Contacts of the helix formed by residues 522 - 529 (chain A) in PDB entry 1FGR
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 522 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 4.2 0.7 - - - -
149A TYR 3.7 2.7 - - - -
151A PRO* 3.8 10.0 - - + +
162A ARG* 3.6 13.1 - - - +
518A LEU* 4.1 11.2 - - + +
519A SER 2.8 18.2 + - - +
521A LEU* 1.3 78.0 - - - +
523A PRO* 1.3 75.5 - - + +
524A ILE* 3.0 40.3 + - + +
525A TYR* 3.1 16.8 + - + +
526A LYS* 3.1 15.6 + - - +
633A TYR* 3.0 23.3 - - - -
642A ASP* 2.8 23.6 + - - -
644A GLU* 3.2 27.1 - - + +
645A LEU* 4.2 6.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 3.5 24.0 - - + -
149A TYR 3.7 17.9 - - - +
150A VAL* 3.7 21.1 - - + +
522A HIS* 1.3 96.7 - - + +
524A ILE* 1.3 58.9 + - + +
526A LYS* 3.3 1.6 + - + +
527A LEU 2.9 16.6 + - - -
628A TYR* 2.7 33.6 + - + +
632A TYR* 3.5 26.5 - - + -
633A TYR* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 3.8 13.9 - - + -
522A HIS* 3.0 24.9 + - + +
523A PRO* 1.3 77.6 - - + +
525A TYR* 1.3 66.5 + - - +
527A LEU* 3.6 19.2 - - + +
528A LEU* 2.9 46.8 + - + +
628A TYR* 4.7 5.6 - - + -
629A VAL* 4.8 6.5 - - + -
633A TYR* 3.9 15.5 - - + +
645A LEU* 4.0 15.5 - - + -
648A TRP* 4.7 3.1 - - + -
675A LEU* 4.3 19.7 - - + -
679A CYS* 4.1 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 3.8 15.5 - - + -
515A HIS* 3.2 33.2 + + - -
518A LEU* 3.2 33.0 - - + +
519A SER 3.2 18.6 - - - +
520A VAL* 3.5 43.0 - - + +
522A HIS* 3.1 12.1 + - + +
524A ILE* 1.3 78.3 - - - +
526A LYS* 1.3 63.0 + - + +
529A THR* 2.9 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA 5.2 0.2 + - - -
146A ASN* 3.2 19.4 + - - +
147A HIS 3.2 17.9 + - - -
148A THR* 2.9 30.6 + - + +
520A VAL 3.3 23.3 - - - +
521A LEU* 4.0 9.2 - - - +
522A HIS 3.1 10.5 + - - +
523A PRO 3.7 6.7 - - - +
525A TYR* 1.3 82.2 - - + +
527A LEU* 1.3 57.8 + - - +
529A THR* 4.2 2.9 - - - -
530A PRO* 3.3 8.5 - - - +
628A TYR* 3.9 7.4 - - - +
767A ARG* 2.7 28.2 + - - +
772A TRP* 3.4 32.1 + - + +
773A THR* 4.2 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PRO 2.9 16.2 + - - +
524A ILE* 3.2 13.2 + - + +
526A LYS* 1.3 75.8 - - - +
528A LEU* 1.3 64.5 + - + +
530A PRO* 3.7 0.7 - - - +
531A HIS* 3.5 19.6 + - - -
624A TRP* 3.5 42.6 - - + +
625A VAL* 4.6 12.1 - - + -
628A TYR* 3.7 31.4 + - + -
629A VAL* 5.0 1.3 - - + -
679A CYS* 3.9 35.7 - - + -
683A ILE* 4.3 7.2 - - + -
767A ARG* 3.5 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 4.8 3.1 - - + +
518A LEU* 5.4 0.9 - - + -
524A ILE* 2.9 37.4 + - + +
525A TYR 4.4 0.2 - - - +
527A LEU* 1.3 80.7 - - + +
529A THR* 1.3 65.2 + - - +
530A PRO* 3.3 4.3 - - - -
531A HIS* 2.9 23.0 + - - +
532A TYR* 3.6 33.0 + - + +
648A TRP* 3.8 23.1 - - + -
679A CYS* 4.1 20.9 - - + +
682A ILE* 4.2 16.2 - - + -
683A ILE* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 3.9 13.5 - - + -
515A HIS* 4.4 8.3 - - - +
525A TYR* 2.9 74.0 + - + +
526A LYS* 4.2 2.6 - - - -
528A LEU* 1.3 71.3 - - - +
530A PRO* 1.3 69.6 - - - +
532A TYR* 3.0 29.3 + - + +
533A ARG* 3.8 4.0 + - - -
----------------------------------------------------------
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