Contacts of the helix formed by residues 594 - 599 (chain B) in PDB entry 5QSY
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 GLN 594 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B VAL* 4.0 13.9 - - + -
590B ALA* 2.8 23.8 + - - +
591B ASN* 3.5 24.0 - - - +
592B LEU 3.1 1.0 + - - -
593B LEU* 1.3 79.2 + - - +
595B ILE* 1.3 61.0 + - - +
596B PRO 3.8 0.2 - - - -
597B GLN* 2.9 35.0 + - - +
598B TYR* 3.2 13.1 - - + +
635B ALA* 4.1 15.0 - - - +
638B LYS* 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B MET* 4.8 3.1 - - + -
530B VAL* 4.2 15.9 - - + -
533B ILE* 3.9 29.6 - - + -
567B LEU* 5.4 0.2 - - + -
571B PHE* 4.1 28.3 - - + -
575B LEU* 4.1 16.6 - - + -
578B LEU* 5.1 0.4 - - + -
592B LEU* 2.8 40.2 + - + +
594B GLN* 1.3 75.4 - - - +
596B PRO* 1.4 59.8 - - + +
597B GLN 3.2 2.5 - - - -
598B TYR* 2.8 40.1 + - - +
599B PHE* 3.7 24.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU* 3.5 23.3 - - + -
592B LEU 3.9 0.7 - - - +
593B LEU* 3.4 17.3 - - + +
595B ILE* 1.4 93.2 - - + +
597B GLN* 1.3 61.0 + - - +
598B TYR 3.0 1.7 + - - -
599B PHE* 3.3 36.9 + - + +
601B LEU* 4.9 1.4 - - - +
616B LEU* 4.5 8.5 - - + -
639B THR* 3.7 32.1 - - + -
642B ILE* 4.1 12.2 - - + +
643B LEU* 4.5 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B LEU 5.1 1.0 + - - +
594B GLN* 2.9 44.9 + - - +
595B ILE 3.0 1.2 + - - -
596B PRO* 1.3 76.3 - - - +
598B TYR* 1.3 93.0 + - + +
599B PHE 3.5 3.5 - - - +
642B ILE* 3.3 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B VAL* 5.1 7.7 - - + +
533B ILE* 3.8 28.0 - - + -
534B ARG* 3.2 36.0 - - + +
537B ALA* 3.8 24.8 - - + +
538B GLU* 3.2 27.4 + - + -
564B ARG* 3.9 22.9 + - - +
567B LEU* 4.2 8.0 - - + +
568B THR* 4.5 1.4 + - - -
594B GLN* 3.2 30.7 - - + +
595B ILE* 2.8 20.6 + - - +
597B GLN* 1.3 96.0 + - + +
599B PHE* 1.3 71.1 + - - +
600B ASP 3.4 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B ARG* 4.8 2.3 + - - -
567B LEU* 4.2 4.7 - - + -
568B THR* 3.5 26.7 - - + -
571B PHE* 3.8 17.0 - - + -
572B ILE* 3.8 23.8 - - + -
575B LEU* 4.2 9.6 - - + -
595B ILE* 3.7 27.8 - - + -
596B PRO* 3.3 34.3 + - + +
597B GLN 4.5 4.0 - - - +
598B TYR* 1.3 83.2 - - - +
600B ASP* 1.3 61.6 + - - +
601B LEU* 3.4 20.5 + - + +
604B TYR* 3.7 37.5 - + - -
616B LEU* 4.9 1.6 - - + -
643B LEU* 5.6 0.2 - - + -
----------------------------------------------------------
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