Contacts of the helix formed by residues 263 - 279 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ASN* 5.3 0.9 - - - -
108G SER* 3.7 18.0 + - - -
262G TYR* 1.3 83.9 - - - +
264G GLN* 1.3 65.9 + - - +
265G ASP* 2.7 10.6 + - - +
267G ARG* 2.9 41.0 - - - +
445G GLU* 3.4 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 264 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ASN* 5.1 3.4 + - - +
37G ASN* 4.9 10.5 - - - +
259G VAL* 2.7 35.6 - - - +
260G MET 3.9 0.7 - - - -
261G GLY* 3.0 31.6 + - - +
262G TYR 3.2 3.6 + - - +
263G GLY* 1.3 70.7 - - - +
265G ASP* 1.3 54.6 + - - +
266G ASP 2.8 11.1 + - - -
267G ARG* 4.9 0.4 - - - -
268G ILE* 3.2 43.4 + - - +
343G VAL* 3.8 0.3 - - - +
437G LEU* 3.6 9.5 - - + +
445G GLU* 2.8 33.9 + - + +
447G SER* 2.8 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G HIS* 3.2 4.2 + - - +
107G ASP 4.3 0.5 - - - +
108G SER* 3.5 18.0 + - - +
109G PRO* 5.1 2.0 - - + -
263G GLY 2.7 8.9 + - - +
264G GLN* 1.3 68.0 - - - +
266G ASP* 1.3 57.1 + - - +
267G ARG* 2.6 13.9 + - - +
296G GLU* 2.9 14.3 - - - +
343G VAL* 3.4 13.0 - - + +
437G LEU* 3.6 2.0 - - - +
440G MSE 3.1 11.1 - - - +
441G HIS* 3.0 17.0 + - + -
445G GLU* 3.0 21.4 + - - +
6013G MN 2.8 18.4 + - - -
6014G MN 2.3 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 266 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G ALA* 3.2 4.3 - - - +
105G HIS* 2.4 69.2 + - + +
264G GLN 2.8 5.4 + - - -
265G ASP* 1.3 72.5 + - - +
267G ARG* 1.3 48.6 + - - +
268G ILE 2.9 6.3 - - - +
269G CYS* 2.8 9.6 + - - +
270G ALA* 2.6 34.5 + - - +
341G SER 2.7 26.1 - - - +
342G ASP* 2.8 19.1 - - - +
343G VAL* 3.3 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ASN* 4.9 2.2 + - - +
36G SER* 5.7 4.3 - - - +
37G ASN* 4.6 14.3 - - + +
40G THR* 3.6 11.0 + - - -
41G GLU* 3.3 44.0 + - - +
43G GLU* 4.3 6.1 - - - +
45G VAL* 4.1 23.3 - - + +
105G HIS 4.2 3.3 + - - -
106G ILE* 2.8 30.1 + - - +
107G ASP* 3.9 1.0 - - - +
108G SER* 3.6 29.2 + - - +
110G ARG* 6.0 0.8 - - - +
262G TYR* 4.0 5.3 + - - -
263G GLY* 2.9 34.9 - - - +
264G GLN* 4.9 0.2 - - - -
265G ASP 2.6 11.9 + - - +
266G ASP* 1.3 72.9 - - - +
268G ILE* 1.3 56.3 + - - +
270G ALA* 3.7 10.4 - - + +
271G TYR* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ASN* 3.9 23.3 - - - +
264G GLN* 3.2 45.1 + - - +
266G ASP 4.4 0.2 - - - +
267G ARG* 1.3 77.5 - - - +
269G CYS* 1.3 68.8 + - - +
271G TYR* 3.3 2.4 + - - +
272G THR* 3.1 24.4 + - - +
343G VAL* 3.6 21.5 - - + -
435G VAL* 3.9 23.1 - - + -
437G LEU* 4.7 0.7 - - + -
447G SER* 3.8 10.5 - - - +
452G ILE* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 269 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G ALA* 4.4 1.8 - - + -
266G ASP* 2.8 22.1 + - - +
268G ILE* 1.3 86.4 - - - +
270G ALA* 1.3 53.0 + - - +
271G TYR 3.0 2.0 - - - -
272G THR* 3.0 7.9 + - - -
273G SER* 2.6 42.1 + - - -
341G SER* 3.4 18.4 - - - +
342G ASP 4.0 3.1 - - - -
343G VAL* 4.1 7.4 - - - -
434G GLY* 3.4 32.8 - - - -
435G VAL* 3.7 12.6 - - - -
459G TYR* 3.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G VAL* 5.9 2.5 - - + -
49G ILE* 4.9 3.4 - - + +
104G ALA* 3.8 11.8 - - + +
105G HIS 4.3 1.6 - - - +
106G ILE* 4.0 17.9 - - + -
266G ASP 2.6 19.7 + - - +
267G ARG* 3.7 12.8 - - + +
269G CYS* 1.3 71.8 - - - +
271G TYR* 1.3 56.7 + - - +
273G SER* 2.8 17.1 + - - -
