Contacts of the helix formed by residues 263 - 279 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J ASN* 5.4 0.9 - - - -
108J SER* 3.6 18.8 + - - -
262J TYR* 1.3 88.2 - - - +
264J GLN* 1.3 65.9 + - - +
265J ASP* 2.6 11.7 + - - +
267J ARG* 3.0 35.6 - - - +
445J GLU* 3.3 7.3 + - - -
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Residues in contact with GLN 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ASN* 5.1 4.0 + - - +
37J ASN* 4.8 9.8 + - - +
259J VAL* 2.7 32.9 - - - +
260J MET 3.9 0.3 - - - -
261J GLY* 2.9 34.4 + - - +
262J TYR 3.2 3.7 + - - +
263J GLY* 1.3 75.3 - - - +
265J ASP* 1.3 60.6 + - - +
266J ASP 2.9 4.7 + - - -
267J ARG* 4.9 0.4 - - - -
268J ILE* 3.2 42.4 + - - +
343J VAL* 3.8 0.5 - - - +
437J LEU* 3.6 9.5 - - + +
445J GLU* 2.8 30.2 + - + +
446J ILE 4.4 0.2 - - - -
447J SER* 2.8 31.0 + - - -
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Residues in contact with ASP 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J HIS* 3.1 5.9 + - - +
107J ASP 4.3 0.7 - - - +
108J SER* 3.5 16.1 + - - +
109J PRO* 5.1 2.0 - - + -
263J GLY 2.6 10.9 + - - +
264J GLN* 1.3 69.4 - - - +
266J ASP* 1.3 57.7 + - - +
267J ARG* 2.6 14.2 + - - -
296J GLU* 3.0 13.1 - - - +
343J VAL* 3.4 13.2 - - + +
437J LEU* 3.9 1.8 - - - -
440J MSE 3.1 13.5 - - - +
441J HIS* 3.0 12.4 + - + -
445J GLU* 3.0 21.0 + - - +
6019J MN 2.9 21.0 + - - -
6020J MN 2.3 27.4 + - - -
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Residues in contact with ASP 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J ALA* 3.2 3.9 - - - +
105J HIS* 2.4 69.6 + - + +
264J GLN 2.9 4.6 + - - -
265J ASP* 1.3 71.8 + - - +
267J ARG* 1.3 48.2 + - - -
268J ILE 2.9 5.6 - - - -
269J CYS* 2.8 9.9 + - - +
270J ALA* 2.6 34.5 + - - +
341J SER 2.7 26.2 - - - +
342J ASP* 2.9 18.4 - - - +
343J VAL* 3.3 16.0 - - - +
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Residues in contact with ARG 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ASN* 4.9 2.7 + - - +
36J SER* 5.7 3.8 - - - +
37J ASN* 4.6 17.2 - - + +
40J THR* 3.5 11.2 + - - -
41J GLU* 3.2 45.4 + - - +
43J GLU* 4.3 6.5 + - - +
45J VAL* 4.1 23.3 - - + +
105J HIS 4.2 3.9 + - - -
106J ILE* 2.8 31.4 + - + +
107J ASP* 4.1 0.8 - - - +
108J SER* 3.7 28.0 + - - +
110J ARG* 6.0 0.8 - - - +
262J TYR* 4.1 5.1 + - - -
263J GLY* 3.0 30.3 - - - +
264J GLN* 4.9 0.2 - - - -
265J ASP 2.6 10.9 + - - +
266J ASP* 1.3 72.5 - - - +
268J ILE* 1.3 60.4 + - - +
270J ALA* 3.7 10.4 - - + +
271J TYR* 3.2 21.1 + - - +
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Residues in contact with ILE 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ASN* 3.9 23.1 - - - +
264J GLN* 3.2 45.0 + - - +
266J ASP 2.9 0.6 - - - +
267J ARG* 1.3 77.4 - - - +
269J CYS* 1.3 68.6 + - - +
271J TYR* 3.3 2.3 + - - +
272J THR* 3.1 24.7 + - + +
343J VAL* 3.6 22.2 - - + -
435J VAL* 3.9 23.1 - - + -
437J LEU* 4.7 0.9 - - + -
447J SER* 3.8 10.8 - - - +
452J ILE* 3.6 35.2 - - + -
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Residues in contact with CYS 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J ALA* 4.5 1.3 - - + -
266J ASP* 2.8 21.6 + - - +
268J ILE* 1.3 81.1 - - - +
270J ALA* 1.3 55.0 + - - +
271J TYR 3.0 1.8 - - - -
272J THR* 3.0 7.9 + - - -
273J SER* 2.7 42.3 + - - -
341J SER* 3.4 18.2 - - - +
342J ASP 4.0 3.6 - - - -
343J VAL* 4.1 7.4 - - - -
434J GLY* 3.4 33.7 - - - -
435J VAL* 3.7 15.3 - - - -
459J TYR* 3.8 6.4 - - - +
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Residues in contact with ALA 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J VAL* 5.9 2.5 - - + -
49J ILE* 4.8 3.2 - - + +
104J ALA* 3.8 11.6 - - + +
105J HIS 4.3 1.8 - - - +
106J ILE* 4.0 17.7 - - + -
266J ASP 2.6 19.2 + - - +
267J ARG* 3.8 13.0 - - + +
269J CYS* 1.3 73.5 - - - +
271J TYR* 1.3 57.1 + - - +
273J SER* 2.8 16.5 + - - -
274J PHE* 3.3 13.3 + - - +
291J LEU* 3.9 26.5 - - + +
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Residues in contact with TYR 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ASP* 4.6 4.5 - - - -
