Contacts of the helix formed by residues 263 - 279 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ASN* 5.3 0.9 - - - -
108S SER* 3.6 17.4 + - - -
262S TYR* 1.3 90.2 - - - +
264S GLN* 1.3 66.1 + - - +
265S ASP* 2.6 11.0 + - - +
267S ARG* 2.9 34.9 - - - +
445S GLU* 3.3 7.1 + - - -
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Residues in contact with GLN 264 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S ASN* 5.1 3.6 + - - -
37S ASN* 4.8 9.9 + - - +
259S VAL* 2.7 33.3 - - - +
260S MET 3.9 0.3 - - - -
261S GLY* 3.0 33.2 + - - +
262S TYR 3.2 3.0 + - - +
263S GLY* 1.3 75.4 - - - +
265S ASP* 1.3 56.5 + - - +
266S ASP 2.8 10.2 + - - -
267S ARG* 4.9 0.2 - - - -
268S ILE* 3.2 43.1 + - - +
343S VAL* 3.8 0.3 - - - +
437S LEU* 3.6 9.7 - - + +
445S GLU* 2.8 27.8 + - + +
447S SER* 2.8 32.3 + - - -
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Residues in contact with ASP 265 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105S HIS* 3.1 4.8 + - - +
107S ASP 4.2 0.7 - - - +
108S SER* 3.4 17.8 + - - +
109S PRO* 5.1 2.7 - - + -
263S GLY 2.6 8.7 + - - +
264S GLN* 1.3 68.6 - - - +
266S ASP* 1.3 56.7 + - - +
267S ARG* 2.6 13.5 + - - +
296S GLU* 3.0 12.6 - - - +
343S VAL* 3.4 13.6 - - + +
437S LEU* 3.7 1.8 - - - +
440S MSE 3.0 13.3 - - - +
441S HIS* 3.0 11.8 + - + -
445S GLU* 3.0 21.7 + - - +
6037S MN 2.8 21.5 + - - -
6038S MN 2.2 29.8 + - - -
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Residues in contact with ASP 266 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104S ALA* 3.2 5.1 - - - +
105S HIS* 2.4 68.4 + - + +
264S GLN 2.8 5.4 + - - -
265S ASP* 1.3 71.7 + - - +
267S ARG* 1.3 48.5 + - - +
268S ILE 2.9 5.8 - - - +
269S CYS* 2.8 9.8 + - - +
270S ALA* 2.6 34.3 + - - +
341S SER 2.7 24.6 - - - +
342S ASP* 2.9 18.5 - - - +
343S VAL* 3.3 14.9 - - - +
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Residues in contact with ARG 267 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S ASN* 4.9 3.0 + - - +
36S SER* 5.7 4.3 - - - +
37S ASN* 4.6 15.5 - - + +
40S THR* 3.6 11.5 + - - -
41S GLU* 3.3 44.4 + - - +
43S GLU* 4.3 6.7 - - - +
45S VAL* 4.0 23.7 - - + +
105S HIS 4.2 3.9 + - - -
106S ILE* 2.8 29.3 + - - +
107S ASP* 3.9 1.0 - - - +
108S SER* 3.7 29.0 + - - +
110S ARG* 6.0 1.2 - - - +
262S TYR* 4.0 5.5 + - - -
263S GLY* 2.9 33.8 - - - +
265S ASP 2.6 11.2 + - - +
266S ASP* 1.3 72.2 - - - +
268S ILE* 1.3 56.5 + - - +
270S ALA* 3.7 11.4 - - + +
271S TYR* 3.1 25.8 + - - +
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Residues in contact with ILE 268 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S ASN* 3.9 24.2 - - - +
264S GLN* 3.2 44.2 + - - +
266S ASP 2.9 0.4 - - - -
267S ARG* 1.3 77.0 - - - +
269S CYS* 1.3 67.3 + - - +
271S TYR* 3.4 1.7 + - - +
272S THR* 3.1 25.0 + - - +
343S VAL* 3.6 21.3 - - + -
435S VAL* 3.8 24.2 - - + -
437S LEU* 4.8 0.4 - - + -
447S SER* 3.7 11.0 - - - +
452S ILE* 3.7 35.4 - - + -
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Residues in contact with CYS 269 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104S ALA* 4.4 0.9 - - + -
266S ASP* 2.8 16.4 + - - +
268S ILE* 1.3 80.3 - - - +
270S ALA* 1.3 54.7 + - - +
271S TYR 3.0 2.2 - - - -
272S THR* 3.1 7.0 + - - -
273S SER* 2.6 42.0 + - - -
341S SER* 3.4 19.7 - - - +
342S ASP 4.0 6.3 - - - -
343S VAL 4.2 5.6 - - - -
434S GLY* 3.4 33.7 - - - -
435S VAL* 3.7 17.0 - - - -
459S TYR* 3.6 7.7 - - - +
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Residues in contact with ALA 270 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S VAL* 5.9 2.2 - - + -
49S ILE* 4.8 2.7 - - - +
104S ALA* 3.8 12.5 - - + +
105S HIS 4.4 1.8 - - - +
106S ILE* 4.0 19.7 - - + -
266S ASP 2.6 20.2 + - - +
267S ARG* 3.7 10.5 - - + +
269S CYS* 1.3 72.9 - - - +
271S TYR* 1.3 58.1 + - - +
273S SER* 2.8 16.1 + - - -
274S PHE* 3.3 15.4 + - - +
291S LEU* 3.9 26.9 - - + +
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Residues in contact with TYR 271 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S ASP* 4.6 5.2 - - - -
