Contacts of the helix formed by residues 526 - 532 (chain B) in PDB entry 4Z4Q
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 MET 526 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B MET 5.3 0.7 - - - +
480B ILE* 5.3 9.4 - - - -
483B ILE* 3.8 37.2 - - + -
486B GLY 4.5 8.3 - - - +
487B VAL* 4.9 2.5 - - - -
491B PHE* 3.2 42.4 - - + -
521B PHE* 3.8 26.7 + - + -
522B PHE* 2.8 36.5 + - + +
525B TYR* 1.3 90.6 - - + +
527B ARG* 1.3 65.5 + - - +
528B PRO* 3.2 8.3 - - - -
529B LEU* 3.1 25.1 + - + +
530B VAL 3.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B PHE 3.1 8.4 + - - -
523B TYR* 3.5 22.1 + - + +
524B ARG 5.2 1.3 + - - +
525B TYR 3.9 0.8 - - - -
526B MET* 1.3 74.4 - - - +
528B PRO* 1.3 72.1 - - + +
530B VAL* 2.9 16.4 + - - +
531B GLU* 2.9 14.5 + - + +
608B ILE* 5.2 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B GLY 5.8 1.1 - - - +
491B PHE* 3.4 36.6 - - + +
493B ILE* 4.5 14.3 - - + +
526B MET* 3.2 5.8 - - - -
527B ARG* 1.3 95.0 - - + +
529B LEU* 1.3 55.5 + - - +
531B GLU* 3.8 7.4 - - + +
532B ALA* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ILE* 5.8 2.2 - - + -
491B PHE* 4.2 20.6 - - + -
493B ILE* 6.0 3.4 - - + -
496B ALA* 5.6 9.6 - - + -
498B TYR 5.9 1.8 - - - +
501B ILE* 4.9 11.4 - - + -
522B PHE* 5.8 2.2 - - + -
526B MET* 3.1 23.0 + - + +
528B PRO* 1.3 77.9 - - - +
530B VAL* 1.3 60.5 + - - +
532B ALA* 3.6 2.7 + - - -
533B GLY 3.5 3.3 + - - -
534B HIS* 3.1 50.1 + - + +
535B VAL* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B LEU* 6.2 3.1 - - + -
522B PHE* 4.7 16.8 - - + +
523B TYR* 5.4 5.4 - - + -
526B MET 3.8 1.2 + - - -
527B ARG* 2.9 10.4 + - - +
529B LEU* 1.3 77.0 - - - +
531B GLU* 1.3 64.2 + - - +
533B GLY* 3.2 9.5 + - - -
534B HIS 5.0 0.2 - - - +
535B VAL* 4.3 15.8 - - + +
606B VAL* 3.6 21.9 - - + +
607B THR* 4.4 6.2 - - - -
608B ILE* 4.5 17.2 + - + -
1009B LEU* 6.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ARG* 2.9 14.0 + - + +
528B PRO* 4.0 8.1 - - + +
530B VAL* 1.3 76.0 - - - +
532B ALA* 1.3 58.0 + - - +
533B GLY 3.2 3.9 + - - -
607B THR* 5.8 1.2 - - - -
608B ILE* 4.6 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B ILE* 6.2 3.8 - - + -
528B PRO 3.0 19.2 + - - +
529B LEU* 3.8 4.0 - - - +
530B VAL 3.3 0.4 - - - -
531B GLU* 1.3 74.3 - - - +
533B GLY* 1.3 63.9 + - - +
534B HIS* 2.9 29.7 + - + +
----------------------------------------------------------
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