - -
32V LYS* 2.8 20.3 + - + +
33V ASN* 3.5 40.6 - - + +
36V SER* 3.7 28.0 - - - +
45V VAL* 6.5 0.4 - - + -
49V ILE* 5.4 9.9 - - + -
267V ARG 3.1 17.1 + - - +
268V ILE 3.6 5.2 - - - +
269V CYS 3.0 0.6 - - - -
270V ALA* 1.3 75.1 - - - +
272V THR* 1.3 65.9 + - + +
273V SER 3.1 1.3 - - - -
274V PHE* 2.7 46.5 + + + +
275V GLU* 2.7 46.5 + - + +
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Residues in contact with THR 272 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29V ASP* 5.2 3.8 - - - +
33V ASN* 6.1 0.2 - - + -
268V ILE* 3.1 15.9 + - + +
269V CYS* 3.0 12.5 + - - -
271V TYR* 1.3 82.0 - - + +
273V SER* 1.3 65.6 + - - +
275V GLU* 3.4 2.4 + - - +
276V ALA* 2.9 26.5 + - - +
435V VAL* 5.6 0.7 - - + -
452V ILE* 3.7 40.8 - - + +
455V THR* 3.6 5.7 - - + +
456V LYS* 3.9 26.8 - - + +
459V TYR* 3.2 14.4 - - - -
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Residues in contact with SER 273 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102V LEU* 3.8 23.5 - - - +
103V GLY 5.6 0.7 - - - -
104V ALA* 4.6 3.6 - - - +
269V CYS 2.6 25.3 + - - -
270V ALA* 2.8 21.8 + - - -
272V THR* 1.3 77.4 + - - +
274V PHE* 1.3 56.2 + - - +
276V ALA* 3.8 1.6 - - - +
277V MET* 3.0 30.3 + - - +
289V THR* 4.1 5.8 + - - +
291V LEU* 4.4 7.1 - - - +
341V SER* 5.2 2.7 - - - -
459V TYR* 3.3 23.6 - - - -
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Residues in contact with PHE 274 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49V ILE* 3.2 47.8 - - + -
52V ALA* 4.0 11.2 - - + -
53V GLU* 3.2 39.0 - - + -
87V MET* 3.3 20.9 - - + -
270V ALA 3.3 12.3 - - - +
271V TYR* 2.7 32.4 + + - +
273V SER* 1.3 79.2 + - - +
275V GLU* 1.3 58.2 + - + -
277V MET* 3.0 6.3 + - - +
278V LEU* 2.6 53.8 + - + +
289V THR* 5.1 2.0 - - - -
291V LEU* 5.1 3.4 - - + -
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Residues in contact with GLU 275 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V ASP* 3.5 6.9 - - - +
32V LYS* 3.0 35.9 + - - +
271V TYR* 2.7 55.2 + - + +
272V THR* 4.1 4.5 - - - +
274V PHE* 1.3 78.1 - - + +
276V ALA* 1.3 65.2 + - - +
278V LEU* 3.0 10.3 + - + +
279V GLU* 2.8 29.9 + - - +
456V LYS* 2.7 42.1 + - + +
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Residues in contact with ALA 276 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102V LEU* 4.8 2.2 - - + -
272V THR 2.9 19.0 + - - +
273V SER 3.8 3.1 - - - +
275V GLU* 1.3 79.8 - - - +
277V MET* 1.3 61.5 + - - +
279V GLU* 3.8 5.1 - - - +
280V MET* 3.4 23.7 + - - +
456V LYS* 4.0 14.3 - - + +
459V TYR* 3.7 28.0 - - + -
460V SER* 3.8 21.4 - - - +
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Residues in contact with MET 277 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57V TYR* 4.0 11.2 + - - +
87V MET* 3.2 43.3 - - + +
88V PHE 3.9 9.2 - - - +
89V LEU* 4.2 7.6 - - + +
102V LEU* 4.8 6.4 - - + +
273V SER 3.0 15.6 + - - +
274V PHE 3.5 3.4 - - - +
276V ALA* 1.3 76.0 - - - +
278V LEU* 1.3 64.1 + - - +
280V MET* 3.3 20.4 - - - +
287V CYS* 3.1 44.4 - - - +
288V ILE* 3.4 8.3 - - - -
289V THR* 3.0 28.7 - - - +
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Residues in contact with LEU 278 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52V ALA* 4.9 2.5 - - + -
53V GLU* 3.2 49.9 + - + +
55V SER* 4.9 9.6 - - - +
57V TYR* 4.6 6.9 + - - -
75V LYS* 5.3 6.4 + - - -
274V PHE* 2.6 42.1 + - + +
275V GLU* 3.0 9.6 + - + +
277V MET* 1.3 71.1 - - - +
279V GLU* 1.3 69.0 + - + +
280V MET 2.9 14.0 + - - +
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Residues in contact with GLU 279 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275V GLU* 2.8 23.5 + - - +
276V ALA* 3.8 6.5 - - - +
278V LEU* 1.3 80.6 - - + +
280V MET* 1.3 58.1 + - - +
281V LYS* 3.7 11.8 + - - +
456V LYS* 3.5 30.5 + - - -
460V SER* 5.6 6.0 - - - -
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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
------------------------------------------------------------
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