Contacts of the helix formed by residues 263 - 279 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T ASN* 5.3 0.7 - - - -
108T SER* 3.6 17.8 + - - -
262T TYR* 1.3 84.3 - - - +
264T GLN* 1.3 65.5 + - - +
265T ASP* 2.7 11.0 + - - +
267T ARG* 2.9 40.7 - - - +
445T GLU* 3.3 8.0 + - - -
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Residues in contact with GLN 264 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T ASN* 5.2 3.0 + - - +
37T ASN* 4.9 9.3 + - - +
259T VAL* 2.7 34.6 - - - +
260T MET 3.9 0.3 - - - -
261T GLY* 3.0 32.3 + - - +
262T TYR 3.1 3.4 + - - +
263T GLY* 1.3 74.7 - - - +
265T ASP* 1.3 57.2 + - - +
266T ASP 2.8 10.9 + - - -
267T ARG* 4.0 0.7 - - - -
268T ILE* 3.2 42.3 + - - +
343T VAL* 3.8 0.5 - - - +
437T LEU* 3.6 9.4 - - + +
445T GLU* 2.8 28.5 + - + +
447T SER* 2.8 31.6 + - - -
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Residues in contact with ASP 265 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105T HIS* 3.2 5.8 + - - +
107T ASP 4.3 0.5 - - - +
108T SER* 3.4 18.3 + - - +
109T PRO* 5.1 2.5 - - + -
263T GLY 2.7 8.7 + - - +
264T GLN* 1.3 68.8 - - - +
266T ASP* 1.3 56.4 + - - +
267T ARG* 2.6 14.6 + - - +
296T GLU* 3.0 12.2 - - - +
343T VAL* 3.4 13.6 - - + +
437T LEU* 3.9 0.4 - - - -
440T MSE 3.1 11.3 - - - +
441T HIS* 3.0 15.2 + - + -
445T GLU* 3.0 21.8 + - - +
6039T MN 2.9 21.0 + - - -
6040T MN 2.4 26.6 + - - -
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Residues in contact with ASP 266 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104T ALA* 3.2 4.2 - - - +
105T HIS* 2.4 69.1 + - + +
264T GLN 2.8 5.4 + - - -
265T ASP* 1.3 72.2 + - - +
267T ARG* 1.3 48.6 + - - -
268T ILE 2.9 5.8 - - - -
269T CYS* 2.8 9.7 + - - +
270T ALA* 2.6 34.3 + - - +
341T SER 2.7 25.8 - - - +
342T ASP* 2.9 18.2 - - - +
343T VAL* 3.3 15.2 - - - +
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Residues in contact with ARG 267 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T ASN* 4.9 2.4 + - - +
36T SER* 5.7 4.3 - - - +
37T ASN* 4.6 15.0 - - + +
40T THR* 3.6 11.5 + - - -
41T GLU* 3.3 45.8 + - - +
43T GLU* 4.3 5.9 - - - +
45T VAL* 4.1 23.5 - - + +
105T HIS 4.2 3.5 + - - -
106T ILE* 2.8 29.2 + - - +
107T ASP* 3.9 1.0 - - - +
108T SER* 3.6 28.6 + - - +
110T ARG* 6.0 0.8 - - - +
262T TYR* 4.1 4.8 + - - -
263T GLY* 2.9 34.7 - - - +
264T GLN* 4.9 0.2 - - - -
265T ASP 2.6 10.4 + - - +
266T ASP* 1.3 72.2 - - - +
268T ILE* 1.3 55.8 + - - +
270T ALA* 3.7 10.2 - - + +
271T TYR* 3.1 26.2 + - - +
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Residues in contact with ILE 268 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T ASN* 4.0 22.9 - - - +
264T GLN* 3.2 45.3 + - - +
266T ASP 2.9 0.6 - - - +
267T ARG* 1.3 77.4 - - - +
269T CYS* 1.3 68.6 + - - +
271T TYR* 3.3 2.4 + - - +
272T THR* 3.1 24.3 + - - +
343T VAL* 3.6 21.1 - - + -
435T VAL* 3.9 23.8 - - + -
437T LEU* 4.7 0.7 - - + -
447T SER* 3.7 10.5 - - - +
452T ILE* 3.7 35.2 - - + -
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Residues in contact with CYS 269 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104T ALA* 4.5 1.6 - - + -
266T ASP* 2.8 22.0 + - - +
268T ILE* 1.3 81.0 - - - +
270T ALA* 1.3 54.6 + - - +
271T TYR 3.0 1.8 - - - -
272T THR* 3.0 7.2 + - - -
273T SER* 2.7 42.6 + - - -
341T SER* 3.4 18.2 - - - +
342T ASP 4.0 2.5 - - - -
343T VAL 4.1 7.4 - - - -
434T GLY* 3.4 33.4 - - - -
435T VAL* 3.7 15.9 - - - -
459T TYR* 3.7 7.9 - - - +
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Residues in contact with ALA 270 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T VAL* 5.9 2.7 - - + -
49T ILE* 4.8 2.4 - - + +
104T ALA* 3.8 13.1 - - + +
105T HIS 4.3 1.6 - - - +
106T ILE* 4.0 18.2 - - + -
266T ASP 2.6 19.3 + - - +
267T ARG* 3.7 12.8 - - + +
269T CYS* 1.3 72.4 - - - +
271T TYR* 1.3 56.2 + - - +
273T SER* 2.8 17.0 + - - -
274T PHE* 3.3 15.6 + - - +
291T LEU* 3.9 25.7 - - + +
