Contacts of the helix formed by residues 263 - 279 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ASN* 5.4 0.9 - - - -
108H SER* 3.6 17.6 + - - -
262H TYR* 1.3 83.3 - - - +
264H GLN* 1.3 65.6 + - - +
265H ASP* 2.6 11.1 + - - +
267H ARG* 2.9 41.2 - - - +
445H GLU* 3.3 7.3 + - - -
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Residues in contact with GLN 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ASN* 5.1 3.7 + - - +
37H ASN* 4.9 9.8 + - - +
259H VAL* 2.7 35.1 - - - +
260H MET 3.9 0.3 - - - -
261H GLY* 3.0 32.6 + - - +
262H TYR 3.2 3.2 + - - +
263H GLY* 1.3 71.1 - - - +
265H ASP* 1.3 53.9 + - - +
266H ASP 2.9 10.9 + - - -
267H ARG* 4.0 0.9 - - - -
268H ILE* 3.2 42.3 + - - +
343H VAL* 3.8 0.5 - - - +
437H LEU* 3.6 9.5 - - + +
445H GLU* 2.7 33.7 + - + +
446H ILE 4.4 0.2 - - - -
447H SER* 2.8 31.2 + - - -
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Residues in contact with ASP 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H HIS* 3.2 6.1 + - - +
107H ASP 4.3 0.5 - - - +
108H SER* 3.5 16.6 + - - +
109H PRO* 5.1 2.2 - - + -
263H GLY 2.6 9.1 + - - +
264H GLN* 1.3 68.4 - - - +
266H ASP* 1.3 55.5 + - - +
267H ARG* 2.7 13.9 + - - +
296H GLU* 3.0 20.3 - - - +
343H VAL* 3.4 12.5 - - + +
437H LEU* 3.7 1.1 - - - +
440H MSE 3.0 31.7 - - - +
441H HIS* 3.0 9.2 + - + -
445H GLU* 3.0 22.5 + - - +
6015H MN 3.0 0.2 + - - -
6016H MN 2.4 26.0 + - - -
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Residues in contact with ASP 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ALA* 3.2 4.7 - - - +
105H HIS* 2.4 68.5 + - + +
264H GLN 2.9 4.9 + - - -
265H ASP* 1.3 71.8 + - - +
267H ARG* 1.3 48.2 + - - -
268H ILE 2.8 6.1 - - - +
269H CYS* 2.7 10.2 + - - +
270H ALA* 2.6 34.7 + - - +
341H SER 2.7 25.3 - - - +
342H ASP* 2.9 18.5 - - - +
343H VAL* 3.3 15.2 - - - +
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Residues in contact with ARG 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ASN* 4.9 2.8 + - - +
36H SER* 5.7 4.9 - - - +
37H ASN* 4.6 15.4 - - + +
40H THR* 3.7 12.0 + - - -
41H GLU* 3.4 42.2 + - - +
43H GLU* 4.3 6.5 - - - +
45H VAL* 4.1 24.1 - - + +
105H HIS 4.3 4.0 + - - -
106H ILE* 2.8 29.9 + - - +
107H ASP* 4.1 1.0 - - - +
108H SER* 3.6 29.4 + - - +
110H ARG* 6.0 1.0 - - - +
262H TYR* 4.0 6.3 + - - -
263H GLY* 2.9 34.9 - - - +
264H GLN* 4.8 0.4 - - - -
265H ASP 2.7 11.2 + - - +
266H ASP* 1.3 72.0 - - - +
268H ILE* 1.3 56.7 + - - +
270H ALA* 3.7 9.8 - - + +
271H TYR* 3.1 26.3 + - - +
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Residues in contact with ILE 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ASN* 3.9 22.7 - - - +
264H GLN* 3.2 43.8 + - - +
266H ASP 2.8 0.4 - - - -
267H ARG* 1.3 77.9 - - - +
269H CYS* 1.3 68.3 + - - +
271H TYR* 3.4 2.6 + - - +
272H THR* 3.1 24.5 + - - +
343H VAL* 3.6 21.3 - - + -
435H VAL* 3.9 24.7 - - + -
437H LEU* 4.7 0.7 - - + -
447H SER* 3.8 11.7 - - - +
452H ILE* 3.7 34.5 - - + -
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Residues in contact with CYS 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ALA* 4.5 1.3 - - + -
266H ASP* 2.7 24.8 + - - +
268H ILE* 1.3 81.4 - - - +
270H ALA* 1.3 55.0 + - - +
271H TYR 3.0 2.2 - - - -
272H THR* 3.0 8.2 + - - -
273H SER* 2.6 42.0 + - - -
341H SER* 3.4 18.8 - - - +
342H ASP 4.0 2.9 - - - -
343H VAL 4.1 7.6 - - - -
434H GLY* 3.4 33.0 - - - -
435H VAL* 3.7 12.1 - - - -
459H TYR* 3.8 6.4 - - - +
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Residues in contact with ALA 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H VAL* 5.9 2.5 - - + -
49H ILE* 4.9 1.2 - - - +
104H ALA* 3.8 12.9 - - + +
105H HIS 4.4 1.6 - - - +
106H ILE* 4.0 17.7 - - + -
266H ASP 2.6 19.5 + - - +
267H ARG* 3.7 12.3 - - + +
269H CYS* 1.3 72.4 - - - +
271H TYR* 1.3 58.2 + - - +
273H SER* 2.8 16.7 + - - -
274H PHE* 3.3 13.7 + - - +
291H LEU* 3.9 26.0 - - + +
