Contacts of the helix formed by residues 263 - 279 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q ASN* 5.4 0.9 - - - -
108Q SER* 3.6 18.6 + - - -
262Q TYR* 1.3 84.1 - - - +
264Q GLN* 1.3 66.0 + - - +
265Q ASP* 2.6 10.8 + - - +
267Q ARG* 2.9 40.7 - - - +
445Q GLU* 3.3 7.3 + - - -
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Residues in contact with GLN 264 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q ASN* 5.1 3.2 + - - -
37Q ASN* 4.9 10.0 + - - +
259Q VAL* 2.7 35.6 - - - +
260Q MET 3.9 0.2 - - - -
261Q GLY* 3.0 31.8 + - - +
262Q TYR 3.1 3.0 + - - +
263Q GLY* 1.3 74.9 - - - +
265Q ASP* 1.3 55.2 - - - +
266Q ASP 2.8 11.1 + - - -
267Q ARG* 4.8 0.4 - - - -
268Q ILE* 3.2 42.7 + - - +
343Q VAL* 3.8 0.3 - - - +
437Q LEU* 3.6 9.4 - - + +
445Q GLU* 2.8 28.1 + - + +
446Q ILE 4.4 0.2 - - - -
447Q SER* 2.7 32.3 + - - -
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Residues in contact with ASP 265 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Q HIS* 3.1 6.2 + - - -
106Q ILE 5.8 0.2 - - - -
107Q ASP 4.3 0.5 - - - +
108Q SER* 3.5 15.7 + - - +
109Q PRO* 5.1 2.2 - - + -
263Q GLY 2.6 10.0 + - - +
264Q GLN* 1.3 68.9 - - - +
266Q ASP* 1.3 56.5 + - - +
267Q ARG* 2.6 14.6 + - - +
296Q GLU* 3.0 13.8 - - - +
343Q VAL* 3.4 14.7 - - + +
437Q LEU* 3.9 1.8 - - - -
440Q MSE 3.0 16.5 - - - +
441Q HIS* 3.0 8.1 + - + -
445Q GLU* 3.0 21.4 + - - +
6033Q MN 2.6 22.7 + - - -
6034Q MN 2.6 24.3 + - - -
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Residues in contact with ASP 266 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q ALA* 3.2 5.1 - - - +
105Q HIS* 2.4 62.8 + - + +
264Q GLN 2.8 5.2 + - - -
265Q ASP* 1.3 71.6 + - - +
267Q ARG* 1.3 48.1 + - - +
268Q ILE 2.9 5.8 - - - +
269Q CYS* 2.8 10.2 + - - +
270Q ALA* 2.6 34.7 + - - +
341Q SER 2.7 25.2 - - - +
342Q ASP* 2.8 25.2 - - - +
343Q VAL* 3.3 15.4 - - - +
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Residues in contact with ARG 267 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q ASN* 4.9 3.0 + - - +
36Q SER* 5.7 3.8 - - - +
37Q ASN* 4.6 15.9 - - + +
40Q THR* 3.6 11.3 + - - -
41Q GLU* 3.3 43.2 + - - +
42Q ARG* 4.9 0.2 - - - +
43Q GLU* 4.3 6.1 - - - +
45Q VAL* 4.1 23.9 - - + +
105Q HIS 4.2 3.9 + - - -
106Q ILE* 2.8 30.1 + - - +
107Q ASP* 3.9 1.2 - - - +
108Q SER* 3.6 29.7 + - - +
110Q ARG* 6.0 0.8 - - - +
262Q TYR* 4.0 5.1 + - - -
263Q GLY* 2.9 34.5 - - - +
264Q GLN* 4.8 0.4 - - - -
265Q ASP 2.6 11.4 + - - +
266Q ASP* 1.3 72.2 - - - +
268Q ILE* 1.3 55.7 + - - +
270Q ALA* 3.7 10.6 - - + +
271Q TYR* 3.2 25.3 + - - +
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Residues in contact with ILE 268 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q ASN* 3.9 23.7 - - - +
264Q GLN* 3.2 44.9 + - - +
266Q ASP 2.9 0.2 - - - -
267Q ARG* 1.3 77.4 - - - +
269Q CYS* 1.3 68.4 + - - +
271Q TYR* 3.4 2.6 + - - +
272Q THR* 3.1 24.0 + - + +
343Q VAL* 3.6 21.8 - - + -
435Q VAL* 3.9 24.0 - - + -
437Q LEU* 4.7 0.7 - - + -
447Q SER* 3.7 11.2 - - - +
452Q ILE* 3.7 36.6 - - + -
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Residues in contact with CYS 269 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q ALA* 4.5 1.1 - - + -
266Q ASP* 2.8 21.4 + - - +
268Q ILE* 1.3 84.6 - - - +
270Q ALA* 1.3 55.5 + - - +
271Q TYR 3.0 1.8 - - - -
272Q THR* 3.0 7.6 + - - -
273Q SER* 2.6 42.0 + - - -
341Q SER* 3.4 19.5 - - - +
342Q ASP 4.0 3.4 - - - -
343Q VAL* 4.1 7.9 - - - -
434Q GLY* 3.4 32.5 - - - -
435Q VAL* 3.7 12.1 - - - -
459Q TYR* 3.8 6.4 - - - +
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Residues in contact with ALA 270 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Q VAL* 5.9 2.7 - - + -
49Q ILE* 4.9 3.1 - - - +
104Q ALA* 3.8 12.1 - - + +
105Q HIS 4.4 1.3 - - - +
106Q ILE* 4.0 17.5 - - + -
266Q ASP 2.6 19.7 + - - +
267Q ARG* 3.7 12.8 - - + +
269Q CYS* 1.3 73.4 - - - +
271Q TYR* 1.3 58.4 + - - +
273Q SER* 2.8 17.2 + - - -
274Q PHE* 3.3 13.7 + - - +
291Q LEU* 3.9 26.0 - - + +
