Contacts of the helix formed by residues 517 - 525 (chain V) in PDB entry 5IY8
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 GLU 517 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ALA 2.8 10.3 + - - -
161 MET* 3.9 1.0 - - - +
191 PHE* 3.5 30.5 - - + -
515V SER 3.5 0.2 + - - -
516V PRO* 1.3 93.0 - - - +
518V PHE* 1.3 61.8 + - - +
519V TYR 3.2 3.9 + - - -
520V ARG* 3.4 18.7 - - - +
521V GLU* 3.3 23.0 + - - +
706V LYS* 3.4 20.6 + - - +
709V GLN* 4.4 3.2 - - - +
710V GLN* 2.7 40.8 + - - +
713V LEU* 3.0 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 518 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 MET* 3.3 23.6 - - + +
515V SER* 3.4 4.1 + - - +
516V PRO 3.1 18.8 + - - -
517V GLU* 1.3 76.7 - - - +
519V TYR* 1.4 54.8 + - - +
520V ARG 3.7 0.2 - - - -
521V GLU 3.7 1.1 + - - -
522V TYR* 3.0 24.6 + - - +
533V LEU* 3.7 43.2 - - + +
536V MET* 4.2 14.1 - - + -
537V ASN* 4.1 3.4 - - - +
538V PRO* 3.7 37.7 - - + -
709V GLN* 3.7 26.2 - - + -
712V LEU* 4.2 15.7 - - + -
713V LEU* 3.5 32.3 - - + -
716V VAL* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 519 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 MET* 3.1 34.4 - - + +
171 LYS* 3.3 44.0 + - + -
201 LEU* 3.3 32.6 - - + +
211 LEU* 5.8 0.4 - - + -
581 GLY* 3.7 14.6 + - - -
611 MET* 4.9 0.3 - - - +
621 ASP 2.9 24.5 + - - -
514V MET* 5.7 0.4 - - + -
517V GLU 3.3 0.8 - - - -
518V PHE* 1.4 72.3 - - - +
520V ARG* 1.3 55.2 + - - +
521V GLU 2.9 2.9 - - - -
522V TYR* 3.8 11.9 - + - -
523V VAL* 2.5 65.2 + - + +
665V GLN 5.5 0.2 - - - -
666V ASP* 3.2 29.0 + - + +
667V THR* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 520 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 MET 3.6 6.5 + - - -
191 PHE* 3.3 70.5 - - + -
201 LEU 4.6 0.9 - - - +
221 TYR* 6.0 2.2 - - - -
231 LEU* 3.2 30.6 - - + +
517V GLU* 3.4 19.7 + - - +
519V TYR* 1.3 71.2 - - - +
521V GLU* 1.3 97.1 + - - +
524V ALA* 2.8 34.4 + - + +
710V GLN* 5.1 5.7 + - - +
713V LEU* 4.0 18.0 - - - +
717V LEU* 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 521 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517V GLU 3.3 17.4 + - - +
518V PHE 4.2 1.1 - - - +
519V TYR 2.9 0.2 - - - -
520V ARG* 1.3 136.6 + - - +
522V TYR* 1.4 56.9 + - - +
524V ALA* 3.8 5.6 - - - +
525V ILE* 3.0 40.0 + - + +
533V LEU* 3.7 21.1 - - + -
713V LEU* 4.5 6.1 - - + -
717V LEU* 3.9 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 522 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 MET* 5.0 2.7 - - + -
621 ASP* 1.4 52.5 + - + -
514V MET* 5.3 1.6 - - + -
518V PHE 3.0 20.7 + - - +
519V TYR* 3.0 18.8 + + + +
521V GLU* 1.4 74.8 - - - +
523V VAL* 1.3 58.7 + - - +
525V ILE 3.1 9.9 - - - +
530V ARG* 2.7 86.1 + - + -
533V LEU* 3.5 13.2 - - + +
534V TYR* 4.0 18.8 - + + -
666V ASP 3.8 1.6 - - - -
667V THR* 3.7 22.2 - - + -
668V GLN* 2.9 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 523 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 LEU* 2.4 33.4 - - + -
231 LEU* 4.9 0.7 - - + -
611 MET* 3.7 20.4 - - + -
621 ASP* 4.6 6.5 - - - +
519V TYR* 2.5 68.6 + - + +
520V ARG 3.8 1.3 - - - +
522V TYR* 1.3 76.9 - - + +
524V ALA* 1.3 58.5 + - - +
525V ILE 3.5 0.2 + - - -
526V LYS* 2.7 31.6 + - - +
530V ARG* 3.8 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 524 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231 LEU* 3.6 17.5 - - + -
520V ARG* 2.8 24.3 + - + +
521V GLU* 3.9 9.2 - - - +
523V VAL* 1.3 74.4 - - - +
525V ILE* 1.4 60.8 + - + +
526V LYS* 3.9 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 525 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521V GLU* 3.0 27.9 + - + +
522V TYR 3.1 5.9 - - - +
524V ALA* 1.4 74.9 - - + +
526V LYS* 1.3 52.8 + - - +
527V THR* 3.1 35.7 - - + +
529V LYS* 4.6 15.9 - - + -
530V ARG* 2.8 39.8 + - + +
533V LEU* 4.4 10.3 - - + -
717V LEU* 3.8 29.4 - - + +
----------------------------------------------------------
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