274G PHE* 3.3 14.9 + - - +
291G LEU* 3.9 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 271 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASP* 4.6 4.9 - - - -
32G LYS* 2.8 20.2 + - + +
33G ASN* 3.5 38.8 - - + +
36G SER* 3.7 27.6 - - - +
45G VAL* 6.4 0.2 - - + -
49G ILE* 5.4 10.1 - - + -
267G ARG 3.1 16.9 + - - +
268G ILE 3.6 5.8 - - - +
269G CYS 3.0 0.4 - - - -
270G ALA* 1.3 75.6 - - - +
272G THR* 1.3 68.3 + - + +
273G SER 3.1 1.3 - - - -
274G PHE* 2.7 37.3 + + + +
275G GLU* 2.7 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASP* 5.2 3.1 - - - +
268G ILE* 3.1 14.5 + - + +
269G CYS* 3.0 12.6 + - - -
271G TYR* 1.3 82.9 - - + +
273G SER* 1.3 62.9 + - - +
275G GLU* 3.9 2.4 - - - +
276G ALA* 2.9 32.2 + - - +
435G VAL* 5.6 0.7 - - + -
452G ILE* 3.7 41.7 - - + +
455G THR* 3.6 6.2 - - + +
456G LYS* 3.9 27.0 - - + +
459G TYR* 3.2 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 273 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LEU* 3.8 25.5 - - - +
103G GLY 5.6 0.4 - - - -
104G ALA* 4.6 3.3 - - - +
269G CYS 2.6 24.1 + - - -
270G ALA* 2.8 21.8 + - - -
272G THR* 1.3 78.2 + - - +
274G PHE* 1.3 56.8 + - - +
276G ALA* 4.4 0.2 - - - -
277G MET* 3.0 30.5 + - - +
289G THR* 4.1 5.5 + - - +
291G LEU* 4.4 7.6 - - - +
341G SER* 5.2 2.9 - - - -
459G TYR* 3.3 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ILE* 3.2 50.5 - - + -
52G ALA* 4.0 11.7 - - + -
53G GLU* 3.2 36.3 - - + -
87G MET* 3.3 20.0 - - + -
270G ALA 3.3 12.6 - - - +
271G TYR* 2.7 29.5 + + - +
273G SER* 1.3 78.7 + - - +
275G GLU* 1.3 63.4 + - + +
277G MET* 3.0 6.1 + - - +
278G LEU* 2.6 53.4 + - + +
289G THR* 5.1 2.5 - - - -
291G LEU* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASP* 3.5 6.8 - - - +
32G LYS* 3.0 33.3 + - - +
271G TYR* 2.7 56.5 + - + +
272G THR* 4.0 4.3 - - - +
274G PHE* 1.3 77.7 - - + +
276G ALA* 1.3 65.4 + - - +
278G LEU* 3.0 10.3 + - + -
279G GLU* 2.9 30.6 + - - +
456G LYS* 2.7 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LEU* 4.8 2.9 - - + -
272G THR 2.9 19.3 + - - +
273G SER 3.8 2.9 - - - +
275G GLU* 1.3 78.8 - - - +
277G MET* 1.3 61.9 + - - +
279G GLU* 3.6 6.3 + - - +
280G MET* 3.4 24.3 + - - +
456G LYS* 4.0 14.4 - - + +
459G TYR* 3.7 27.6 - - + -
460G SER* 3.8 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 277 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TYR* 4.0 9.8 + - - +
87G MET* 3.2 43.3 - - + +
88G PHE 3.9 9.6 - - - +
89G LEU* 4.1 7.4 - - + +
102G LEU* 4.8 5.3 - - + +
273G SER 3.0 14.2 + - - +
274G PHE 3.0 4.3 + - - +
276G ALA* 1.3 75.6 - - - +
278G LEU* 1.3 65.5 + - - +
280G MET* 3.3 19.4 - - - +
287G CYS* 3.1 45.3 - - - +
288G ILE* 3.4 9.0 - - - -
289G THR* 3.0 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ALA* 4.9 2.0 - - + -
53G GLU* 3.2 49.3 - - + +
55G SER* 4.9 9.6 - - - +
57G TYR* 4.6 6.5 + - - -
75G LYS* 5.3 6.4 + - - -
274G PHE* 2.6 43.0 + - + +
275G GLU* 3.4 9.4 - - + +
277G MET* 1.3 71.9 - - - +
279G GLU* 1.3 69.3 + - + +
280G MET 2.9 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G GLU* 2.9 23.6 + - - +
276G ALA* 3.9 7.0 - - - +
278G LEU* 1.3 80.2 - - + +
280G MET* 1.3 58.5 + - - +
281G LYS* 3.6 12.5 + - - +
456G LYS* 3.5 30.8 + - - -
460G SER* 5.6 6.4 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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