Contacts of the helix formed by residues 263 - 279 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N ASN* 5.4 0.9 - - - -
108N SER* 3.6 17.4 + - - -
262N TYR* 1.3 84.0 - - - +
264N GLN* 1.3 66.2 + - - +
265N ASP* 2.6 10.7 + - - +
267N ARG* 3.0 40.4 - - - +
445N GLU* 3.3 7.3 + - - -
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Residues in contact with GLN 264 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N ASN* 5.1 3.6 + - - +
37N ASN* 4.9 9.8 + - - +
259N VAL* 2.7 35.1 - - - +
260N MET 3.9 0.5 - - - -
261N GLY* 3.0 31.9 + - - +
262N TYR 3.2 3.4 + - - +
263N GLY* 1.3 74.1 - - - +
265N ASP* 1.3 54.5 + - - +
266N ASP 2.8 11.1 + - - -
267N ARG* 4.9 0.2 - - - -
268N ILE* 3.2 43.2 + - - +
343N VAL* 3.8 0.5 - - - +
437N LEU* 3.6 9.5 - - + +
445N GLU* 2.8 30.5 + - + +
446N ILE 4.4 0.2 - - - -
447N SER* 2.8 32.0 + - - -
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Residues in contact with ASP 265 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105N HIS* 3.1 5.6 + - - -
107N ASP 4.3 0.9 - - - +
108N SER* 3.5 18.0 + - - +
109N PRO* 5.1 2.7 - - + -
263N GLY 2.6 10.1 + - - +
264N GLN* 1.3 68.0 - - - +
266N ASP* 1.3 56.6 + - - +
267N ARG* 2.6 14.2 + - - +
296N GLU* 3.0 13.4 - - - +
342N ASP* 3.2 0.2 - - - +
343N VAL* 3.4 14.5 - - + +
437N LEU* 3.7 2.2 - - - +
440N MSE 3.0 10.7 - - - +
441N HIS* 3.0 14.3 + - + -
445N GLU* 3.0 20.3 + - - +
6027N MN 2.4 23.2 + - - -
6028N MN 2.5 25.5 + - - -
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Residues in contact with ASP 266 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104N ALA* 3.2 4.0 - - - +
105N HIS* 2.4 69.4 + - + +
264N GLN 2.8 4.9 + - - -
265N ASP* 1.3 72.3 + - - +
267N ARG* 1.3 47.4 + - - -
268N ILE 2.9 6.3 - - - +
269N CYS* 2.7 10.5 + - - +
270N ALA* 2.6 34.5 + - - +
341N SER 2.7 25.6 - - - +
342N ASP* 2.9 18.6 - - - +
343N VAL* 3.3 15.2 - - - +
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Residues in contact with ARG 267 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N ASN* 4.9 2.8 + - - +
36N SER* 5.7 3.8 - - - +
37N ASN* 4.7 13.4 - - + +
40N THR* 3.6 10.6 + - - -
41N GLU* 3.3 44.2 + - - +
43N GLU* 4.3 6.5 - - - +
45N VAL* 4.1 24.7 - - + +
105N HIS 4.2 3.9 + - - -
106N ILE* 2.8 30.3 + - - +
107N ASP* 4.1 1.2 - - - +
108N SER* 3.6 28.8 + - - +
110N ARG* 6.0 0.8 - - - +
262N TYR* 4.1 5.5 + - - -
263N GLY* 3.0 34.3 - - - +
264N GLN* 4.9 0.2 - - - -
265N ASP 2.6 11.2 + - - +
266N ASP* 1.3 73.3 - - - +
268N ILE* 1.3 54.9 + - - +
270N ALA* 3.7 10.5 - - + +
271N TYR* 3.1 26.5 + - - +
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Residues in contact with ILE 268 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N ASN* 4.0 24.0 - - - +
264N GLN* 3.2 45.7 + - - +
266N ASP 2.9 0.2 - - - -
267N ARG* 1.3 76.4 - - - +
269N CYS* 1.3 68.8 + - - +
271N TYR* 3.3 2.8 + - - +
272N THR* 3.1 24.8 + - + +
343N VAL* 3.6 22.2 - - + -
435N VAL* 3.9 23.1 - - + -
437N LEU* 4.7 0.4 - - + -
447N SER* 3.8 10.8 - - - +
452N ILE* 3.7 36.1 - - + -
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Residues in contact with CYS 269 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104N ALA* 4.5 1.3 - - + -
266N ASP* 2.7 23.4 + - - +
268N ILE* 1.3 86.9 - - - +
270N ALA* 1.3 54.4 + - - +
271N TYR 3.0 2.2 - - - -
272N THR* 3.0 8.0 + - - -
273N SER* 2.7 42.0 + - - -
341N SER* 3.4 18.4 - - - +
342N ASP 4.0 3.4 - - - -
343N VAL 4.0 7.4 - - - -
434N GLY* 3.4 33.0 - - - -
435N VAL* 3.7 11.9 - - - -
459N TYR* 3.8 5.9 - - - +
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Residues in contact with ALA 270 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N VAL* 5.9 2.2 - - + -
49N ILE* 4.8 2.8 - - + +
104N ALA* 3.8 13.0 - - + +
105N HIS 4.4 1.1 - - - +
106N ILE* 4.0 17.5 - - + -
266N ASP 2.6 19.7 + - - +
267N ARG* 3.7 12.8 - - + +
269N CYS* 1.3 72.6 - - - +
271N TYR* 1.3 57.3 + - - +
273N SER* 2.8 16.7 + - - -
274N PHE* 3.3 14.7 + - - +
291N LEU* 3.9 26.4 - - + +