32S LYS* 2.8 20.9 - - + +
33S ASN* 3.5 39.0 - - + +
36S SER* 3.7 28.3 - - - +
45S VAL* 6.4 0.2 - - + -
49S ILE* 5.4 9.9 - - + -
267S ARG 3.1 17.2 + - - +
268S ILE 3.6 5.4 - - - +
269S CYS 3.0 0.6 - - - -
270S ALA* 1.3 76.6 - - - +
272S THR* 1.3 64.6 + - + +
273S SER 3.1 1.1 - - - -
274S PHE* 2.7 40.6 + + + +
275S GLU* 2.7 52.5 + - + +
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Residues in contact with THR 272 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S ASP* 5.2 3.4 - - - +
268S ILE* 3.1 15.6 + - + +
269S CYS* 3.1 11.8 + - - -
271S TYR* 1.3 82.9 - - + +
273S SER* 1.3 69.2 + - - +
274S PHE 3.1 0.2 + - - -
275S GLU* 3.3 2.8 + - - +
276S ALA* 2.9 26.3 + - - +
435S VAL* 5.6 0.9 - - + -
452S ILE* 3.7 41.7 - - + +
455S THR* 3.6 6.7 - - + +
456S LYS* 4.0 26.4 - - + +
459S TYR* 3.2 15.3 - - - -
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Residues in contact with SER 273 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S LEU* 3.8 25.4 - - - +
103S GLY 5.6 0.2 - - - -
104S ALA* 4.6 3.3 - - - +
269S CYS 2.6 24.5 + - - -
270S ALA* 2.8 21.3 + - - -
272S THR* 1.3 77.2 + - - +
274S PHE* 1.3 55.0 + - - +
276S ALA* 4.0 0.4 - - - -
277S MET* 3.0 29.8 + - - +
289S THR* 4.0 5.9 + - - +
291S LEU* 4.4 7.5 - - - +
341S SER* 5.2 3.1 - - - -
459S TYR* 3.3 23.6 - - - -
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Residues in contact with PHE 274 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S ILE* 3.2 50.0 - - + -
52S ALA* 4.0 12.3 - - + -
53S GLU* 3.2 37.2 - - + -
87S MET* 3.3 20.9 - - + -
270S ALA 3.3 13.0 - - - +
271S TYR* 2.7 32.3 + + - +
273S SER* 1.3 79.0 + - - +
275S GLU* 1.3 59.5 - - + -
277S MET* 3.0 6.1 + - - +
278S LEU* 2.6 53.7 + - + +
289S THR* 5.1 2.2 - - - -
291S LEU* 5.1 3.4 - - + -
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Residues in contact with GLU 275 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S ASP* 3.5 7.1 - - - +
32S LYS* 3.1 32.1 + - - +
271S TYR* 2.7 55.8 + - + +
272S THR* 4.0 4.3 - - - +
274S PHE* 1.3 77.8 - - + +
276S ALA* 1.3 65.3 + - - +
278S LEU* 3.0 11.3 + - + +
279S GLU* 2.9 30.5 + - - +
456S LYS* 2.6 43.6 + - + +
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Residues in contact with ALA 276 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S LEU* 4.7 2.7 - - + -
272S THR 2.9 17.9 + - - +
273S SER 3.8 3.4 - - - +
275S GLU* 1.3 80.6 - - - +
277S MET* 1.3 62.2 + - - +
279S GLU* 3.6 4.9 + - - +
280S MET* 3.5 22.4 + - - +
456S LYS* 4.0 15.3 - - + +
459S TYR* 3.7 27.1 - - + -
460S SER* 3.8 21.8 - - - +
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Residues in contact with MET 277 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57S TYR* 4.0 10.6 + - - +
87S MET* 3.1 47.1 - - + +
88S PHE 3.9 9.4 - - - +
89S LEU* 4.2 7.0 - - + +
102S LEU* 4.8 6.8 - - + +
273S SER 3.0 11.0 + - - +
274S PHE 3.0 4.3 + - - +
276S ALA* 1.3 78.3 - - - +
278S LEU* 1.3 65.6 + - - +
280S MET* 3.2 19.3 - - - +
287S CYS* 3.1 41.1 - - - +
288S ILE* 3.4 8.5 - - - -
289S THR* 3.1 29.2 - - - +
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Residues in contact with LEU 278 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S ALA* 4.9 2.5 - - + -
53S GLU* 3.2 49.4 - - + +
55S SER* 4.9 9.4 - - - +
57S TYR* 4.5 7.2 + - - -
75S LYS* 5.3 6.2 + - - -
274S PHE* 2.6 41.9 + - + +
275S GLU* 3.4 9.0 - - + +
277S MET* 1.3 71.4 - - - +
279S GLU* 1.3 68.6 + - + +
280S MET 2.9 14.1 + - - +
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Residues in contact with GLU 279 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275S GLU* 2.9 24.4 + - - +
276S ALA* 3.8 6.7 - - - +
278S LEU* 1.3 79.1 - - + +
280S MET* 1.3 57.7 + - - +
281S LYS* 3.7 11.3 + - - +
456S LYS* 3.5 29.5 + - - -
460S SER* 5.6 6.4 - - - -
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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