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Residues in contact with TYR 271 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T ASP* 4.6 4.5 - - - -
32T LYS* 2.8 20.8 - - + +
33T ASN* 3.5 38.8 - - + +
36T SER* 3.7 27.4 - - - +
45T VAL* 6.5 0.2 - - + -
49T ILE* 5.4 9.4 - - + -
267T ARG 3.1 17.0 + - - +
268T ILE 3.6 5.2 - - - +
269T CYS 3.0 0.8 - - - -
270T ALA* 1.3 76.7 - - - +
272T THR* 1.3 64.6 + - + +
273T SER 3.1 0.9 - - - -
274T PHE* 2.7 40.3 + + - +
275T GLU* 2.7 52.3 + - + +
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Residues in contact with THR 272 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T ASP* 5.2 3.4 - - - +
268T ILE* 3.1 14.9 + - + +
269T CYS* 3.0 12.1 + - - -
271T TYR* 1.3 82.8 - - + +
273T SER* 1.3 68.3 + - - +
275T GLU* 3.4 3.2 + - - +
276T ALA* 2.9 26.7 + - - +
435T VAL* 5.5 0.8 - - + +
452T ILE* 3.7 42.4 - - + +
455T THR* 3.6 6.7 - - + +
456T LYS* 4.0 26.7 - - + +
459T TYR* 3.2 14.2 - - - -
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Residues in contact with SER 273 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102T LEU* 3.9 24.2 - - - +
103T GLY 5.6 0.4 - - - -
104T ALA* 4.6 3.2 - - - +
269T CYS 2.7 24.5 + - - -
270T ALA* 2.8 21.5 + - - -
272T THR* 1.3 77.2 + - - +
274T PHE* 1.3 57.2 + - - +
276T ALA* 3.8 1.3 - - - +
277T MET* 3.0 30.3 + - - +
289T THR* 4.0 5.8 + - - +
291T LEU* 4.4 7.6 - - - +
341T SER* 5.2 2.9 - - - -
459T TYR* 3.3 23.8 - - - -
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Residues in contact with PHE 274 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T ILE* 3.2 50.9 - - + -
52T ALA* 4.0 11.9 - - + -
53T GLU* 3.2 38.1 - - + -
87T MET* 3.2 19.5 - - + -
270T ALA 3.3 12.8 - - - +
271T TYR* 2.7 30.3 + + - +
273T SER* 1.3 79.8 + - - +
275T GLU* 1.3 61.7 + - + +
277T MET* 2.9 7.4 + - - +
278T LEU* 2.6 52.3 + - + +
289T THR* 5.1 2.2 - - - -
291T LEU* 5.1 3.1 - - + -
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Residues in contact with GLU 275 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T ASP* 3.5 7.5 - - - +
32T LYS* 3.1 33.0 + - - +
271T TYR* 2.7 56.0 + - + +
272T THR* 4.0 4.3 - - - +
274T PHE* 1.3 78.0 - - + +
276T ALA* 1.3 65.8 + - - +
278T LEU* 4.0 10.3 - - + -
279T GLU* 2.9 31.1 + - - +
456T LYS* 2.6 41.6 + - + +
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Residues in contact with ALA 276 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T LEU* 4.8 2.7 - - + -
272T THR 2.9 16.9 + - - +
273T SER 3.8 2.9 - - - +
275T GLU* 1.3 80.1 - - - +
277T MET* 1.3 64.1 + - - +
279T GLU* 3.6 6.2 + - - +
280T MET* 3.4 23.7 + - - +
456T LYS* 4.0 14.5 - - + +
459T TYR* 3.7 27.8 - - + -
460T SER* 3.7 20.9 - - - +
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Residues in contact with MET 277 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57T TYR* 4.0 10.8 + - - +
87T MET* 3.2 42.8 - - + +
88T PHE 3.9 8.7 - - - +
89T LEU* 4.1 7.1 - - + +
102T LEU* 4.8 6.4 - - + +
273T SER 3.0 14.6 + - - +
274T PHE 2.9 4.8 + - - +
276T ALA* 1.3 75.8 - - - +
278T LEU* 1.3 64.0 + - - +
280T MET* 3.3 18.7 - - - +
287T CYS* 3.1 46.4 - - - +
288T ILE* 3.4 8.1 - - - -
289T THR* 3.1 28.9 - - - +
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Residues in contact with LEU 278 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52T ALA* 4.9 2.0 - - + -
53T GLU* 3.2 49.7 - - + +
55T SER* 4.9 9.4 - - - +
57T TYR* 4.5 7.2 + - - -
75T LYS* 5.3 6.4 + - - -
274T PHE* 2.6 42.5 + - + +
275T GLU* 3.5 9.4 - - + +
277T MET* 1.3 70.9 - - - +
279T GLU* 1.3 67.7 + - + +
280T MET* 2.9 13.8 + - - +
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Residues in contact with GLU 279 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275T GLU* 2.9 23.7 + - - +
276T ALA* 3.8 6.2 - - - +
278T LEU* 1.3 81.7 - - + +
280T MET* 1.3 58.1 + - - +
281T LYS* 3.6 12.2 + - - +
456T LYS* 3.5 30.3 + - - -
460T 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