Contacts of the strand formed by residues 758 - 765 (chain B) in PDB entry 2H5G
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 LEU 758 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B SER 3.5 22.2 - - - +
451B VAL* 4.4 10.3 - - + -
453B ARG* 6.1 0.7 - - - +
470B THR* 4.3 14.8 - - + +
471B VAL 3.5 19.3 - - - +
473B ILE* 3.8 2.2 - - - -
497B SER* 3.6 31.0 - - - +
747B HIS* 3.6 21.5 - - - -
754B LEU* 3.9 17.5 - - + +
755B GLU* 3.4 35.4 + - + +
756B GLY 3.3 0.6 - - - -
757B LEU* 1.3 83.3 - - - +
759B THR* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 759 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B THR* 3.3 9.7 - - - +
471B VAL* 2.9 43.1 + - + +
472B PRO 3.8 11.2 - - - +
473B ILE* 4.0 17.4 - - + +
747B HIS* 5.5 2.2 - - - -
758B LEU* 1.3 76.9 - - - +
760B THR* 1.3 79.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 760 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU* 3.6 28.5 - - + -
468B GLN* 3.2 27.6 + - - +
469B VAL 3.1 9.9 - - - +
470B THR* 5.1 0.7 - - + -
471B VAL* 4.0 8.6 - - - +
759B THR* 1.3 96.5 + - - +
761B LYS* 1.3 64.5 + - - +
762B TRP* 4.4 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 761 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B GLU 3.9 0.7 - - - +
468B GLN* 3.4 2.3 - - - -
469B VAL* 2.8 36.3 + - + +
471B VAL* 4.0 29.5 - - + +
760B THR* 1.3 77.6 - - - +
762B TRP* 1.3 70.2 + - - +
763B LEU* 3.9 31.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 762 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ARG* 3.7 31.6 - - + -
466B LEU* 3.7 41.3 - - + -
467B GLU 3.5 4.3 - - - -
468B GLN* 3.4 44.7 - - + +
760B THR* 4.4 4.8 + - - -
761B LYS* 1.3 81.7 - - - +
763B LEU* 1.3 65.8 + - - +
764B LEU* 4.2 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 763 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B GLU 3.8 1.4 - - - +
466B LEU* 3.3 5.7 - - - +
467B GLU* 2.8 57.6 + - + +
469B VAL* 4.0 23.8 - - + -
761B LYS* 4.0 29.4 - - + +
762B TRP* 1.3 78.8 - - - +
764B LEU* 1.3 60.2 + - - +
765B ARG* 3.8 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 764 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B ILE* 3.9 19.7 - - + -
464B LEU* 3.7 32.8 - - + -
465B GLU 3.5 22.0 - - - +
466B LEU* 3.9 13.2 - - + -
762B TRP 4.2 2.0 + - - -
763B LEU* 1.3 73.1 - - - +
765B ARG* 1.3 63.3 + - - +
766B GLY 4.0 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 765 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ASN 3.7 2.4 - - - +
464B LEU* 3.6 3.2 - - - -
465B GLU* 3.0 41.3 + - + +
466B LEU 6.0 0.2 - - - -
467B GLU* 2.9 34.9 + - - +
763B LEU* 3.8 27.1 + - + +
764B LEU* 1.3 77.7 - - - +
766B GLY* 1.3 59.6 + - - +
----------------------------------------------------------
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