Contacts of the helix formed by residues 276 - 281 (chain A) in PDB entry 2QJK
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 HIS 276 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 3.6 22.3 + - - +
154A MET* 3.7 21.3 - - + -
275A GLY* 1.3 69.9 - - - -
277A PRO* 1.3 61.3 - - + +
278A ASP* 2.8 67.8 + - + +
279A ASN* 2.8 22.2 + - - +
280A TYR* 5.0 3.8 - - - -
291A HIS* 3.0 27.9 + - + +
293A VAL* 3.8 26.1 - - + +
294A PRO 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ASN 5.7 1.8 - - - +
275A GLY 3.1 11.2 - - - +
276A HIS* 1.3 91.6 - - + +
278A ASP* 1.3 64.1 + - - +
279A ASN 3.2 1.0 + - - -
280A TYR* 3.4 13.9 + - + +
281A ILE* 4.4 0.3 - - - +
105B LYS 3.9 18.2 - - - +
106B ALA* 3.4 34.5 - - - +
107B ARG* 4.3 4.7 - - - +
108B ALA* 4.5 9.6 - - + +
120B GLN* 5.5 3.1 - - - +
125B ILE* 4.3 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 3.2 13.8 - - + +
154A MET* 3.6 15.3 - - + -
276A HIS* 2.8 32.1 + - + +
277A PRO* 1.3 80.0 - - - +
279A ASN* 1.3 57.3 + - - +
280A TYR 3.1 5.6 - - - -
281A ILE* 3.1 32.5 + - + +
289A PRO* 3.0 28.8 - - - +
291A HIS* 4.6 9.4 + - - +
106B ALA 4.5 5.5 - - - +
107B ARG* 5.2 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.7 15.6 - - - -
94A ARG* 5.6 3.1 + - - +
147A TYR* 3.5 33.5 + - + +
150A PRO* 4.6 11.8 - - - +
152A GLY* 3.0 12.6 - - - -
153A GLN 4.2 0.4 - - - +
154A MET* 2.9 29.3 + - + +
155A SER* 2.9 26.3 + - - +
276A HIS 2.8 13.9 + - - +
278A ASP* 1.3 76.0 - - - +
280A TYR* 1.3 61.7 + - + +
281A ILE 3.0 8.4 + - - +
502A HEM 5.6 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.8 11.6 - + - -
81A GLU* 4.6 4.7 - - - -
84A MET* 4.5 0.5 - - - +
94A ARG* 4.5 22.3 + - - -
95A TYR* 3.6 9.9 + - - -
272A ASN* 2.5 29.7 + - + -
276A HIS 5.0 2.2 - - - -
277A PRO* 3.7 16.2 - - + +
278A ASP 3.1 1.2 - - - -
279A ASN* 1.3 82.7 - - + +
281A ILE* 1.3 62.5 + - - +
282A GLU 4.2 0.3 + - - -
102B LEU* 3.7 43.7 - - + +
105B LYS* 3.2 63.7 + - + +
106B ALA* 4.0 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 4.4 1.8 - - - -
152A GLY* 3.3 6.2 - - - -
153A GLN* 3.0 40.8 + - + +
277A PRO 4.4 3.1 - - - +
278A ASP* 3.1 28.7 - - + +
279A ASN 3.0 0.5 - - - +
280A TYR* 1.3 84.0 - - - +
282A GLU* 1.3 71.8 + - - +
284A ASN* 6.0 0.2 - - + -
103B MET* 5.8 1.3 - - - -
106B ALA* 4.3 10.1 - - + -
107B ARG* 3.7 31.9 - - - +
----------------------------------------------------------
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