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Residues in contact with TYR 271 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q ASP* 4.6 5.2 - - - -
32Q LYS* 2.8 20.1 - - + +
33Q ASN* 3.5 39.5 - - + +
36Q SER* 3.7 28.0 - - - +
45Q VAL* 6.5 0.2 - - + -
49Q ILE* 5.4 9.9 - - + -
267Q ARG 3.2 16.8 + - - +
268Q ILE 3.6 5.4 - - - +
269Q CYS 3.0 0.8 - - - -
270Q ALA* 1.3 75.1 - - - +
272Q THR* 1.3 66.5 + - + +
273Q SER 3.1 1.1 - - - -
274Q PHE* 2.7 46.4 + + + +
275Q GLU* 2.7 47.1 + - + +
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Residues in contact with THR 272 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q ASP* 5.2 3.4 - - - +
33Q ASN* 6.2 0.2 - - + -
268Q ILE* 3.1 14.4 + - + +
269Q CYS* 3.0 12.5 + - - -
271Q TYR* 1.3 84.2 - - + +
273Q SER* 1.3 70.1 + - - +
275Q GLU* 3.9 2.6 - - - +
276Q ALA* 2.9 27.2 + - - +
435Q VAL* 5.6 0.7 - - + -
452Q ILE* 3.7 40.8 - - + +
455Q THR* 3.6 6.3 - - + +
456Q LYS* 4.0 27.3 - - + +
459Q TYR* 3.1 15.0 - - - -
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Residues in contact with SER 273 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q LEU* 3.8 24.8 - - - +
103Q GLY 5.6 0.9 - - - -
104Q ALA* 4.6 3.4 - - - +
269Q CYS 2.6 24.2 + - - -
270Q ALA* 2.8 22.3 + - - -
272Q THR* 1.3 78.1 + - - +
274Q PHE* 1.3 55.2 + - - +
276Q ALA* 3.8 1.3 - - - +
277Q MET* 3.0 30.1 + - - +
289Q THR* 4.0 6.6 + - - +
291Q LEU* 4.4 7.1 - - - +
341Q SER* 5.2 3.4 - - - -
459Q TYR* 3.2 22.7 - - - -
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Residues in contact with PHE 274 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q ILE* 3.2 50.9 - - + -
52Q ALA* 3.9 12.3 - - + -
53Q GLU* 3.2 36.1 - - + -
87Q MET* 3.4 20.6 - - + -
270Q ALA 3.3 12.8 - - - +
271Q TYR* 2.7 31.9 + + - +
273Q SER* 1.3 78.9 + - - +
275Q GLU* 1.3 60.3 + - + -
277Q MET* 3.0 6.4 + - - +
278Q LEU* 2.6 53.4 + - + +
289Q THR* 5.1 2.0 - - - -
291Q LEU* 5.1 3.6 - - + -
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Residues in contact with GLU 275 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q ASP* 3.5 6.3 - - - +
32Q LYS* 3.0 34.4 + - - +
271Q TYR* 2.7 53.5 + - + +
272Q THR* 4.0 3.8 - - - +
274Q PHE* 1.3 80.8 - - + +
276Q ALA* 1.3 65.7 + - - +
278Q LEU* 3.5 9.6 - - + +
279Q GLU* 2.9 30.9 + - - +
456Q LYS* 2.7 42.7 + - + +
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Residues in contact with ALA 276 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Q LEU* 4.8 2.5 - - + -
272Q THR 2.9 18.6 + - - +
273Q SER 3.8 2.5 - - - +
275Q GLU* 1.3 80.3 - - - +
277Q MET* 1.3 63.4 + - - +
279Q GLU* 3.6 4.9 + - - +
280Q MET* 3.4 23.1 + - - +
456Q LYS* 4.0 14.4 - - + +
459Q TYR* 3.7 28.3 - - + -
460Q SER* 3.8 21.1 - - - +
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Residues in contact with MET 277 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q TYR* 4.0 10.2 + - - +
87Q MET* 3.2 47.8 - - + +
88Q PHE 3.9 9.0 - - - +
89Q LEU* 4.2 6.8 - - + +
102Q LEU* 4.8 6.4 - - + +
273Q SER 3.0 15.2 + - - +
274Q PHE 3.4 2.7 - - - +
276Q ALA* 1.3 76.8 - - - +
278Q LEU* 1.3 65.4 + - - +
280Q MET* 3.2 20.3 - - - +
287Q CYS* 3.1 44.9 - - - +
288Q ILE* 3.4 7.9 - - - -
289Q THR* 3.0 25.6 - - - +
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Residues in contact with LEU 278 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Q ALA* 4.9 2.2 - - + -
53Q GLU* 3.1 49.9 - - + +
55Q SER* 4.9 9.2 - - - +
57Q TYR* 4.5 7.0 + - - -
75Q LYS* 5.3 6.2 + - - -
274Q PHE* 2.6 41.3 + - + +
275Q GLU* 3.5 9.6 - - + +
277Q MET* 1.3 76.6 - - - +
279Q GLU* 1.3 68.0 + - + +
280Q MET 2.9 9.5 + - - +
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Residues in contact with GLU 279 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Q GLU* 2.9 24.1 + - - +
276Q ALA* 3.8 6.5 - - - +
278Q LEU* 1.3 80.3 - - + +
280Q MET* 1.3 57.7 + - - +
281Q LYS* 3.7 12.0 + - - +
456Q LYS* 3.6 30.6 + - - -
460Q SER* 5.6 6.1 - - - -
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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