Contacts of the helix formed by residues 263 - 279 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W ASN* 5.3 0.9 - - - -
108W SER* 3.6 18.6 + - - -
262W TYR* 1.3 84.5 - - - +
264W GLN* 1.3 66.4 + - - +
265W ASP* 2.7 10.4 + - - +
267W ARG* 2.9 41.3 - - - +
445W GLU* 3.4 7.3 + - - -
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Residues in contact with GLN 264 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W ASN* 5.1 3.7 + - - +
37W ASN* 4.8 10.4 + - - +
259W VAL* 2.7 35.1 - - - +
260W MET 3.9 0.5 - - - -
261W GLY* 3.0 31.6 + - - +
262W TYR 3.1 3.6 + - - +
263W GLY* 1.3 74.9 - - - +
265W ASP* 1.3 56.1 + - - +
266W ASP 2.9 10.6 + - - -
268W ILE* 3.2 42.1 + - - +
343W VAL* 3.8 0.3 - - - +
437W LEU* 3.6 9.0 - - + +
445W GLU* 2.8 28.9 + - + +
447W SER* 2.7 31.8 + - - -
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Residues in contact with ASP 265 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105W HIS* 3.2 6.9 + - - +
107W ASP 4.3 0.5 - - - +
108W SER* 3.5 17.8 + - - +
109W PRO* 5.1 2.5 - - + -
263W GLY 2.7 9.4 + - - +
264W GLN* 1.3 69.2 - - - +
266W ASP* 1.3 56.2 + - - +
267W ARG* 2.7 13.7 + - - +
296W GLU* 3.0 13.8 - - - +
343W VAL* 3.4 12.3 - - + +
437W LEU* 3.7 0.9 - - - +
440W MSE 3.0 12.8 - - - +
441W HIS* 3.0 12.1 + - + -
445W GLU* 3.0 21.7 + - - +
6045W MN 2.6 22.0 + - - -
6046W MN 2.5 24.7 + - - -
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Residues in contact with ASP 266 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104W ALA* 3.2 5.2 - - - +
105W HIS* 2.4 68.0 + - + +
264W GLN 2.9 4.8 + - - -
265W ASP* 1.3 72.4 + - - +
267W ARG* 1.3 48.8 + - - +
268W ILE 2.9 6.3 - - - +
269W CYS* 2.8 10.9 + - - +
270W ALA* 2.6 34.1 + - - +
341W SER 2.7 24.9 - - - +
342W ASP* 2.9 18.6 - - - +
343W VAL* 3.3 15.6 - - - +
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Residues in contact with ARG 267 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W ASN* 4.9 2.3 + - - +
36W SER* 5.6 5.2 - - - +
37W ASN* 4.6 14.6 - - + +
40W THR* 3.6 11.9 + - - -
41W GLU* 3.3 43.9 + - - +
43W GLU* 4.3 6.7 - - - +
45W VAL* 4.1 23.9 - - + +
105W HIS 4.2 3.5 + - - -
106W ILE* 2.8 29.7 + - - +
107W ASP* 3.9 0.8 - - - +
108W SER* 3.6 28.8 + - - +
110W ARG* 6.0 1.2 - - - +
262W TYR* 4.0 5.7 + - - -
263W GLY* 2.9 34.6 - - - +
264W GLN* 4.8 0.2 - - - -
265W ASP 2.7 10.9 + - - +
266W ASP* 1.3 72.7 - - - +
268W ILE* 1.3 56.9 + - - +
270W ALA* 3.7 11.1 - - + +
271W TYR* 3.1 25.3 + - - +
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Residues in contact with ILE 268 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W ASN* 3.9 20.0 - - - +
264W GLN* 3.2 46.2 + - - +
266W ASP 4.4 0.2 - - - +
267W ARG* 1.3 77.2 - - - +
269W CYS* 1.3 67.6 + - - +
271W TYR* 3.3 5.2 + - - +
272W THR* 3.1 25.3 + - - +
343W VAL* 3.6 22.0 - - + -
435W VAL* 3.9 23.6 - - + -
437W LEU* 4.7 0.4 - - + -
447W SER* 3.7 10.5 - - - +
452W ILE* 3.7 35.7 - - + -
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Residues in contact with CYS 269 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104W ALA* 4.5 1.8 - - + -
266W ASP* 2.8 22.3 + - - +
268W ILE* 1.3 80.5 - - - +
270W ALA* 1.3 54.6 + - - +
271W TYR 3.0 1.8 - - - -
272W THR* 3.0 8.0 + - - -
273W SER* 2.6 41.3 + - - -
341W SER* 3.4 17.7 - - - +
342W ASP 4.0 3.4 - - - -
343W VAL 4.1 7.0 - - - -
434W GLY* 3.4 33.2 - - - -
435W VAL* 3.8 15.0 - - - -
459W TYR* 3.7 7.5 - - - +
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Residues in contact with ALA 270 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45W VAL* 5.9 2.9 - - + -
49W ILE* 4.8 3.1 - - - +
104W ALA* 3.8 12.1 - - + +
105W HIS 4.4 1.6 - - - +
106W ILE* 4.0 17.3 - - + -
266W ASP 2.6 19.6 + - - +
267W ARG* 3.7 13.5 - - + +
269W CYS* 1.3 72.4 - - - +
271W TYR* 1.3 59.2 + - - +
273W SER* 2.8 15.8 + - - -
274W PHE* 3.3 13.2 + - - +
291W LEU* 3.9 26.8 - - + +
