Contacts of the helix formed by residues 504 - 511 (chain A) in PDB entry 2C31
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 ARG 504 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ARG 5.4 2.9 - - - +
503A GLY* 1.3 71.3 - - - -
505A TYR* 1.3 55.8 + - - +
506A ASP* 2.7 40.7 + - - +
507A MET* 2.8 55.6 + - + +
518A VAL* 4.0 15.2 - - - +
542A ASN* 4.5 4.5 - - - +
544A MET* 6.5 0.2 - - - -
510B GLU 5.8 0.4 - - - +
511B ALA* 3.0 27.4 + - - +
512B PHE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ASP* 4.1 13.1 + - + +
455A PHE* 3.7 31.4 - + - -
476A ILE* 3.8 24.9 - - + -
478A ASN* 3.7 28.0 - - - -
500A LEU* 5.1 1.2 - - - +
501A THR 4.2 10.5 + - - -
503A GLY 3.1 11.7 + - - -
504A ARG* 1.3 75.7 - - - +
506A ASP* 1.3 62.6 + - - +
508A MET* 3.1 10.7 + - - +
509A MET 3.1 17.8 + - - -
540A LEU* 3.9 30.7 - - + +
542A ASN* 3.6 5.1 - - - +
54B ARG* 3.1 29.8 + - - -
460B MET* 4.4 6.1 - - + -
463B GLU* 5.0 0.2 - - - +
511B ALA* 5.3 0.2 - - - -
512B PHE* 3.5 32.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ARG* 2.7 47.8 + - - -
505A TYR* 1.3 79.2 - - - +
507A MET* 1.3 64.4 + - - +
509A MET* 3.4 4.2 + - - +
510A GLU* 3.0 34.8 + - - +
516A GLY* 3.9 6.0 - - - -
517A TYR 3.5 32.3 - - - +
518A VAL* 3.5 11.9 - - - +
540A LEU* 4.0 10.5 - - - +
542A ASN* 3.1 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ARG* 2.8 48.2 + - + +
506A ASP* 1.3 84.5 - - - +
508A MET* 1.3 64.6 + - - +
510A GLU* 3.4 10.6 + - - +
511A ALA* 3.0 19.6 + - - +
507B MET* 3.5 42.6 - - + +
510B GLU* 4.1 16.4 - - + +
511B ALA* 3.8 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A PHE* 4.7 6.1 - - + -
459A GLY* 3.2 35.0 - - - +
460A MET* 4.1 4.9 - - - +
462A LEU* 4.0 17.7 - - + -
504A ARG 3.4 2.2 + - - -
505A TYR* 3.1 16.9 + - - +
507A MET* 1.3 78.9 - - - +
509A MET* 1.3 64.9 + - - +
511A ALA* 3.1 20.3 + - - +
512A PHE* 3.3 20.0 - - + -
460B MET* 3.9 9.4 - - - +
508B MET* 3.6 43.1 - - + +
511B ALA* 4.0 12.9 - - + +
512B PHE* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 3.8 34.0 - - + +
465A ILE* 4.9 7.4 - - + -
466A CYS* 3.5 27.1 - - - -
472A VAL 4.9 0.2 - - - +
474A VAL* 5.1 1.6 - - + -
505A TYR 3.1 6.8 + - - +
506A ASP 3.6 9.2 - - - +
507A MET 3.3 0.2 - - - -
508A MET* 1.3 77.2 - - - +
510A GLU* 1.3 63.4 + - - +
512A PHE* 3.0 16.2 + - - +
514A GLY* 3.2 19.4 + - - -
515A LYS 3.7 19.7 - - - +
538A PRO* 3.8 10.5 - - + -
539A CYS 3.4 38.1 - - - +
540A LEU* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ASP* 3.0 22.5 + - - +
507A MET* 3.8 12.5 - - - +
508A MET 3.3 0.2 - - - -
509A MET* 1.3 74.8 - - - +
511A ALA* 1.3 62.1 + - - +
512A PHE 3.1 0.2 - - - -
513A GLY* 3.2 12.0 + - - -
514A GLY 3.2 13.5 - - - +
515A LYS* 4.0 2.9 - - - -
516A GLY* 3.0 37.6 + - - +
507B MET* 4.2 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A MET 3.0 12.8 + - - +
508A MET* 3.2 15.3 - - - +
509A MET 3.1 1.0 - - - -
510A GLU* 1.3 77.5 - - - +
512A PHE* 1.3 62.7 + - + +
513A GLY 3.4 0.4 + - - -
503B GLY* 3.8 2.9 - - - -
504B ARG* 3.0 51.6 + - - +
507B MET* 3.7 19.1 - - + -
508B MET* 4.0 11.7 - - + +
----------------------------------------------------------
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