Contacts of the helix formed by residues 500 - 512 (chain A) in PDB entry 4Z4H
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 SER 500 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PHE* 3.2 16.1 - - - -
495A ALA* 3.6 14.0 - - - +
496A GLN 3.0 17.2 + - - -
497A GLY 2.9 16.3 + - - -
499A ASP* 1.3 76.9 - - - +
501A VAL* 1.3 62.8 + - - +
503A PRO* 3.4 8.0 - - - +
504A MET* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PHE* 3.6 30.7 - - + -
498A ALA* 3.4 23.3 - - - +
499A ASP 3.2 1.8 - - - -
500A SER* 1.3 77.0 - - - +
502A GLU* 1.3 61.4 + - - +
504A MET* 3.0 5.4 + - - +
505A PHE* 2.9 39.1 + - + -
528A VAL* 4.1 11.7 - - + -
531A GLU* 3.7 23.1 - - + -
532A VAL* 4.0 20.4 - - + -
535A VAL* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ALA 4.6 1.0 + - - -
499A ASP 4.3 1.5 + - - +
501A VAL* 1.3 77.2 - - - +
503A PRO* 1.3 71.7 - - + +
505A PHE* 3.9 0.3 - - - +
506A ARG* 2.9 62.8 + - + +
531A GLU* 4.5 4.5 + - - +
534A ARG* 3.0 27.2 + - - -
535A VAL* 4.0 26.4 - - + +
539A VAL* 4.4 9.9 - - - +
540A LEU* 4.5 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ASP 3.1 24.0 - - - +
500A SER* 3.4 12.8 - - - +
501A VAL 3.5 1.3 - - - -
502A GLU* 1.3 94.8 - - + +
504A MET* 1.3 59.3 + - - +
506A ARG* 3.9 8.1 - - + +
507A HIS* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ALA* 3.5 29.6 - - - -
456A PHE* 4.4 10.3 - - - -
491A PHE* 4.4 16.2 - - + -
493A LYS* 4.2 19.1 - - + +
494A TYR 4.2 7.6 - - - +
495A ALA* 3.6 29.2 - - + -
500A SER* 3.1 19.3 + - - +
501A VAL 3.0 4.9 + - - +
503A PRO* 1.3 80.3 - - - +
505A PHE* 1.3 65.1 + - + +
507A HIS* 3.4 7.1 + - - +
508A LEU* 3.1 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ALA* 4.6 4.3 - - + -
456A PHE* 5.0 4.5 - + - -
501A VAL* 2.9 27.1 + - + +
502A GLU 3.3 2.0 + - - +
504A MET* 1.3 93.6 - - + +
506A ARG* 1.3 65.9 + - - +
508A LEU* 3.4 9.7 + - + +
509A LYS* 3.1 18.4 + - - +
518A VAL* 4.1 18.6 - - + -
520A VAL* 4.0 23.6 - - + -
532A VAL* 4.1 21.8 - - + -
535A VAL* 3.9 18.8 - - + -
536A GLY* 4.6 4.0 - - - -
540A LEU* 3.6 15.7 - - + -
542A MET* 3.6 24.9 - - + +
544A THR* 3.6 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GLU* 2.9 52.7 + - - +
503A PRO* 3.9 6.7 - - + +
505A PHE* 1.3 76.8 - - - +
507A HIS* 1.3 61.4 + - - +
509A LYS* 3.4 3.6 + - - +
510A ASN* 3.1 37.5 + - - +
539A VAL* 3.9 16.4 - - - +
540A LEU* 3.7 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A PHE* 4.3 24.6 - + - -
503A PRO 3.1 18.1 + - - +
504A MET* 3.6 7.1 + - - +
506A ARG* 1.3 76.8 - - - +
508A LEU* 1.3 60.5 + - - +
510A ASN* 3.3 4.9 + - - +
511A THR* 2.7 65.5 + - + +
512A TYR* 4.5 6.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ALA* 4.2 9.4 - - + -
454A ALA* 5.6 0.7 - - + -
491A PHE* 3.4 48.2 - - + -
504A MET* 3.1 24.7 + - + +
505A PHE* 3.7 17.9 - - + +
506A ARG 3.3 0.2 - - - -
507A HIS* 1.3 79.6 - - - +
509A LYS* 1.3 62.6 + - - +
512A TYR* 3.0 45.9 + - + +
515A LEU* 3.9 15.0 - - + +
518A VAL* 3.8 34.3 - - + -
542A MET* 4.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A PHE 3.1 17.4 + - - +
506A ARG* 3.9 6.1 - - - +
507A HIS 3.3 0.2 - - - -
508A LEU* 1.3 76.8 - - - +
510A ASN* 1.3 67.4 + - - +
512A TYR 4.2 9.9 - - - +
513A ALA* 5.5 0.9 - - - -
515A LEU* 4.7 4.0 - - - -
540A LEU* 2.9 42.1 + - + +
541A GLY 5.5 0.4 - - - -
542A MET* 3.8 23.3 - - + +
849A HIS* 4.2 14.6 + - - -
851A ASP* 4.4 7.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ARG* 3.1 26.8 + - - +
507A HIS* 3.9 5.2 - - - +
509A LYS* 1.3 84.7 - - - +
511A THR* 1.3 63.5 + - - +
512A TYR 5.3 0.2 - - - -
513A ALA 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A HIS* 2.7 47.9 + - + +
510A ASN* 1.3 81.1 - - - +
512A TYR* 1.3 95.3 + - + +
513A ALA* 3.7 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A VAL* 4.3 9.4 - - + -
490A CYS* 3.4 51.6 + - + -
491A PHE* 3.6 17.8 - + + -
507A HIS* 4.5 6.3 - + - -
508A LEU* 3.0 48.8 + - + +
509A LYS 4.2 6.9 - - - +
510A ASN 3.7 0.4 - - - -
511A THR* 1.3 100.6 - - + +
513A ALA* 1.3 65.3 + - - +
514A GLY 3.5 0.2 + - - -
515A LEU* 3.4 22.1 + - + +
----------------------------------------------------------
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