Contacts of the helix formed by residues 788 - 792 (chain C) in PDB entry 3RMD
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 ILE 788 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785C ALA* 4.1 21.3 - - + +
786C ASN 3.3 0.2 - - - -
787C ASN* 1.3 76.6 - - - +
789C ALA* 1.3 65.0 + - - +
791C TYR* 3.1 14.7 + - - +
792C ASP* 3.4 10.1 + - - +
805C ILE* 4.0 17.9 - - + +
808C ILE* 3.6 28.0 - - + -
809C LEU* 4.5 10.1 - - + +
812C ASN* 5.0 4.7 - - - +
824C VAL* 4.1 28.0 - - + +
826C GLU* 3.1 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 789 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787C ASN* 3.3 0.4 - - - -
788C ILE* 1.3 75.2 - - - +
790C LYS* 1.3 53.6 + - - +
791C TYR 2.7 6.7 + - - -
792C ASP* 2.6 41.5 + - + +
826C GLU* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 790 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787C ASN* 3.3 31.1 + - + +
789C ALA* 1.3 77.3 - - - +
791C TYR* 1.3 85.4 + - + +
792C ASP 3.5 1.3 - - - +
799C PRO* 6.1 0.5 - - - +
109J C 4.1 5.9 + - - -
110J A 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 791 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786C ASN 5.0 2.0 - - - -
787C ASN* 3.3 19.7 - - + -
788C ILE 3.1 7.2 + - - +
789C ALA 2.7 2.0 + - - -
790C LYS* 1.3 112.4 + - + +
792C ASP* 1.3 59.6 + - - +
793C VAL* 4.7 1.1 - - - -
796C PHE 3.5 2.6 - - - +
797C PRO* 3.6 3.3 - - - +
798C GLY* 2.7 33.5 + - - +
799C PRO* 3.5 15.9 - - - -
800C LYS* 3.2 24.8 + - + +
801C CYS* 3.3 34.5 - - + -
802C PRO* 3.4 18.6 - - + -
805C ILE* 4.2 4.9 - - + -
809C LEU* 4.0 3.0 - - - +
109J C 3.4 8.7 + - - -
110J A 2.8 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 792 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C ILE* 3.4 5.6 + - - +
789C ALA* 2.6 35.3 + - + +
790C LYS 5.0 0.7 - - - +
791C TYR* 1.3 71.2 - - - +
793C VAL* 1.3 69.7 + - - +
794C GLY 3.4 1.8 + - - -
795C GLY* 2.6 36.5 + - - -
796C PHE 4.0 1.8 - - - -
809C LEU* 3.8 21.3 - - + +
812C ASN* 4.7 7.4 + - - -
----------------------------------------------------------
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