Contacts of the strand formed by residues 823 - 827 (chain D) in PDB entry 2HVH
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 823 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D ALA* 4.4 17.2 - - + +
643D SER* 5.1 0.9 - - - -
647D TRP* 3.9 14.3 - + - -
815D LEU* 4.5 5.8 - - - -
821D GLN 3.5 11.5 + - - +
822D ALA* 1.3 75.1 - - - +
824D LEU* 1.3 77.1 + - - +
825D LEU* 3.7 10.6 - - + +
834D LEU* 3.3 7.9 - - - +
835D GLU* 2.8 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 824 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D ILE* 3.8 26.7 - - + -
488D MET* 3.7 30.0 - - + +
491D ALA* 5.1 0.3 - - - +
808D MET* 4.2 30.1 - - + +
811D LEU* 4.1 17.0 - - + -
812D ASN* 4.9 6.7 - - + +
815D LEU* 5.1 3.9 - - + +
823D HIS* 1.3 87.9 - - - +
825D LEU* 1.3 59.8 + - - +
826D LEU 4.4 6.3 - - - +
832D LEU* 4.0 22.7 - - + -
833D ILE 3.7 6.3 - - - +
834D LEU* 4.0 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 825 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D MET* 3.6 24.2 - - - +
491D ALA* 5.0 2.9 - - + -
492D GLY 3.5 22.5 - - - +
493D VAL* 4.2 30.2 - - + +
494D LYS 5.9 0.2 - - - +
604D THR* 5.7 0.5 - - - +
606D PHE* 4.4 2.8 - - - -
641D VAL 5.5 0.9 - - - +
649D ILE* 3.7 29.4 - - + -
823D HIS* 3.7 18.2 - - + +
824D LEU* 1.3 74.3 - - - +
826D LEU* 1.3 70.7 + - + +
833D ILE* 2.7 20.0 + - + +
834D LEU 4.4 2.0 - - - -
835D GLU* 3.7 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 826 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D MET* 3.5 10.4 - - - +
493D VAL* 4.1 19.5 - - + -
604D THR* 4.6 3.1 - - + -
606D PHE* 3.9 17.7 - - + -
623D LEU* 3.8 40.8 - - + +
624D GLN* 6.3 0.2 - - + -
640D PHE* 5.7 0.2 - - + -
824D LEU* 4.4 1.7 - - - +
825D LEU* 1.3 89.5 - - + +
827D GLN* 1.3 65.0 + - - +
828D VAL* 4.7 2.5 - - + -
832D LEU* 3.7 5.9 - - - +
833D ILE* 3.1 44.9 + - + +
872D TRP* 3.9 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 827 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D LEU* 5.7 0.2 - - + -
488D MET* 4.8 0.7 - - + -
606D PHE* 3.9 11.2 - - + -
616D LEU* 3.5 32.9 - - + +
624D GLN* 2.9 39.5 + - - +
804D ILE* 4.0 20.2 - - + +
805D LYS* 5.3 4.2 - - - +
808D MET* 3.8 23.9 - - + -
826D LEU* 1.3 77.1 - - - +
828D VAL* 1.3 64.5 + - - +
829D HIS* 2.8 35.5 + - - +
831D GLU 3.4 5.2 - - - +
832D LEU* 3.8 21.1 - - + -
----------------------------------------------------------
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