32J LYS* 2.9 20.1 + - + +
33J ASN* 3.5 41.1 - - + +
36J SER* 3.7 27.6 - - - +
45J VAL* 6.4 0.2 - - + -
49J ILE* 5.4 10.1 - - + -
267J ARG 3.2 15.9 + - - +
268J ILE 3.6 4.7 - - - +
269J CYS 3.0 0.6 - - - -
270J ALA* 1.3 75.5 - - - +
272J THR* 1.3 74.2 + - + +
273J SER 3.1 1.1 - - - -
274J PHE* 2.8 32.7 + + + +
275J GLU* 2.7 52.1 + - + +
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Residues in contact with THR 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ASP* 5.2 4.0 - - - +
268J ILE* 3.1 14.9 + - + +
269J CYS* 3.0 12.5 + - - -
271J TYR* 1.3 85.9 - - + +
273J SER* 1.3 62.7 + - - +
275J GLU* 3.4 2.8 + - - +
276J ALA* 2.8 32.7 + - - +
435J VAL* 5.6 0.7 - - + -
452J ILE* 3.7 42.0 - - + +
455J THR* 3.6 6.1 - - + +
456J LYS* 4.0 27.7 - - + +
459J TYR* 3.2 14.1 - - - -
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Residues in contact with SER 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102J LEU* 3.8 24.3 - - - +
103J GLY 5.6 0.7 - - - -
104J ALA* 4.6 3.5 - - - +
269J CYS 2.7 24.2 + - - -
270J ALA* 2.8 22.5 + - - -
272J THR* 1.3 78.6 + - - +
274J PHE* 1.3 55.0 + - - +
276J ALA* 3.7 1.3 - - - +
277J MET* 3.0 30.1 + - - +
289J THR* 4.1 5.9 + - - +
291J LEU* 4.4 7.1 - - - +
341J SER* 5.2 3.1 - - - -
459J TYR* 3.3 23.3 - - - -
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Residues in contact with PHE 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J ILE* 3.2 51.8 - - + -
52J ALA* 4.0 11.0 - - + -
53J GLU* 3.2 37.9 - - + -
87J MET* 3.3 20.4 - - + -
270J ALA 3.3 12.8 - - - +
271J TYR* 2.8 30.6 + + - +
273J SER* 1.3 79.0 + - - +
275J GLU* 1.3 61.6 + - + +
277J MET* 3.0 6.6 + - - +
278J LEU* 2.6 52.0 + - + +
289J THR* 5.1 2.5 - - - -
291J LEU* 5.1 2.9 - - + -
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Residues in contact with GLU 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ASP* 3.5 7.2 - - - +
32J LYS* 3.0 35.7 + - - +
271J TYR* 2.7 49.7 + - + +
272J THR* 4.0 4.3 - - - +
274J PHE* 1.3 81.2 - - + +
276J ALA* 1.3 65.9 - - - +
278J LEU* 3.0 10.8 + - + -
279J GLU* 2.9 30.6 + - - +
456J LYS* 2.6 43.6 + - + +
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Residues in contact with ALA 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J LEU* 4.8 2.5 - - + -
272J THR 2.8 19.5 + - - +
273J SER 3.7 3.4 - - - +
275J GLU* 1.3 79.8 - - - +
277J MET* 1.3 61.5 + - - +
279J GLU* 3.6 5.9 + - - +
280J MET* 3.5 23.2 + - - +
456J LYS* 4.0 13.8 - - + +
459J TYR* 3.6 28.5 - - + -
460J SER* 3.8 19.5 - - - +
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Residues in contact with MET 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J TYR* 4.0 10.1 + - - +
87J MET* 3.2 43.5 - - + +
88J PHE 3.9 9.0 - - - +
89J LEU* 4.1 8.4 - - + +
102J LEU* 4.8 5.3 - - + +
273J SER 3.0 14.0 + - - +
274J PHE 3.0 4.5 + - - +
276J ALA* 1.3 76.6 - - - +
278J LEU* 1.3 64.8 + - - +
280J MET* 3.3 20.1 - - - +
287J CYS* 3.1 45.1 - - - +
288J ILE* 3.4 9.0 - - - -
289J THR* 3.0 27.4 - - - +
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Residues in contact with LEU 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J ALA* 4.9 2.7 - - + -
53J GLU* 3.2 50.3 + - + +
55J SER* 4.9 9.4 - - - +
57J TYR* 4.5 6.8 + - - -
75J LYS* 5.3 6.6 + - - -
274J PHE* 2.6 41.9 + - + +
275J GLU* 3.0 9.4 + - + +
277J MET* 1.3 75.6 - - - +
279J GLU* 1.3 67.8 + - + +
280J MET* 2.9 9.6 + - - +
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Residues in contact with GLU 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J GLU* 2.9 22.9 + - - +
276J ALA* 3.9 6.1 - - - +
278J LEU* 1.3 80.3 - - + +
280J MET* 1.3 58.8 + - - +
281J LYS* 3.6 11.3 + - - +
456J LYS* 3.6 31.3 + - - -
460J SER* 5.6 5.8 - - - -
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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
------------------------------------------------------------
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