Contacts of the helix formed by residues 526 - 533 (chain A) in PDB entry 2FY2
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 ASP 526 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.5 4.0 + - - -
40A GLN* 4.8 2.9 - - - +
43A LYS* 5.9 1.4 - - - +
44A SER* 2.5 37.2 + - - +
47A ILE* 3.8 23.8 - - + +
48A VAL* 5.6 1.0 - - - +
522A GLU* 2.8 16.9 + - - +
523A MET 3.7 11.4 - - - +
524A PHE 3.3 0.2 - - - -
525A MET* 1.3 78.1 - - - +
527A GLU* 1.3 77.0 + - - +
528A THR* 3.1 16.5 + - - -
529A TYR* 2.9 17.0 + - + +
530A LEU* 3.2 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLN* 3.8 19.3 - - - +
525A MET 3.3 4.7 + - - -
526A ASP* 1.3 76.4 + - - +
528A THR* 1.3 56.6 + - - +
530A LEU* 3.3 18.0 + - - +
531A MET* 2.8 34.2 + - + +
534A ARG* 2.8 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.7 13.5 - - + +
29A LEU* 6.3 0.9 - - + -
32A MET* 3.6 33.2 - - + +
36A VAL* 4.1 10.4 - - + +
40A GLN* 3.0 26.6 + - - +
41A PHE* 6.3 0.7 - - + -
44A SER* 2.6 33.2 + - - +
526A ASP* 3.0 7.9 + - - -
527A GLU* 1.3 79.1 - - - +
529A TYR* 1.3 57.3 + - - +
531A MET* 3.6 3.1 + - - -
532A SER* 3.0 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.1 27.0 + + - +
506A LEU* 4.1 32.4 + - + +
507A LEU* 4.5 2.9 + - - +
510A ARG* 3.1 39.0 + - - -
523A MET* 3.7 15.9 - - + +
524A PHE* 3.4 48.4 - + - -
526A ASP* 2.9 10.2 + - - +
528A THR* 1.3 76.5 - - - +
530A LEU* 1.3 72.1 + - + +
532A SER* 2.6 24.9 + - - -
533A ASN* 3.3 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A PHE 3.7 17.7 - - - +
525A MET* 3.8 24.0 - - + +
526A ASP 3.2 8.7 + - - +
527A GLU* 3.3 22.9 + - - +
529A TYR* 1.3 84.6 - - + +
531A MET* 1.3 60.6 + - - +
533A ASN* 3.4 14.0 + - - +
534A ARG* 3.5 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 3.0 28.9 - - + -
35A LEU* 3.4 31.2 - - + +
36A VAL* 3.6 10.8 - - - -
40A GLN* 5.4 1.3 - - - +
434A PRO* 2.9 50.6 - - + +
527A GLU* 2.8 22.2 + - + +
528A THR* 3.9 2.0 - - - +
530A LEU* 1.3 72.2 - - - +
532A SER* 1.3 64.2 + - - +
533A ASN 3.0 4.3 + - - -
534A ARG* 3.1 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.2 8.9 - - - -
32A MET* 3.4 37.0 - - - +
434A PRO* 3.6 5.9 - - - +
453A ARG* 2.9 33.7 + - - -
506A LEU* 6.0 0.2 - - - +
528A THR 3.0 13.1 + - - -
529A TYR* 2.6 24.8 + - - -
531A MET* 1.3 76.2 - - - +
533A ASN* 1.3 66.2 + - - +
534A ARG 3.5 0.2 - - - -
535A PHE* 3.3 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 3.1 22.2 + - - -
503A ASP* 4.0 4.5 - - - +
510A ARG* 4.6 4.6 - - - +
529A TYR* 3.3 51.0 + - - -
530A LEU* 3.4 9.1 + - - +
531A MET 3.0 1.2 - - - -
532A SER* 1.3 80.6 + - - +
534A ARG* 1.3 60.2 + - - +
535A PHE* 3.5 27.0 + - + -
556A VAL* 5.5 0.7 - - - +
----------------------------------------------------------
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