Contacts of the helix formed by residues 263 - 279 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASN* 5.4 0.7 - - - -
108E SER* 3.7 18.4 + - - -
262E TYR* 1.3 83.8 - - - +
264E GLN* 1.3 67.0 + - - +
265E ASP* 2.6 10.0 + - - +
267E ARG* 2.9 40.8 - - - +
445E GLU* 3.3 8.3 + - - -
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Residues in contact with GLN 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ASN* 5.1 3.2 + - - -
37E ASN* 4.8 9.1 + - - +
259E VAL* 2.7 35.0 - - - +
260E MET 3.9 0.2 - - - -
261E GLY* 3.0 32.9 + - - +
262E TYR 3.2 2.8 + - - +
263E GLY* 1.3 74.9 - - - +
265E ASP* 1.3 56.2 + - - +
266E ASP 2.8 11.3 + - - -
267E ARG* 4.9 0.2 - - - -
268E ILE* 3.2 42.5 + - - +
343E VAL* 3.8 0.5 - - - +
437E LEU* 3.6 9.7 - - + +
445E GLU* 2.8 29.0 + - + +
446E ILE 4.4 0.2 - - - -
447E SER* 2.8 31.6 + - - -
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Residues in contact with ASP 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E HIS* 3.2 5.0 + - - -
107E ASP 4.3 0.5 - - - +
108E SER* 3.5 17.4 + - - +
109E PRO* 5.1 2.0 - - + -
263E GLY 2.6 9.3 + - - +
264E GLN* 1.3 68.6 - - - +
266E ASP* 1.3 56.5 + - - +
267E ARG* 2.6 14.4 + - - +
296E GLU* 3.0 11.1 - - - +
343E VAL* 3.4 12.1 - - + -
437E LEU* 3.9 1.6 - - - -
440E MSE 3.1 11.6 - - - +
441E HIS* 3.0 15.3 + - + -
445E GLU* 3.0 21.6 + - - +
6009E MN 2.8 20.4 + - - -
6010E MN 2.2 30.7 + - - -
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Residues in contact with ASP 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E ALA* 3.2 4.5 - - - +
105E HIS* 2.4 68.3 + - + +
264E GLN 2.8 5.0 + - - -
265E ASP* 1.3 73.1 + - - +
267E ARG* 1.3 47.7 + - - +
268E ILE 2.8 5.8 - - - +
269E CYS* 2.7 10.1 + - - +
270E ALA* 2.6 34.7 + - - +
341E SER 2.7 25.7 - - - +
342E ASP* 2.8 18.9 - - - +
343E VAL* 3.3 15.6 - - - +
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Residues in contact with ARG 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ASN* 4.9 2.2 + - - +
36E SER* 5.7 4.3 - - - +
37E ASN* 4.6 14.8 - - + +
40E THR* 3.6 11.3 + - - -
41E GLU* 3.3 43.4 + - - +
43E GLU* 4.3 6.5 - - - +
45E VAL* 4.1 23.9 - - + +
105E HIS 4.2 3.7 + - - -
106E ILE* 2.8 31.2 + - - +
107E ASP* 4.1 1.0 - - - +
108E SER* 3.7 28.0 + - - +
110E ARG* 6.0 1.0 - - - +
262E TYR* 4.1 5.9 + - - -
263E GLY* 2.9 33.2 - - - +
264E GLN* 4.9 0.2 - - - -
265E ASP 2.6 11.0 + - - +
266E ASP* 1.3 74.0 - - - +
268E ILE* 1.3 56.8 + - - +
270E ALA* 3.7 10.5 - - + +
271E TYR* 3.1 25.1 + - - +
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Residues in contact with ILE 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ASN* 3.9 22.9 - - - +
264E GLN* 3.2 46.8 + - - +
266E ASP 2.8 0.2 - - - -
267E ARG* 1.3 78.3 - - - +
269E CYS* 1.3 68.2 + - - +
271E TYR* 3.3 2.1 + - - +
272E THR* 3.1 24.3 + - - +
343E VAL* 3.6 22.0 - - + -
435E VAL* 3.8 23.3 - - + -
437E LEU* 4.7 0.9 - - + -
447E SER* 3.8 10.3 - - - +
452E ILE* 3.7 36.6 - - + -
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Residues in contact with CYS 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E ALA* 4.4 1.6 - - + -
266E ASP* 2.7 22.2 + - - +
268E ILE* 1.3 80.2 - - - +
270E ALA* 1.3 55.6 + - - +
271E TYR 3.0 1.8 - - - -
272E THR* 3.1 8.0 + - - -
273E SER* 2.6 42.0 + - - -
341E SER* 3.4 17.9 - - - +
342E ASP 4.0 2.9 - - - -
343E VAL 4.1 7.2 - - - -
434E GLY* 3.4 33.7 - - - -
435E VAL* 3.7 15.5 - - - -
459E TYR* 3.7 7.1 - - - +
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Residues in contact with ALA 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E VAL* 5.9 2.2 - - + -
49E ILE* 4.8 3.2 - - + +
104E ALA* 3.8 13.0 - - + +
105E HIS 4.4 1.1 - - - +
106E ILE* 4.0 17.5 - - + -
266E ASP 2.6 19.4 + - - +
267E ARG* 3.7 13.2 - - + +
269E CYS* 1.3 72.3 - - - +
271E TYR* 1.3 57.2 + - - +
273E SER* 2.8 16.6 + - - -
274E PHE* 3.3 14.9 + - - +
291E LEU* 3.9 27.1 - - + +