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Residues in contact with TYR 271 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N ASP* 4.6 5.2 - - - -
32N LYS* 2.8 19.7 + - + +
33N ASN* 3.5 37.9 - - + +
36N SER* 3.7 26.9 - - - +
45N VAL* 6.4 0.2 - - + -
49N ILE* 5.4 9.9 - - + -
267N ARG 3.1 16.5 + - - +
268N ILE 3.6 5.4 - - - +
269N CYS 3.0 0.6 - - - -
270N ALA* 1.3 76.4 - - - +
272N THR* 1.3 66.2 + - + +
273N SER 3.1 0.9 - - - -
274N PHE* 2.7 47.0 + + + +
275N GLU* 2.6 46.9 + - + +
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Residues in contact with THR 272 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N ASP* 5.2 3.6 - - - +
268N ILE* 3.1 14.8 + - + +
269N CYS* 3.0 12.6 + - - -
271N TYR* 1.3 86.0 - - + +
273N SER* 1.3 67.8 + - - +
275N GLU* 3.4 2.4 + - - +
276N ALA* 2.9 27.0 + - - +
435N VAL* 5.6 0.9 - - + -
452N ILE* 3.7 41.7 - - + +
455N THR* 3.6 6.4 - - + +
456N LYS* 3.9 27.4 - - + +
459N TYR* 3.1 14.9 - - - -
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Residues in contact with SER 273 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N LEU* 3.8 24.3 - - - +
103N GLY 5.6 0.4 - - - -
104N ALA* 4.6 3.6 - - - +
269N CYS 2.7 24.1 + - - -
270N ALA* 2.8 22.7 + - - -
272N THR* 1.3 78.8 + - - +
274N PHE* 1.3 56.4 + - - +
276N ALA* 3.8 1.1 - - - +
277N MET* 3.0 30.5 + - - +
289N THR* 4.1 5.9 + - - +
291N LEU* 4.4 6.9 - - - +
341N SER* 5.2 3.1 - - - -
459N TYR* 3.3 23.1 - - - -
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Residues in contact with PHE 274 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N ILE* 3.2 50.5 - - + -
52N ALA* 4.0 11.7 - - + -
53N GLU* 3.2 38.6 - - + -
87N MET* 3.3 20.2 - - + -
270N ALA 3.3 12.8 - - - +
271N TYR* 2.7 32.5 + + - +
273N SER* 1.3 79.4 + - - +
275N GLU* 1.3 60.0 + - + -
277N MET* 2.9 6.2 + - - +
278N LEU* 2.6 51.6 + - + +
289N THR* 5.1 1.6 - - - -
291N LEU* 5.1 3.4 - - + -
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Residues in contact with GLU 275 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N ASP* 3.5 6.9 - - - +
32N LYS* 3.0 33.6 + - - +
271N TYR* 2.6 54.5 + - + +
272N THR* 4.0 4.5 - - - +
274N PHE* 1.3 78.7 - - + +
276N ALA* 1.3 64.5 + - - +
278N LEU* 4.0 10.8 - - + -
279N GLU* 2.9 31.4 + - - +
456N LYS* 2.7 42.2 + - + +
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Residues in contact with ALA 276 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N LEU* 4.8 2.2 - - + -
272N THR 2.9 18.8 + - - +
273N SER 3.8 3.1 - - - +
275N GLU* 1.3 79.6 - - - +
277N MET* 1.3 61.3 + - - +
279N GLU* 3.6 5.8 + - - +
280N MET* 3.4 23.6 + - - +
456N LYS* 4.0 14.9 - - + +
459N TYR* 3.7 27.8 - - + -
460N SER* 3.8 21.3 - - - +
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Residues in contact with MET 277 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57N TYR* 4.0 10.8 + - - +
87N MET* 3.2 44.0 - - + +
88N PHE 3.9 8.5 - - - +
89N LEU* 4.2 8.0 - - + +
102N LEU* 4.8 6.2 - - + +
273N SER 3.0 14.8 + - - +
274N PHE 2.9 3.7 + - - +
276N ALA* 1.3 76.2 - - - +
278N LEU* 1.3 64.1 + - - +
280N MET* 3.3 19.5 - - - +
287N CYS* 3.1 44.4 - - - +
288N ILE* 3.4 9.4 - - - -
289N THR* 3.0 29.4 - - - +
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Residues in contact with LEU 278 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N ALA* 4.9 2.7 - - + -
53N GLU* 3.1 49.8 - - + +
55N SER* 4.9 10.3 - - - +
57N TYR* 4.5 6.6 + - - -
75N LYS* 5.3 6.9 + - - -
274N PHE* 2.6 41.0 + - + +
275N GLU* 3.1 10.3 + - + +
277N MET* 1.3 72.1 - - - +
279N GLU* 1.3 68.1 + - + +
280N MET* 2.9 13.8 + - - +
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Residues in contact with GLU 279 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275N GLU* 2.9 22.2 + - - +
276N ALA* 3.9 6.5 - - - +
278N LEU* 1.3 81.2 - - + +
280N MET* 1.3 57.7 + - - +
281N LYS* 3.6 11.9 + - - +
456N LYS* 3.5 31.6 + - - -
460N 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