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Residues in contact with TYR 271 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W ASP* 4.6 5.4 - - - -
32W LYS* 2.9 20.0 - - + +
33W ASN* 3.5 37.9 - - + +
36W SER* 3.7 27.4 - - - +
45W VAL* 6.4 0.2 - - + -
49W ILE* 5.4 9.6 - - + -
267W ARG 3.1 16.2 + - - +
268W ILE 3.6 4.9 - - - +
269W CYS 3.0 0.8 - - - -
270W ALA* 1.3 75.6 - - - +
272W THR* 1.3 68.3 + - + +
273W SER 3.1 1.3 - - - -
274W PHE* 2.7 37.3 + + + +
275W GLU* 2.6 52.7 + - + +
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Residues in contact with THR 272 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W ASP* 5.2 3.4 - - - +
268W ILE* 3.1 14.5 + - + +
269W CYS* 3.0 12.3 + - - -
271W TYR* 1.3 84.9 - - + +
273W SER* 1.3 67.8 + - - +
275W GLU* 3.4 2.5 + - - +
276W ALA* 2.9 26.7 + - - +
435W VAL* 5.6 0.9 - - + -
452W ILE* 3.7 42.2 - - + +
455W THR* 3.6 6.1 - - + +
456W LYS* 3.9 27.8 - - + +
459W TYR* 3.2 14.2 - - - -
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Residues in contact with SER 273 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102W LEU* 3.9 24.5 - - - +
103W GLY 5.6 0.7 - - - -
104W ALA* 4.6 3.3 - - - +
269W CYS 2.6 24.6 + - - -
270W ALA* 2.8 22.3 + - - -
272W THR* 1.3 78.0 + - - +
274W PHE* 1.3 56.5 + - - +
276W ALA* 3.8 1.1 - - - +
277W MET* 3.0 30.3 + - - +
289W THR* 4.1 5.6 + - - +
291W LEU* 4.4 7.3 - - - +
341W SER* 5.2 3.1 - - - -
459W TYR* 3.3 22.4 - - - -
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Residues in contact with PHE 274 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W ILE* 3.2 49.6 - - + -
52W ALA* 4.0 11.7 - - + -
53W GLU* 3.2 38.4 - - + -
87W MET* 3.3 20.6 - - + -
270W ALA 3.3 12.3 - - - +
271W TYR* 2.7 30.7 + + - +
273W SER* 1.3 79.7 + - - +
275W GLU* 1.3 62.2 + - + +
277W MET* 3.0 6.4 + - - +
278W LEU* 2.6 51.2 + - + +
289W THR* 5.1 1.6 - - - -
291W LEU* 5.1 3.6 - - + -
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Residues in contact with GLU 275 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W ASP* 3.5 7.1 - - - +
32W LYS* 3.1 32.8 + - - +
271W TYR* 2.6 52.7 + - + +
272W THR* 4.0 4.0 - - - +
274W PHE* 1.3 81.0 - - + +
276W ALA* 1.3 64.8 + - - +
278W LEU* 3.5 10.3 - - + +
279W GLU* 2.8 30.6 + - - +
456W LYS* 2.6 43.6 + - + +
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Residues in contact with ALA 276 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102W LEU* 4.8 2.7 - - + -
272W THR 2.9 17.9 + - - +
273W SER 3.8 3.1 - - - +
275W GLU* 1.3 78.8 - - - +
277W MET* 1.3 62.9 + - - +
279W GLU* 3.6 5.6 + - - +
280W MET* 3.4 24.0 + - - +
456W LYS* 4.0 14.2 - - + +
459W TYR* 3.7 27.8 - - + -
460W SER* 3.8 20.7 - - - +
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Residues in contact with MET 277 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57W TYR* 4.0 10.2 + - - +
87W MET* 3.2 44.6 - - + +
88W PHE 3.9 8.7 - - - +
89W LEU* 4.1 7.2 - - + +
102W LEU* 4.8 6.4 - - + +
273W SER 3.0 15.1 + - - +
274W PHE 3.0 4.4 + - - +
276W ALA* 1.3 75.6 - - - +
278W LEU* 1.3 64.3 + - - +
280W MET* 3.2 20.5 - - - +
287W CYS* 3.1 44.6 - - - +
288W ILE* 3.4 7.9 - - - -
289W THR* 3.0 28.0 - - - +
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Residues in contact with LEU 278 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52W ALA* 4.9 1.8 - - + -
53W GLU* 3.2 50.4 - - + +
55W SER* 4.9 9.2 - - - +
57W TYR* 4.5 6.8 + - - -
75W LYS* 5.3 6.2 + - - -
274W PHE* 2.6 41.3 + - + +
275W GLU* 3.5 9.0 - - + +
277W MET* 1.3 71.1 - - - +
279W GLU* 1.3 68.2 + - + +
280W MET 2.9 14.3 + - - +
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Residues in contact with GLU 279 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275W GLU* 2.8 23.3 + - - +
276W ALA* 3.8 6.3 - - - +
278W LEU* 1.3 80.6 - - + +
280W MET* 1.3 58.0 + - - +
281W LYS* 3.6 13.0 + - - +
456W LYS* 3.6 30.3 + - - -
460W SER* 5.6 6.7 - - - -
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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