Contacts of the helix formed by residues 263 - 279 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U ASN* 5.4 0.9 - - - -
108U SER* 3.6 18.9 + - - -
262U TYR* 1.3 84.6 - - - +
264U GLN* 1.3 65.7 + - - +
265U ASP 2.6 11.0 + - - +
267U ARG* 3.0 40.1 - - - +
445U GLU* 3.3 7.5 + - - -
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Residues in contact with GLN 264 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U ASN* 5.1 3.6 + - - +
37U ASN* 4.8 9.7 + - - +
259U VAL* 2.7 34.3 - - - +
260U MET 3.9 0.5 - - - -
261U GLY* 3.0 32.0 + - - +
262U TYR 3.2 3.2 + - - +
263U GLY* 1.3 73.8 - - - +
265U ASP* 1.3 61.1 + - - +
266U ASP 2.9 4.3 + - - -
267U ARG* 4.0 0.4 - - - -
268U ILE* 3.2 44.6 + - - +
343U VAL* 3.8 0.5 - - - +
437U LEU* 3.6 9.2 - - + +
445U GLU* 2.8 32.6 + - + +
447U SER* 2.8 31.3 + - - -
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Residues in contact with ASP 265 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105U HIS* 3.2 5.4 + - - -
107U ASP 4.3 0.7 - - - +
108U SER* 3.5 17.0 + - - +
109U PRO* 5.1 1.8 - - + -
263U GLY 2.6 11.7 + - - +
264U GLN* 1.3 68.4 - - - +
266U ASP* 1.3 56.1 + - - +
267U ARG* 2.6 14.5 + - - +
296U GLU* 2.9 14.0 - - - +
342U ASP* 3.2 0.3 - - - +
343U VAL* 3.4 15.6 - - + +
437U LEU* 3.9 1.8 - - - -
440U MSE 3.1 10.6 - - - +
441U HIS* 3.0 14.7 + - + -
445U GLU* 3.0 21.2 + - - +
6041U MN 2.8 20.8 + - - -
6042U MN 2.5 25.3 + - - -
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Residues in contact with ASP 266 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104U ALA* 3.2 3.8 - - - +
105U HIS* 2.4 69.4 + - + +
264U GLN 2.9 5.2 + - - -
265U ASP* 1.3 73.3 + - - +
267U ARG* 1.3 48.7 + - - +
268U ILE 2.9 5.6 - - - +
269U CYS* 2.7 10.4 + - - +
270U ALA* 2.6 33.6 + - - +
341U SER 2.7 25.5 - - - +
342U ASP* 2.9 17.4 - - - +
343U VAL* 3.3 14.8 - - - +
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Residues in contact with ARG 267 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U ASN* 4.9 2.6 + - - +
36U SER* 5.7 4.7 - - - +
37U ASN* 4.6 15.2 - - + +
40U THR* 3.6 11.0 + - - -
41U GLU* 3.3 44.6 + - - +
43U GLU* 4.3 6.5 - - - +
45U VAL* 4.1 23.9 - - + +
105U HIS 4.2 3.9 + - - -
106U ILE* 2.8 29.4 + - - +
107U ASP* 4.1 1.4 - - - +
108U SER* 3.7 28.0 + - - +
110U ARG* 6.0 1.0 - - - +
262U TYR* 4.1 5.3 + - - -
263U GLY* 3.0 32.9 + - - +
264U GLN* 4.9 0.7 - - - -
265U ASP 2.6 11.2 + - - +
266U ASP* 1.3 72.3 - - - +
268U ILE* 1.3 59.3 + - - +
270U ALA* 3.7 10.2 - - + +
271U TYR* 3.2 22.0 + - - +
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Residues in contact with ILE 268 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U ASN* 3.9 23.6 - - - +
264U GLN* 3.2 45.1 + - - +
266U ASP 2.9 0.2 - - - -
267U ARG* 1.3 77.5 - - - +
269U CYS* 1.3 68.9 + - - +
271U TYR* 3.3 2.1 + - - +
272U THR* 3.1 24.3 + - - +
343U VAL* 3.6 22.9 - - + -
435U VAL* 3.8 24.5 - - + -
437U LEU* 4.7 0.4 - - + -
447U SER* 3.7 11.0 - - - +
452U ILE* 3.7 36.1 - - + -
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Residues in contact with CYS 269 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104U ALA* 4.5 0.9 - - + -
266U ASP* 2.7 17.5 + - - +
268U ILE* 1.3 79.7 - - - +
270U ALA* 1.3 54.6 + - - +
271U TYR 3.0 2.2 - - - -
272U THR* 3.0 8.0 + - - -
273U SER* 2.7 41.6 + - - -
341U SER* 3.4 18.6 - - - +
342U ASP 3.9 8.3 - - - -
343U VAL 4.1 7.4 - - - -
434U GLY* 3.4 33.9 - - - -
435U VAL* 3.7 15.0 - - - -
459U TYR* 3.7 6.7 - - - +
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Residues in contact with ALA 270 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45U VAL* 5.9 2.7 - - + -
49U ILE* 4.8 2.8 - - + +
104U ALA* 3.8 12.7 - - + +
105U HIS 4.4 1.1 - - - +
106U ILE* 4.0 17.9 - - + -
266U ASP 2.6 18.8 + - - +
267U ARG* 3.8 13.2 - - + +
269U CYS* 1.3 73.3 - - - +
271U TYR* 1.3 54.8 + - - +
273U SER* 2.8 16.8 + - - -
274U PHE* 3.3 14.7 + - - +
291U LEU* 3.9 26.7 - - + +
