Contacts of the helix formed by residues 277 - 287 (chain B) in PDB entry 2Q06
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 PRO 277 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.0 16.6 - - + -
60B SER* 3.6 12.3 - - - +
64B GLU* 3.2 10.3 - - - +
139B TRP* 3.4 36.8 - - + +
276B LEU* 1.3 94.3 - - + +
278B ALA* 1.3 58.7 + - - +
279B CYS* 2.9 21.6 + - - -
280B VAL* 2.9 30.7 + - + +
281B TYR* 3.7 3.3 + - - -
307B LEU* 6.1 0.2 - - + -
312B VAL* 5.5 2.9 - - + -
329B VAL* 5.4 0.7 - - + -
333B CYS* 4.7 8.1 - - - -
381B LEU* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.8 25.1 - - + +
39B PHE* 5.9 2.9 - - + -
40B TYR* 3.5 31.5 - - + +
60B SER* 3.1 2.2 + - - +
63B ILE* 5.5 1.6 - - + -
64B GLU* 2.6 33.8 + - + +
136B MET* 5.0 4.3 - - - -
276B LEU 3.8 1.2 + - - -
277B PRO* 1.3 69.7 - - - +
279B CYS* 1.3 57.1 + - - +
280B VAL 3.4 0.2 - - - -
281B TYR* 3.6 6.6 + - - +
282B GLY 3.0 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.3 34.9 - - + +
54B GLY 3.7 7.6 - - - +
55B ARG* 4.7 7.2 - - - -
57B ILE* 4.7 2.7 - - - -
60B SER* 3.3 21.6 + - - -
277B PRO* 2.9 13.2 + - - -
278B ALA* 1.3 77.1 - - - +
280B VAL* 1.3 65.5 + - - +
282B GLY 2.9 0.5 + - - -
283B LEU* 2.8 40.0 + - + +
312B VAL* 4.1 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 4.2 10.1 - - + -
277B PRO* 2.9 34.9 + - + +
279B CYS* 1.3 77.2 - - - +
281B TYR* 1.3 62.5 + - + +
283B LEU* 3.5 6.7 + - - +
284B ALA* 3.1 26.0 + - - +
306B LEU* 3.8 31.5 - - + +
307B LEU* 4.1 22.2 - - + -
310B SER* 4.2 9.6 - - - -
312B VAL* 4.0 23.8 - - + -
381B LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.5 33.0 - - + +
36B ILE* 3.7 24.2 - - + -
37B GLY* 3.3 17.7 - - - +
135B HIS* 2.7 43.2 + + - -
274B SER 4.3 0.3 + - - -
276B LEU* 3.1 49.0 + - + +
277B PRO 3.7 3.3 + - - -
278B ALA* 3.6 3.9 + - - +
279B CYS 3.3 0.2 - - - -
280B VAL* 1.3 76.5 - - + +
282B GLY* 1.3 58.9 + - - +
284B ALA* 3.8 4.2 - - - +
285B VAL* 2.9 33.4 + - - +
291B PHE* 4.5 1.6 - + - -
296B TYR* 4.0 20.4 + + - -
306B LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY* 3.5 17.2 - - - -
40B TYR* 4.1 11.0 - - - -
41B ILE* 3.5 9.2 - - - +
278B ALA 3.0 13.2 + - - -
279B CYS 2.9 8.8 + - - -
281B TYR* 1.3 72.2 - - - +
283B LEU* 1.3 53.3 + - - -
284B ALA 3.0 1.3 - - - -
285B VAL* 2.9 7.3 + - - +
286B ALA 2.8 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 5.5 2.2 - - + -
44B CYS* 6.5 0.4 - - - -
51B ASP* 5.0 2.5 - - - +
54B GLY 4.6 7.4 - - - +
55B ARG* 3.1 60.3 - - + +
279B CYS* 2.8 30.3 + - + +
280B VAL* 4.5 4.3 - - - +
282B GLY* 1.3 70.6 - - - -
284B ALA* 1.3 53.8 + - - +
286B ALA* 3.5 10.7 - - + +
287B SER* 2.8 35.4 + - - -
310B SER* 5.7 3.4 - - - -
311B GLN 3.8 20.0 - - - +
312B VAL* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL 3.1 19.9 + - - +
281B TYR 3.8 0.4 - - - +
283B LEU* 1.3 73.5 - - - +
285B VAL* 1.3 59.0 + - - +
287B SER* 2.7 26.7 + - - -
289B TYR* 3.2 26.5 + - + +
291B PHE* 3.5 28.3 - - + -
306B LEU* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL 5.0 0.2 - - - +
34B GLY* 4.1 9.0 - - - +
37B GLY* 3.6 14.8 - - - -
38B ARG* 3.8 26.0 - - + +
41B ILE* 3.9 14.1 - - + -
281B TYR 2.9 20.6 + - - +
282B GLY 2.9 9.8 + - - +
284B ALA* 1.3 77.1 - - - +
286B ALA* 1.3 63.6 + - - +
287B SER 3.2 0.3 + - - -
288B GLY* 3.3 9.5 + - - -
289B TYR 3.7 16.1 + - - +
291B PHE* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 3.3 28.0 - - + +
282B GLY 2.8 11.0 + - - +
283B LEU* 3.5 12.1 - - + +
285B VAL* 1.3 77.4 - - - +
287B SER* 1.3 56.3 + - - +
288B GLY 3.2 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU 2.8 18.0 + - - -
284B ALA* 2.7 17.2 + - - -
286B ALA* 1.3 71.8 - - - +
288B GLY* 1.3 59.9 + - - +
289B TYR* 3.4 2.4 - - - +
----------------------------------------------------------
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