Contacts of the helix formed by residues 754 - 763 (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 ASN 754 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A ASP* 5.1 1.0 - - - -
752A LYS 3.1 6.6 + - - +
753A PRO* 1.3 68.1 - - - +
755A VAL* 1.3 66.4 + - - +
756A ASP* 3.5 13.5 + - - +
757A GLU* 3.0 35.8 + - + +
758A TYR* 3.2 22.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ILE* 4.2 22.3 - - + +
723A TYR* 4.7 19.7 - - + -
728A PHE* 3.5 34.3 - - + -
753A PRO 3.5 2.9 + - - +
754A ASN* 1.3 72.7 + - - +
756A ASP* 1.3 68.6 + - - +
757A GLU 3.1 0.2 + - - -
758A TYR* 3.2 3.8 + - - +
759A LYS* 2.8 30.9 + - + +
115C ASP 5.3 7.4 - - - +
116C ASP* 4.2 19.8 + - - +
117C VAL* 5.2 13.0 - - + +
118C THR* 4.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A TYR* 5.2 3.1 + - - -
754A ASN* 3.3 10.3 + - - +
755A VAL* 1.3 87.3 - - - +
757A GLU* 1.3 56.3 + - - +
759A LYS* 3.9 14.4 - - - +
760A SER* 3.1 27.7 + - - -
115C ASP* 4.8 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A PHE* 4.4 1.0 - - - -
673A ILE* 4.3 18.5 - - + +
747A ASP* 2.7 40.1 - - - +
754A ASN* 3.0 36.6 + - + +
756A ASP* 1.3 74.5 - - - +
758A TYR* 1.3 74.1 + - + +
760A SER* 3.0 18.3 + - - +
761A VAL* 3.2 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A PHE* 3.3 16.9 - + - -
673A ILE* 3.7 29.8 - - + -
722A ILE* 4.1 15.7 - - + -
728A PHE* 4.3 10.1 - + + -
731A VAL* 3.6 24.2 - - + -
732A VAL* 3.7 33.8 + - + +
735A ALA* 4.4 0.9 - - + -
748A ASP* 2.6 44.2 + - - -
753A PRO* 4.3 0.4 - - + -
754A ASN* 3.2 31.6 + - + -
755A VAL 3.8 5.4 - - - +
757A GLU* 1.3 86.5 - - + +
759A LYS* 1.3 62.1 + - - +
761A VAL* 3.4 1.6 + - - +
762A ILE* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ILE* 3.9 26.2 - - + +
723A TYR* 3.7 35.9 - - + +
755A VAL* 2.8 20.1 + - + +
756A ASP* 3.9 15.3 - - - +
758A TYR* 1.3 75.2 - - - +
760A SER* 1.3 59.9 + - - +
762A ILE* 4.2 3.1 - - - +
763A ASP* 2.8 62.0 + - - +
139C LYS* 4.8 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A ASP 3.1 16.3 + - - -
757A GLU* 3.0 10.5 + - - -
759A LYS* 1.3 77.6 - - - +
761A VAL* 1.3 69.4 + - - +
763A ASP* 3.5 5.2 + - - +
764A HIS* 3.2 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A GLU* 3.8 27.4 - - + +
673A ILE* 3.9 37.9 - - + -
674A LYS* 4.1 25.3 - - + +
757A GLU* 3.2 18.2 + - + +
758A TYR 3.8 6.3 - - - +
760A SER* 1.3 81.8 + - - +
762A ILE* 1.3 67.2 + - - +
764A HIS* 3.1 17.1 + - - +
765A MET* 3.4 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A ILE* 4.1 10.8 - - + -
677A ARG* 3.6 46.7 - - + +
720A PHE* 4.1 28.7 - - + -
722A ILE* 4.4 5.2 - - + -
731A VAL* 4.0 26.9 - - + -
758A TYR 3.0 21.7 + - - +
759A LYS* 4.2 3.6 - - - +
761A VAL* 1.3 73.7 - - - +
763A ASP* 1.3 67.1 + - - +
764A HIS 3.0 1.8 + - - -
765A MET* 3.2 24.9 + - - +
767A ILE* 4.6 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A LYS* 2.8 57.6 + - - +
760A SER* 3.8 7.8 - - - +
761A VAL 3.2 0.2 - - - -
762A ILE* 1.3 80.6 - - - +
764A HIS* 1.3 70.5 + - + +
765A MET 3.5 1.5 - - - +
----------------------------------------------------------
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