Contacts of the helix formed by residues 263 - 279 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ASN* 5.4 0.9 - - - -
108P SER* 3.6 17.7 + - - -
262P TYR* 1.3 84.1 - - - +
264P GLN* 1.3 67.2 + - - +
265P ASP* 2.6 11.5 + - - +
267P ARG* 3.0 41.1 - - - +
445P GLU* 3.3 7.5 + - - -
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Residues in contact with GLN 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ASN* 5.2 3.0 + - - -
37P ASN* 4.8 9.3 + - - +
259P VAL* 2.6 35.0 - - - +
260P MET 3.9 0.3 - - - -
261P GLY* 3.0 31.9 + - - +
262P TYR 3.2 2.8 + - - +
263P GLY* 1.3 74.6 - - - +
265P ASP* 1.3 63.5 + - - +
266P ASP 2.8 4.9 + - - -
267P ARG* 4.9 0.2 - - - -
268P ILE* 3.2 42.9 + - - +
343P VAL* 3.8 0.3 - - - +
437P LEU* 3.6 9.9 - - + +
445P GLU* 2.8 29.2 + - + +
447P SER* 2.8 31.8 + - - -
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Residues in contact with ASP 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P HIS* 3.1 5.4 + - - -
107P ASP 4.3 0.7 - - - +
108P SER* 3.5 16.5 + - - +
109P PRO* 5.1 2.0 - - + -
263P GLY 2.6 9.5 + - - +
264P GLN* 1.3 69.9 - - - +
266P ASP* 1.3 56.4 + - - +
267P ARG* 2.6 14.4 + - - +
296P GLU* 2.9 21.6 - - - +
342P ASP* 3.3 0.9 - - - +
343P VAL* 3.4 14.5 - - + +
437P LEU* 3.9 2.0 - - - -
440P MSE 3.0 19.8 - - - +
441P HIS* 3.0 18.7 + - + -
445P GLU* 3.0 21.2 + - - +
6032P MN 2.5 24.9 + - - -
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Residues in contact with ASP 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P ALA* 3.2 3.9 - - - +
105P HIS* 2.4 68.2 + - + +
264P GLN 2.8 5.2 + - - -
265P ASP* 1.3 71.6 + - - +
267P ARG* 1.3 48.1 + - - +
268P ILE 2.9 6.1 - - - +
269P CYS* 2.7 10.7 + - - +
270P ALA* 2.6 34.1 + - - +
341P SER 2.7 26.4 - - - +
342P ASP* 2.8 17.3 - - - +
343P VAL* 3.3 15.4 - - - +
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Residues in contact with ARG 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ASN* 4.9 2.6 + - - +
36P SER* 5.7 4.7 - - - +
37P ASN* 4.6 14.4 - - + +
40P THR* 3.6 11.7 + - - -
41P GLU* 3.2 44.6 + - - +
43P GLU* 4.3 6.1 - - - +
45P VAL* 4.1 23.9 - - + +
105P HIS 4.2 4.1 + - - -
106P ILE* 2.8 29.9 + - - +
107P ASP* 4.1 1.2 - - - +
108P SER* 3.6 29.4 + - - +
110P ARG* 6.0 1.0 - - - +
262P TYR* 4.0 5.5 + - - -
263P GLY* 3.0 34.9 - - - +
264P GLN* 4.9 0.4 - - - -
265P ASP 2.6 10.8 + - - +
266P ASP* 1.3 72.0 - - - +
268P ILE* 1.3 56.2 + - - +
270P ALA* 3.7 10.6 - - + +
271P TYR* 3.1 26.2 + - - +
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Residues in contact with ILE 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ASN* 3.9 23.1 - - - +
264P GLN* 3.2 45.4 + - - +
266P ASP 2.9 0.4 - - - -
267P ARG* 1.3 76.6 - - - +
269P CYS* 1.3 67.9 + - - +
271P TYR* 3.3 2.6 + - - +
272P THR* 3.1 24.5 + - + +
343P VAL* 3.6 22.0 - - + -
435P VAL* 3.9 23.6 - - + -
437P LEU* 4.7 0.4 - - + -
447P SER* 3.7 10.8 - - - +
452P ILE* 3.7 36.1 - - + -
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Residues in contact with CYS 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P ALA* 4.5 1.1 - - + -
266P ASP* 2.7 21.6 + - - +
268P ILE* 1.3 81.0 - - - +
270P ALA* 1.3 55.1 + - - +
271P TYR 3.0 1.8 - - - -
272P THR* 3.0 8.1 + - - -
273P SER* 2.7 41.8 + - - -
341P SER* 3.4 18.4 - - - +
342P ASP 4.0 2.9 - - - -
343P VAL* 4.1 7.6 - - - -
434P GLY* 3.4 33.2 - - - -
435P VAL* 3.7 15.0 - - - -
459P TYR* 3.7 6.9 - - - +
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Residues in contact with ALA 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P VAL* 5.9 2.2 - - + -
49P ILE* 4.9 3.0 - - + +
104P ALA* 3.7 13.4 - - + +
105P HIS 4.4 1.1 - - - +
106P ILE* 4.0 16.8 - - + -
266P ASP 2.6 19.2 + - - +
267P ARG* 3.7 13.2 - - + +
269P CYS* 1.3 73.2 - - - +
271P TYR* 1.3 58.9 + - - +
273P SER* 2.8 16.4 + - - -
274P PHE* 3.3 13.7 + - - +
291P LEU* 3.8 26.8 - - + +
