Contacts of the helix formed by residues 263 - 279 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 5.4 0.7 - - - -
108A SER* 3.6 18.8 + - - -
262A TYR* 1.3 84.3 - - - +
264A GLN* 1.3 65.5 + - - +
265A ASP* 2.6 11.3 + - - +
267A ARG* 2.9 41.3 - - - +
445A GLU* 3.3 7.7 + - - -
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Residues in contact with GLN 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 5.1 3.7 + - - -
37A ASN* 4.8 8.9 - - - +
259A VAL* 2.6 36.0 - - - +
260A MET 3.9 0.2 - - - -
261A GLY* 2.9 31.3 + - - +
262A TYR 3.2 3.2 + - - +
263A GLY* 1.3 74.9 - - - +
265A ASP* 1.3 54.9 - - - +
266A ASP 2.9 10.4 + - - -
267A ARG* 4.9 0.4 - - - -
268A ILE* 3.2 43.6 + - - +
343A VAL* 3.8 0.3 - - - +
437A LEU* 3.6 9.5 - - + +
445A GLU* 2.8 29.6 + - + +
447A SER* 2.8 31.8 + - - -
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS* 3.1 5.2 + - - -
107A ASP 4.3 0.7 - - - +
108A SER* 3.5 16.2 + - - +
109A PRO* 5.1 2.2 - - + -
263A GLY 2.6 10.0 + - - +
264A GLN* 1.3 69.0 - - - +
266A ASP* 1.3 57.3 + - - +
267A ARG* 2.7 14.8 + - - +
296A GLU* 2.9 21.7 - - - +
342A ASP* 3.2 0.3 - - - +
343A VAL* 3.4 15.2 - - + +
437A LEU* 3.7 0.8 - - - +
440A MSE 3.1 11.8 - - - +
441A HIS* 3.0 21.0 + - + -
445A GLU* 3.0 21.9 + - - +
6001A MN 3.0 5.2 + - - -
6002A MN 2.5 25.0 + - - -
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Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 3.2 4.5 - - - +
105A HIS* 2.4 68.1 + - + +
264A GLN 2.9 5.6 + - - -
265A ASP* 1.3 71.7 + - - +
267A ARG* 1.3 49.0 + - - +
268A ILE 2.9 6.3 - - - +
269A CYS* 2.7 9.7 + - - +
270A ALA* 2.6 34.7 + - - +
341A SER 2.7 25.9 - - - +
342A ASP* 2.9 17.5 - - - +
343A VAL* 3.3 15.0 - - - +
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Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 4.9 2.6 + - - +
36A SER* 5.7 4.5 - - - +
37A ASN* 4.6 15.2 - - + +
40A THR* 3.6 11.5 + - - -
41A GLU* 3.3 44.0 + - - +
43A GLU* 4.3 6.3 - - - +
45A VAL* 4.1 24.6 - - + +
105A HIS 4.2 3.7 + - - -
106A ILE* 2.8 30.5 + - - +
107A ASP* 4.1 0.8 - - - +
108A SER* 3.6 29.2 + - - +
110A ARG* 6.0 0.8 - - - +
262A TYR* 4.0 5.1 + - - -
263A GLY* 2.9 34.2 - - - +
264A GLN* 4.9 0.4 - - - -
265A ASP 2.7 11.0 + - - +
266A ASP* 1.3 72.9 - - - +
268A ILE* 1.3 60.5 + - - +
270A ALA* 3.7 9.7 - - + +
271A TYR* 3.1 22.2 + - - +
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 3.9 23.6 - - - +
264A GLN* 3.2 44.9 + - - +
266A ASP 2.9 0.2 - - - -
267A ARG* 1.3 78.4 - - - +
269A CYS* 1.3 68.5 + - - +
271A TYR* 3.3 2.4 + - - +
272A THR* 3.1 24.3 + - - +
343A VAL* 3.6 22.0 - - + -
435A VAL* 3.9 23.6 - - + -
437A LEU* 4.7 0.7 - - + -
447A SER* 3.8 10.3 - - - +
452A ILE* 3.6 36.6 - - + -
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Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 4.5 0.9 - - + -
266A ASP* 2.7 16.4 + - - +
268A ILE* 1.3 85.7 - - - +
270A ALA* 1.3 53.9 + - - +
271A TYR 3.0 2.0 - - - -
272A THR* 3.0 7.8 + - - -
273A SER* 2.7 42.5 + - - -
341A SER* 3.4 18.8 - - - +
342A ASP 4.0 8.3 - - - -
343A VAL* 4.1 7.0 - - - -
434A GLY* 3.4 33.2 - - - -
435A VAL* 3.7 12.6 - - - -
455A THR* 5.3 0.2 - - - -
459A TYR* 3.7 6.4 - - - +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 5.9 2.5 - - + -
49A ILE* 4.9 2.4 - - - +
104A ALA* 3.8 12.7 - - + +
105A HIS 4.3 1.8 - - - +
106A ILE* 4.0 17.9 - - + -
266A ASP 2.6 19.2 + - - +
267A ARG* 3.7 12.3 - - + +
269A CYS* 1.3 73.1 - - - +
271A TYR* 1.3 57.3 + - - +
