Contacts of the helix formed by residues 500 - 505 (chain B) in PDB entry 6WCZ
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 500 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B HIS* 3.1 22.5 + - - +
499B MET* 1.3 79.1 - - - +
501B ARG* 1.3 57.8 + - - -
502B GLU 3.3 2.9 - - - -
503B ASN 3.8 2.0 - - - -
504B SER* 2.6 40.2 + - - -
507B GLY 3.2 5.4 - - - -
509B GLU* 3.6 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B GLY* 1.3 72.4 - - - -
502B GLU* 1.3 72.0 + - + +
505B GLY* 3.1 41.7 + - - +
506B GLY 2.6 27.4 + - - +
507B GLY 2.8 14.7 + - - +
508B VAL* 3.4 30.5 - - + +
509B GLU 5.1 0.8 + - - -
519B ILE* 3.5 31.9 - - + +
523B MET* 5.6 4.4 - - - +
658B LYS 4.6 10.9 + - - -
660B MET 2.5 29.8 + - - -
661B ALA* 3.6 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ARG* 4.5 12.0 + - - -
500B GLY 3.3 0.6 - - - -
501B ARG* 1.3 86.6 - - + +
503B ASN* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 3.3 27.2 - - - +
389B ARG* 4.0 23.3 + - - +
390B LYS* 4.8 11.8 - - - +
496B ASP 4.7 2.2 + - - -
497B HIS* 3.3 29.6 + - + +
498B TRP* 3.4 35.3 + - - +
500B GLY 3.2 1.6 + - - +
501B ARG 3.2 0.2 - - - -
502B GLU* 1.3 79.8 - - - +
504B SER* 1.3 63.9 + - - +
505B GLY 3.4 1.2 + - - -
654B TRP* 3.7 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 3.7 25.3 - - - +
498B TRP 4.4 0.2 - - - -
499B MET* 2.7 38.0 + - - +
500B GLY 2.6 26.3 + - - -
503B ASN* 1.3 76.3 - - - +
505B GLY* 1.3 59.2 + - - -
506B GLY* 3.2 10.0 + - - -
507B GLY 4.0 0.9 + - - -
617B LEU* 5.2 4.0 - - - +
654B TRP* 3.8 10.8 - - - -
657B LEU* 3.4 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B GLY 3.4 0.4 + - - -
501B ARG* 3.1 40.7 + - - -
503B ASN 3.4 1.6 - - - -
504B SER* 1.3 77.5 + - - +
506B GLY* 1.3 56.8 + - - +
654B TRP* 4.3 13.4 - - - -
657B LEU* 2.8 26.9 - - - +
658B LYS* 4.3 6.7 - - - +
----------------------------------------------------------
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