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Residues in contact with TYR 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P ASP* 4.6 5.2 - - - -
32P LYS* 2.9 20.3 - - + +
33P ASN* 3.5 39.5 - - + +
36P SER* 3.7 28.3 - - - +
45P VAL* 6.4 0.2 - - + -
49P ILE* 5.4 9.4 - - + -
267P ARG 3.1 16.5 + - - +
268P ILE 3.6 5.6 - - - +
269P CYS 3.0 0.8 - - - -
270P ALA* 1.3 77.0 - - - +
272P THR* 1.3 66.0 + - + +
273P SER 3.1 0.9 - - - -
274P PHE* 2.7 47.1 + + - +
275P GLU* 2.7 47.1 + - + +
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Residues in contact with THR 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P ASP* 5.2 3.8 - - - +
268P ILE* 3.1 14.4 + - + +
269P CYS* 3.0 12.1 + - - -
271P TYR* 1.3 86.3 - - + +
273P SER* 1.3 69.4 + - - +
275P GLU* 3.4 2.8 + - - +
276P ALA* 2.9 26.3 + - - +
435P VAL* 5.6 0.7 - - + -
452P ILE* 3.7 42.0 - - + +
455P THR* 3.6 6.5 - - + +
456P LYS* 3.9 26.6 - - + +
459P TYR* 3.2 14.0 - - - -
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Residues in contact with SER 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P LEU* 3.8 23.9 - - - +
103P GLY 5.6 0.4 - - - -
104P ALA* 4.6 3.6 - - - +
269P CYS 2.7 23.3 + - - -
270P ALA* 2.8 22.2 + - - -
272P THR* 1.3 78.6 + - - +
274P PHE* 1.3 55.6 + - - +
276P ALA* 3.8 1.3 - - - +
277P MET* 3.0 30.5 + - - +
289P THR* 4.1 5.9 + - - +
291P LEU* 4.4 7.7 - - - +
341P SER* 5.2 2.9 - - - -
459P TYR* 3.3 23.1 - - - -
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Residues in contact with PHE 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P ILE* 3.2 50.5 - - + -
52P ALA* 4.0 11.7 - - + -
53P GLU* 3.3 36.8 - - + -
87P MET* 3.3 20.4 - - + -
270P ALA 3.3 12.1 - - - +
271P TYR* 2.7 32.8 + + - +
273P SER* 1.3 79.8 + - - +
275P GLU* 1.3 59.2 + - + -
277P MET* 3.0 6.6 + - - +
278P LEU* 2.6 53.8 + - + +
289P THR* 5.1 2.0 - - - -
291P LEU* 5.1 3.4 - - + -
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Residues in contact with GLU 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P ASP* 3.5 6.7 - - - +
32P LYS* 3.1 34.1 + - - +
271P TYR* 2.7 55.5 + - + +
272P THR* 4.0 4.3 - - - +
274P PHE* 1.3 77.9 - - + +
276P ALA* 1.3 66.4 + - - +
278P LEU* 3.5 10.0 - - + +
279P GLU* 2.8 32.2 + - - +
456P LYS* 2.7 42.9 + - + +
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Residues in contact with ALA 276 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P LEU* 4.8 2.7 - - + -
272P THR 2.9 19.0 + - - +
273P SER 3.8 3.4 - - - +
275P GLU* 1.3 80.9 - - - +
277P MET* 1.3 61.2 + - - +
279P GLU* 3.8 4.6 - - - +
280P MET* 3.4 24.0 + - - +
456P LYS* 4.0 14.7 - - + +
459P TYR* 3.7 27.1 - - + -
460P SER* 3.7 21.8 - - - +
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Residues in contact with MET 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P TYR* 4.0 9.9 + - - +
87P MET* 3.2 44.0 - - + +
88P PHE 3.9 9.4 - - - +
89P LEU* 4.2 6.9 - - + +
102P LEU* 4.8 6.4 - - + +
273P SER 3.0 16.7 + - - +
274P PHE 3.5 2.9 - - - +
276P ALA* 1.3 76.5 - - - +
278P LEU* 1.3 63.2 + - - +
280P MET* 3.3 20.2 - - - +
287P CYS* 3.1 44.0 - - - +
288P ILE* 3.4 8.1 - - - -
289P THR* 3.0 28.0 - - - +
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Residues in contact with LEU 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P ALA* 4.9 2.5 - - + -
53P GLU* 3.2 49.9 - - + +
55P SER* 4.9 9.0 - - - +
57P TYR* 4.5 6.8 + - - -
75P LYS* 5.3 6.8 + - - -
274P PHE* 2.6 41.1 + - + +
275P GLU* 3.5 9.2 - - + +
277P MET* 1.3 71.8 - - - +
279P GLU* 1.3 68.8 + - + +
280P MET 2.9 13.2 + - - +
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Residues in contact with GLU 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275P GLU* 2.8 22.9 + - - +
276P ALA* 3.8 6.5 - - - +
278P LEU* 1.3 79.9 - - + +
280P MET* 1.3 58.1 + - - +
281P LYS* 3.7 12.4 + - - +
456P LYS* 3.5 29.9 + - - -
460P SER* 5.6 6.6 - - - -
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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