273A SER* 2.7 17.5 + - - -
274A PHE* 3.2 14.6 + - - +
291A LEU* 3.9 26.9 - - + +
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 4.6 5.6 - - - -
32A LYS* 2.8 20.8 + - + +
33A ASN* 3.5 38.6 - - + +
36A SER* 3.7 27.6 - - - +
45A VAL* 6.5 0.4 - - + -
49A ILE* 5.4 9.9 - - + -
267A ARG 3.1 16.1 + - - +
268A ILE 3.6 5.2 - - - +
269A CYS 3.0 0.8 - - - -
270A ALA* 1.3 76.2 - - - +
272A THR* 1.3 69.0 + - + +
273A SER 3.1 1.3 - - - -
274A PHE* 2.7 43.1 + + + +
275A GLU* 2.6 48.6 + - + +
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 5.2 3.6 - - - +
268A ILE* 3.1 15.0 + - + +
269A CYS* 3.0 12.7 + - - -
271A TYR* 1.3 83.0 - - + +
273A SER* 1.3 68.3 + - - +
275A GLU* 3.4 2.2 + - - +
276A ALA* 2.9 27.5 + - - +
435A VAL* 5.6 0.7 - - + -
452A ILE* 3.7 41.1 - - + +
455A THR* 3.6 6.2 - - + +
456A LYS* 3.9 27.4 - - + +
459A TYR* 3.2 13.5 - - - -
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 3.8 24.6 - - - +
103A GLY 5.6 0.7 - - - -
104A ALA* 4.6 3.3 - - - +
269A CYS 2.7 23.7 + - - -
270A ALA* 2.7 22.5 + - - -
272A THR* 1.3 78.8 + - - +
274A PHE* 1.3 56.7 + - - +
276A ALA* 3.8 0.9 - - - +
277A MET* 3.0 30.0 + - - +
289A THR* 4.1 5.9 + - - +
291A LEU* 4.4 7.1 - - - +
341A SER* 5.2 3.4 - - - -
459A TYR* 3.3 21.8 - - - -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.2 51.1 - - + -
52A ALA* 3.9 11.9 - - + -
53A GLU* 3.2 38.8 - - + -
87A MET* 3.3 19.5 - - + -
270A ALA 3.3 12.8 - - - +
271A TYR* 2.7 31.2 + + - +
273A SER* 1.3 78.3 + - - +
275A GLU* 1.3 61.9 + - + +
277A MET* 2.9 6.7 + - - +
278A LEU* 2.6 52.3 + - + +
289A THR* 5.1 2.2 - - - -
291A LEU* 5.1 3.1 - - + -
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 3.5 6.9 - - - +
32A LYS* 3.0 33.2 + - - +
271A TYR* 2.6 53.6 + - + +
272A THR* 4.0 4.3 - - - +
274A PHE* 1.3 82.3 - - + +
276A ALA* 1.3 64.4 + - - +
278A LEU* 4.0 10.3 - - + -
279A GLU* 2.8 31.6 + - - +
456A LYS* 2.7 42.2 + - + +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 4.8 2.2 - - + -
272A THR 2.9 18.4 + - - +
273A SER 3.8 3.1 - - - +
275A GLU* 1.3 81.2 - - - +
277A MET* 1.3 60.6 + - - +
279A GLU* 3.6 5.4 + - - +
280A MET* 3.4 23.3 + - - +
456A LYS* 4.0 14.9 - - + +
459A TYR* 3.7 27.8 - - + -
460A SER* 3.8 20.9 - - - +
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Residues in contact with MET 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 4.0 11.2 + - - +
87A MET* 3.2 42.2 - - + +
88A PHE 3.9 9.4 - - - +
89A LEU* 4.2 7.2 - - + +
102A LEU* 4.8 6.4 - - + +
273A SER 3.0 14.8 + - - +
274A PHE 2.9 4.3 + - - +
276A ALA* 1.3 76.5 - - - +
278A LEU* 1.3 65.6 + - - +
280A MET* 3.3 19.7 - - - +
287A CYS* 3.1 44.9 - - - +
288A ILE* 3.3 9.0 - - - -
289A THR* 3.0 28.9 - - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 4.9 1.8 - - + -
53A GLU* 3.2 49.0 - - + +
55A SER* 4.9 9.9 - - - +
57A TYR* 4.5 7.6 + - - -
75A LYS* 5.3 6.4 + - - -
274A PHE* 2.6 42.0 + - + +
275A GLU* 3.5 10.1 - - + +
277A MET* 1.3 75.8 - - - +
279A GLU* 1.3 68.3 + - + +
280A MET 2.9 9.0 + - - +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLU* 2.8 24.3 + - - +
276A ALA* 3.9 6.2 - - - +
278A LEU* 1.3 80.2 - - + +
280A MET* 1.3 57.9 + - - +
281A LYS* 3.6 12.2 + - - +
456A LYS* 3.6 31.8 + - - -
460A SER* 5.6 6.1 - - - -
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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
------------------------------------------------------------
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