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Residues in contact with TYR 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ASP* 4.6 4.9 - - - -
32H LYS* 2.9 20.0 - - + +
33H ASN* 3.5 41.1 - - + +
36H SER* 3.7 27.1 - - - +
45H VAL* 6.4 0.2 - - + -
49H ILE* 5.4 9.6 - - + -
267H ARG 3.1 16.8 + - - +
268H ILE 3.6 5.2 - - - +
269H CYS 3.0 0.6 - - - -
270H ALA* 1.3 75.5 - - - +
272H THR* 1.3 66.0 + - + +
273H SER 3.1 1.1 - - - -
274H PHE* 2.7 41.7 + + + +
275H GLU* 2.6 52.4 + - + +
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Residues in contact with THR 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ASP* 5.2 3.6 - - - +
268H ILE* 3.1 14.5 + - + +
269H CYS* 3.0 12.5 + - - -
271H TYR* 1.3 82.3 - - + +
273H SER* 1.3 69.6 + - - +
275H GLU* 4.0 2.9 - - - +
276H ALA* 2.9 27.0 + - - +
435H VAL* 5.6 0.7 - - + -
452H ILE* 3.6 41.7 - - + +
455H THR* 3.6 6.0 - - + +
456H LYS* 3.9 26.2 - - + +
459H TYR* 3.1 14.7 - - - -
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Residues in contact with SER 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H LEU* 3.8 25.3 - - - +
103H GLY 5.6 0.9 - - - -
104H ALA* 4.6 3.2 - - - +
269H CYS 2.6 24.8 + - - -
270H ALA* 2.8 22.2 + - - -
272H THR* 1.3 77.9 + - - +
274H PHE* 1.3 55.5 + - - +
276H ALA* 4.4 0.2 - - - -
277H MET* 3.0 29.5 + - - +
289H THR* 4.0 5.9 + - - +
291H LEU* 4.4 7.7 - - - +
341H SER* 5.2 3.1 - - - -
459H TYR* 3.3 22.2 - - - -
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Residues in contact with PHE 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H ILE* 3.2 48.7 - - + -
52H ALA* 4.0 11.9 - - + -
53H GLU* 3.2 39.0 - - + -
87H MET* 3.3 21.3 - - + -
270H ALA 3.3 13.5 - - - +
271H TYR* 2.7 33.4 + + - +
273H SER* 1.3 78.5 + - - +
275H GLU* 1.3 59.6 + - + -
277H MET* 3.0 6.0 + - - +
278H LEU* 2.6 53.9 + - + +
289H THR* 5.1 2.0 - - - -
291H LEU* 5.1 3.4 - - + -
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Residues in contact with GLU 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ASP* 3.5 6.5 - - - +
32H LYS* 3.1 34.5 + - - +
271H TYR* 2.6 57.2 + - + +
272H THR* 4.0 4.0 - - - +
274H PHE* 1.3 77.7 - - + +
276H ALA* 1.3 64.9 + - - +
278H LEU* 4.0 9.6 - - + -
279H GLU* 2.9 31.5 + - - +
456H LYS* 2.7 42.2 + - + +
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Residues in contact with ALA 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H LEU* 4.8 2.5 - - + -
272H THR 2.9 18.6 + - - +
273H SER 3.8 3.1 - - - +
275H GLU* 1.3 79.4 - - - +
277H MET* 1.3 63.7 + - - +
279H GLU* 3.6 4.9 + - - +
280H MET* 3.4 23.0 + - - +
456H LYS* 4.0 15.1 - - + +
459H TYR* 3.7 27.1 - - + -
460H SER* 3.8 21.3 - - - +
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Residues in contact with MET 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H TYR* 4.0 9.7 + - - +
87H MET* 3.2 43.1 - - + +
88H PHE 3.9 9.9 - - - +
89H LEU* 4.1 7.0 - - + +
102H LEU* 4.8 5.8 - - + +
273H SER 3.0 14.9 + - - +
274H PHE 3.0 4.7 + - - +
276H ALA* 1.3 75.4 - - - +
278H LEU* 1.3 65.7 + - - +
280H MET* 3.3 19.2 - - - +
287H CYS* 3.1 45.1 - - - +
288H ILE* 3.4 9.0 - - - -
289H THR* 3.0 28.7 - - - +
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Residues in contact with LEU 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H ALA* 4.9 2.5 - - + -
53H GLU* 3.2 49.5 - - + +
55H SER* 4.9 9.4 - - - +
57H TYR* 4.6 6.2 + - - -
75H LYS* 5.3 6.4 + - - -
274H PHE* 2.6 41.9 + - + +
275H GLU* 3.4 9.9 - - + +
277H MET* 1.3 71.5 - - - +
279H GLU* 1.3 69.4 + - + +
280H MET* 2.9 13.7 + - - +
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Residues in contact with GLU 279 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H GLU* 2.9 23.4 + - - +
276H ALA* 3.8 6.7 - - - +
278H LEU* 1.3 80.5 - - + +
280H MET* 1.3 57.8 + - - +
281H LYS* 3.6 12.0 + - - +
456H LYS* 3.5 31.0 + - - -
460H SER* 5.6 5.3 - - - -
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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