Contacts of the helix formed by residues 506 - 515 (chain B) in PDB entry 5ZR1
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 GLY 506 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ASN* 5.9 0.2 - - - -
368B PRO* 4.4 20.8 - - - +
369B SER* 4.5 14.6 + - - -
492B PHE* 5.1 6.5 + - - -
503B THR 5.4 0.4 - - - -
504B SER 3.5 2.2 - - - -
505B SER* 1.3 76.1 - - - +
507B ALA* 1.3 58.2 + - - +
508B GLU* 3.4 3.3 - - - +
509B GLY* 3.6 7.4 + - - -
510B ALA* 3.2 18.4 + - - +
604B TYR* 3.4 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B SER* 3.1 4.3 + - - -
506B GLY* 1.3 76.5 - - - +
508B GLU* 1.3 59.3 - - - +
510B ALA* 3.2 4.2 + - - +
511B LYS* 3.1 22.0 + - - +
604B TYR* 3.7 31.6 - - + -
608B GLU* 3.5 36.6 - - + +
612B LEU* 3.8 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 4.2 1.2 + - - -
491B THR 3.7 7.0 - - - +
492B PHE 4.2 9.6 - - - +
493B GLN 4.0 5.6 - - - +
494B ASP* 2.9 52.8 - - + +
501B SER* 4.2 13.6 + - - +
505B SER* 5.0 3.8 - - - -
506B GLY* 3.4 1.4 - - - +
507B ALA* 1.3 78.6 - - - +
509B GLY* 1.3 60.2 + - - +
511B LYS* 3.2 46.7 + - - +
512B TYR* 3.6 5.0 + - - +
611B LYS* 4.9 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B THR* 3.6 16.6 + - - +
492B PHE* 3.8 32.1 - - - +
506B GLY 3.6 7.4 + - - -
507B ALA 3.3 0.2 - - - -
508B GLU* 1.3 75.8 - - - +
510B ALA* 1.3 62.2 + - - +
512B TYR* 3.5 10.7 + - - +
513B VAL* 3.3 20.7 + - - +
19C GLN* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLY 3.2 5.8 + - - +
507B ALA 3.4 10.1 - - - +
508B GLU 3.2 0.4 - - - -
509B GLY* 1.3 75.6 - - - +
511B LYS* 1.3 64.8 + - - +
513B VAL* 3.1 17.8 + - - +
514B LEU* 3.2 20.6 + - - +
587B MET* 4.1 17.7 - - + -
604B TYR* 3.3 37.2 - - + +
612B LEU* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 3.5 36.7 - - - +
507B ALA 3.1 11.2 + - - +
508B GLU* 3.2 35.4 + - - +
510B ALA* 1.3 78.2 - - - +
512B TYR* 1.3 61.7 + - - +
513B VAL 3.5 0.2 + - - -
514B LEU* 3.7 12.1 + - - +
515B GLN* 3.3 51.5 + - - +
611B LYS* 5.9 6.1 - - - +
612B LEU* 4.8 10.1 - - + -
615B THR* 4.3 15.3 - - + +
616B VAL* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B THR* 3.5 33.0 - - + +
508B GLU 3.6 5.1 + - - +
509B GLY 3.5 10.5 + - - +
510B ALA 3.2 0.6 - - - -
511B LYS* 1.3 82.3 - - + +
513B VAL* 1.3 64.8 + - + +
515B GLN* 3.5 33.2 + - - +
516B SER* 4.4 3.1 + - - -
19C GLN* 3.8 35.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B PHE* 6.0 1.6 - - + -
509B GLY 3.3 17.0 - - - +
510B ALA* 3.1 8.1 + - - +
512B TYR* 1.3 79.0 - - + +
514B LEU* 1.3 64.0 + - - +
515B GLN 3.2 1.0 + - - -
516B SER* 3.6 8.1 + - - +
517B LEU* 3.3 19.0 - - + +
585B HIS* 4.7 13.5 - - + +
587B MET* 3.7 24.7 - - + -
15C PHE* 3.7 37.2 - - + -
19C GLN* 4.8 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ALA 3.2 28.0 + - - +
511B LYS* 4.1 4.0 - - - +
512B TYR 3.4 0.4 - - - -
513B VAL* 1.3 77.9 - - - +
515B GLN* 1.3 59.8 + - - +
516B SER 3.3 0.5 + - - -
517B LEU* 3.7 27.6 + - + +
522B LYS* 3.2 32.5 + - + +
525B TYR* 3.9 28.5 - - + -
582B PHE* 4.7 0.7 - - + -
587B MET* 3.6 19.1 - - + -
612B LEU* 4.1 13.7 - - + -
616B VAL* 3.7 19.4 - - + +
617B LEU* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 5.9 1.0 - - - +
511B LYS* 3.3 48.3 - - - +
512B TYR* 3.8 26.7 - - - +
513B VAL 3.2 1.6 - - - -
514B LEU* 1.3 78.7 - - - +
516B SER* 1.3 58.4 + - - +
517B LEU 3.8 0.9 + - - -
522B LYS* 4.8 7.6 + - - +
616B VAL* 4.5 16.1 - - + +
----------------------------------------------------------
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