Contacts of the helix formed by residues 687 - 691 (chain A) in PDB entry 2C11
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 HIS 687 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ASN* 4.3 0.9 - - - +
511A VAL* 3.7 10.4 - - - +
685A ILE 3.1 22.0 - - - -
686A PRO* 1.3 74.5 - - - +
688A ALA* 1.3 55.6 + - - +
689A GLU* 2.9 33.1 + - + +
690A ASP* 2.7 45.2 + - - +
1745A CU 2.3 31.2 - - - -
586B TYR* 4.5 4.0 + - - -
706B ARG* 5.2 2.5 + - - -
707B PRO 3.7 17.3 + - - -
708B TYR* 3.5 24.6 - + + -
709B ASN* 3.2 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLN 5.0 1.3 + - - +
511A VAL* 3.9 14.8 - - - +
687A HIS* 1.3 73.0 - - - +
689A GLU* 1.3 57.8 + - - +
690A ASP 3.0 5.4 + - - -
691A ILE* 3.0 17.4 + - - +
595B ASN* 3.8 12.6 - - - +
597B TRP* 4.0 8.3 - - + -
709B ASN* 3.5 8.6 + - - +
711B PHE 3.0 26.5 - - - +
712B ASP 3.6 14.8 - - - +
713B GLU* 3.2 15.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A HIS* 2.9 22.3 + - + +
688A ALA* 1.3 70.9 - - - +
690A ASP* 1.3 59.6 + - - +
691A ILE 3.1 2.5 - - - -
693A ASN 3.4 4.2 - - - +
694A THR* 4.9 0.5 - - - -
695A VAL* 5.1 7.2 + - + +
482B SER 5.6 0.4 - - - +
707B PRO* 3.1 37.3 - - + +
709B ASN* 2.8 23.2 + - - -
710B PHE 2.9 24.4 + - - -
711B PHE* 3.0 30.3 + - + -
713B GLU 4.6 1.8 - - - +
714B ASP* 3.1 33.2 - - + +
715B PRO* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLY 4.9 0.5 - - - +
495A ILE* 4.5 19.8 + - + +
684A HIS* 2.9 21.5 + - - -
686A PRO* 3.3 1.7 - - - +
687A HIS* 2.7 46.5 + - - +
689A GLU* 1.3 70.9 - - - +
691A ILE* 1.3 62.7 + - + +
692A PRO 3.3 7.4 - - - +
693A ASN 3.1 27.1 - - - +
694A THR* 3.0 30.8 + - - +
695A VAL* 4.9 1.0 + - - +
1745A CU 3.5 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.7 21.1 - - + -
298A GLY* 3.6 3.6 - - - +
299A SER* 3.6 36.8 - - - +
495A ILE* 4.1 22.0 - - + -
511A VAL* 4.0 34.8 - - + +
512A SER* 5.7 1.6 - - - -
687A HIS 4.6 0.4 - - - +
688A ALA 3.0 14.0 + - - +
689A GLU 3.1 0.6 - - - -
690A ASP* 1.3 87.1 - - - +
692A PRO* 1.3 64.3 - - + +
693A ASN 3.6 0.4 - - - -
712B ASP 5.4 1.1 - - - +
713B GLU* 3.4 12.5 - - + +
714B ASP* 2.6 32.3 + - - -
----------------------------------------------------------
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