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Residues in contact with TYR 271 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U ASP* 4.6 4.5 - - - -
32U LYS* 2.9 21.2 + - + +
33U ASN* 3.5 39.7 - - + +
36U SER* 3.7 27.8 - - - +
45U VAL* 6.4 0.4 - - + -
49U ILE* 5.4 9.6 - - + -
267U ARG 3.2 17.0 + - - +
268U ILE 3.6 5.2 - - - +
269U CYS 3.0 0.6 - - - -
270U ALA* 1.3 76.0 - - - +
272U THR* 1.3 68.3 + - + +
273U SER 3.1 1.3 - - - -
274U PHE* 2.8 37.9 + + + +
275U GLU* 2.7 52.8 + - + +
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Residues in contact with THR 272 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U ASP* 5.2 3.6 - - - +
268U ILE* 3.1 14.6 + - + +
269U CYS* 3.0 12.5 + - - -
271U TYR* 1.3 83.0 - - + +
273U SER* 1.3 63.8 + - - +
275U GLU* 3.4 2.6 + - - +
276U ALA* 2.9 32.4 + - - +
435U VAL* 5.6 0.7 - - + -
452U ILE* 3.7 41.3 - - + +
455U THR* 3.6 6.5 - - + +
456U LYS* 3.9 26.8 - - + +
459U TYR* 3.1 14.8 - - - -
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Residues in contact with SER 273 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102U LEU* 3.9 24.0 - - - +
103U GLY 5.6 0.2 - - - -
104U ALA* 4.6 4.1 - - - +
269U CYS 2.7 24.6 + - - -
270U ALA* 2.8 21.5 + - - -
272U THR* 1.3 77.6 + - - +
274U PHE* 1.3 56.2 + - - +
276U ALA* 3.8 1.3 - - - +
277U MET* 2.9 30.7 + - - +
289U THR* 4.1 5.3 + - - +
291U LEU* 4.4 7.1 - - - +
341U SER* 5.2 3.1 - - - -
459U TYR* 3.3 22.9 - - - -
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Residues in contact with PHE 274 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U ILE* 3.2 50.0 - - + -
52U ALA* 3.9 11.2 - - + -
53U GLU* 3.2 37.2 - - + -
87U MET* 3.3 20.4 - - + -
270U ALA 3.3 12.8 - - - +
271U TYR* 2.8 30.4 + + - +
273U SER* 1.3 79.4 + - - +
275U GLU* 1.3 59.9 + - + +
277U MET* 2.9 7.2 + - - +
278U LEU* 2.6 53.2 + - + +
289U THR* 5.1 2.0 - - - -
291U LEU* 5.1 3.4 - - + -
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Residues in contact with GLU 275 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U ASP* 3.5 8.0 - - - +
32U LYS* 3.0 33.4 + - - +
271U TYR* 2.7 55.0 + - + +
272U THR* 4.0 4.7 - - - +
274U PHE* 1.3 77.2 - - + +
276U ALA* 1.3 64.6 - - - +
278U LEU* 4.0 10.7 - - + +
279U GLU* 2.9 30.4 + - - +
456U LYS* 2.6 41.9 + - + +
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Residues in contact with ALA 276 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U LEU* 4.8 2.5 - - + -
272U THR 2.9 18.5 + - - +
273U SER 3.8 3.1 - - - +
275U GLU* 1.3 80.4 - - - +
277U MET* 1.3 62.4 + - - +
279U GLU* 3.9 5.3 - - - +
280U MET* 3.4 23.0 + - - +
456U LYS* 4.0 14.9 - - + +
459U TYR* 3.7 27.8 - - + -
460U SER* 3.7 21.2 - - - +
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Residues in contact with MET 277 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57U TYR* 4.0 10.6 + - - +
87U MET* 3.2 42.4 - - + +
88U PHE 3.9 9.6 - - - +
89U LEU* 4.1 6.3 - - + +
102U LEU* 4.8 6.6 - - + +
273U SER 2.9 16.4 + - - +
274U PHE 3.4 2.9 - - - +
276U ALA* 1.3 75.9 - - - +
278U LEU* 1.3 65.1 + - - +
280U MET* 3.3 19.4 - - - +
287U CYS* 3.0 46.0 - - - +
288U ILE* 3.4 8.3 - - - -
289U THR* 3.0 28.0 - - - +
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Residues in contact with LEU 278 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52U ALA* 4.9 1.8 - - + -
53U GLU* 3.1 50.6 - - + +
55U SER* 4.9 9.4 - - - +
57U TYR* 4.5 6.6 + - - -
75U LYS* 5.3 6.4 + - - -
274U PHE* 2.6 41.3 + - + +
275U GLU* 3.5 9.6 - - + +
277U MET* 1.3 71.7 - - - +
279U GLU* 1.3 68.8 + - + +
280U MET 2.9 13.8 + - - +
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Residues in contact with GLU 279 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275U GLU* 2.9 23.3 + - - +
276U ALA* 3.9 6.1 - - - +
278U LEU* 1.3 81.9 - - + +
280U MET* 1.3 58.1 + - - +
281U LYS* 3.6 13.1 + - - +
456U LYS* 3.6 29.8 + - - -
460U SER* 5.6 6.6 - - - -
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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