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Residues in contact with TYR 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ASP* 4.6 5.4 - - - -
32E LYS* 2.9 20.4 - - + +
33E ASN* 3.5 39.7 - - + +
36E SER* 3.7 27.4 - - - +
45E VAL* 6.4 0.2 - - + -
49E ILE* 5.4 9.6 - - + -
267E ARG 3.1 16.8 + - - +
268E ILE 3.6 5.4 - - - +
269E CYS 3.0 0.6 - - - -
270E ALA* 1.3 76.0 - - - +
272E THR* 1.3 66.3 + - + +
273E SER 3.1 1.1 - - - -
274E PHE* 2.7 41.5 + + + +
275E GLU* 2.7 51.8 + - + +
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Residues in contact with THR 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ASP* 5.1 3.8 - - - +
268E ILE* 3.1 15.4 + - + +
269E CYS* 3.1 12.0 + - - -
271E TYR* 1.3 82.6 - - + +
273E SER* 1.3 60.0 + - - +
275E GLU* 4.6 2.5 - - - +
276E ALA* 2.9 32.9 + - - +
435E VAL* 5.6 0.9 - - + -
452E ILE* 3.7 40.8 - - + +
455E THR* 3.6 5.7 - - + +
456E LYS* 3.9 27.4 - - + +
459E TYR* 3.2 14.8 - - - -
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Residues in contact with SER 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 3.8 25.3 - - - +
103E GLY 5.6 0.7 - - - -
104E ALA* 4.6 2.9 - - - +
269E CYS 2.6 24.0 + - - -
270E ALA* 2.8 22.3 + - - -
272E THR* 1.3 78.3 + - - +
274E PHE* 1.3 56.1 + - - +
276E ALA* 3.8 1.3 - - - +
277E MET* 3.0 30.3 + - - +
289E THR* 4.1 6.1 + - - +
291E LEU* 4.4 7.1 - - - +
341E SER* 5.2 3.6 - - - -
459E TYR* 3.3 22.9 - - - -
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Residues in contact with PHE 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 3.2 49.6 - - + -
52E ALA* 4.0 11.0 - - + -
53E GLU* 3.2 38.8 - - + -
87E MET* 3.3 20.9 - - + -
270E ALA 3.3 13.0 - - - +
271E TYR* 2.7 33.7 + + - +
273E SER* 1.3 79.3 + - - +
275E GLU* 1.3 58.9 + - + -
277E MET* 2.9 6.7 + - - +
278E LEU* 2.6 52.9 + - + +
289E THR* 5.1 2.0 - - - -
291E LEU* 5.1 3.1 - - + -
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Residues in contact with GLU 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ASP* 3.5 6.9 - - - +
32E LYS* 3.1 33.4 + - - +
271E TYR* 2.7 56.6 + - + +
272E THR* 4.0 3.8 - - - +
274E PHE* 1.3 77.2 - - + +
276E ALA* 1.3 65.8 + - - +
278E LEU* 3.0 10.7 + - + +
279E GLU* 2.9 30.2 + - - +
456E LYS* 2.7 42.4 + - + +
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Residues in contact with ALA 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU* 4.7 2.2 - - + -
272E THR 2.9 19.2 + - - +
273E SER 3.8 3.1 - - - +
275E GLU* 1.3 79.2 - - - +
277E MET* 1.3 62.8 + - - +
279E GLU* 3.6 6.1 + - - +
280E MET* 3.5 23.0 + - - +
456E LYS* 4.0 14.5 - - + +
459E TYR* 3.7 28.5 - - + -
460E SER* 3.8 20.0 - - - +
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Residues in contact with MET 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E TYR* 4.0 10.4 + - - +
87E MET* 3.2 45.3 - - + +
88E PHE 3.9 8.7 - - - +
89E LEU* 4.1 7.9 - - + +
102E LEU* 4.8 6.0 - - + +
273E SER 3.0 14.2 + - - +
274E PHE 2.9 4.5 + - - +
276E ALA* 1.3 75.6 - - - +
278E LEU* 1.3 63.2 + - - +
280E MET* 3.3 19.7 - - - +
287E CYS* 3.1 44.9 - - - +
288E ILE* 3.4 8.3 - - - -
289E THR* 3.0 28.5 - - - +
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Residues in contact with LEU 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E ALA* 4.9 2.5 - - + -
53E GLU* 3.2 50.0 - - + +
55E SER* 4.9 9.0 - - - +
57E TYR* 4.5 6.9 + - - -
75E LYS* 5.3 6.4 + - - -
274E PHE* 2.6 41.9 + - + +
275E GLU* 3.0 9.8 + - + +
277E MET* 1.3 71.9 - - - +
279E GLU* 1.3 68.8 + - + +
280E MET* 2.9 14.2 + - - +
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Residues in contact with GLU 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E GLU* 2.9 22.6 + - - +
276E ALA* 3.9 6.3 - - - +
278E LEU* 1.3 81.0 - - + +
280E MET* 1.3 58.1 + - - +
281E LYS* 3.6 12.4 + - - +
456E LYS* 3.5 31.3 + - - -
460E SER* 5.6 5.9 - - - -
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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