Contacts of the helix formed by residues 598 - 604 (chain A) in PDB entry 3CMM
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 PRO 598 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A SER 3.7 8.0 - - - +
597A ILE* 1.4 91.5 - - + +
599A LEU* 1.3 61.0 + - - +
600A CYS* 5.4 0.4 - - + -
601A THR* 2.9 40.1 + - + +
602A LEU* 3.1 10.6 + - - +
611A HIS* 5.9 0.9 - - + -
782A ASP* 3.8 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ILE 3.4 4.3 + - - +
598A PRO* 1.3 70.5 - - - +
600A CYS* 1.3 57.5 + - - +
602A LEU* 3.4 14.5 + - + +
603A ARG* 2.8 55.5 + - - +
782A ASP* 3.1 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A PRO* 3.2 1.7 - - + -
599A LEU* 1.3 75.6 - - - +
601A THR* 1.3 61.0 + - - +
603A ARG* 3.9 12.3 - - - -
604A SER* 2.9 24.5 + - - -
605A PHE* 3.2 13.9 + - + -
779A GLN* 3.7 29.8 - - - +
780A VAL 3.3 22.9 - - - +
781A ASN* 3.4 33.0 - - - -
782A ASP* 3.4 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ILE* 4.2 4.3 - - + -
598A PRO* 2.9 29.2 + - + +
600A CYS* 1.3 75.9 - - - +
602A LEU* 1.3 65.1 + - - +
605A PHE* 3.1 25.4 + - - +
606A PRO* 3.0 27.5 - - - +
607A ASN* 5.0 3.4 + - - +
611A HIS* 3.8 37.5 - - + +
711A ALA* 5.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ILE* 3.5 44.4 - - + +
598A PRO 3.1 8.0 + - - +
599A LEU* 3.6 15.7 - - + +
601A THR* 1.3 78.5 - - - +
603A ARG* 1.3 62.8 + - - +
606A PRO* 4.5 1.0 - - - +
611A HIS* 3.6 27.9 - - + +
614A ALA* 3.8 22.2 - - + -
615A TRP* 3.4 18.8 - - + +
841A ARG* 3.1 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A LEU* 2.8 44.8 + - - +
600A CYS* 3.9 15.2 - - - +
602A LEU* 1.3 79.1 - - - +
604A SER* 1.3 67.2 + - - +
615A TRP* 4.3 9.2 + - - +
778A ILE* 5.8 4.1 - - + +
779A GLN* 3.2 40.8 + - - +
787A PRO 5.4 4.1 - - - -
841A ARG* 3.5 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A CYS* 2.9 9.6 + - - -
602A LEU 3.4 0.4 - - - -
603A ARG* 1.3 87.0 + - - +
605A PHE* 1.3 89.5 + - - +
606A PRO* 3.4 6.3 - - - -
691A LEU* 3.6 15.2 - - - +
778A ILE* 3.4 24.4 - - - +
779A GLN 4.7 1.7 + - - -
845A TYR* 2.7 30.3 + - - -
----------------------------------------------------------
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