Contacts of the helix formed by residues 715 - 731 (chain A) in PDB entry 3QHE
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 715 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LEU* 4.6 22.7 - - + +
675A THR* 5.8 1.6 - - - -
678A SER* 3.2 24.8 + - - -
713A SER* 3.2 11.6 + - - +
714A LYS* 1.3 82.0 - - + +
716A LYS* 1.3 67.3 + - - +
717A MET* 3.6 27.5 - - + +
718A ILE* 3.2 35.9 + - + +
719A ALA* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A SER 5.4 0.2 - - - -
714A LYS 3.4 6.3 + - - +
715A HIS* 1.3 71.7 - - - +
717A MET* 1.3 59.4 + - + +
719A ALA* 3.4 6.1 + - + +
720A MET* 2.9 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ARG* 3.7 30.5 - - - +
678A SER* 3.3 16.3 - - - +
681A CYS* 4.4 4.1 - - - +
682A GLY 5.5 0.5 + - - -
685A TRP* 5.3 2.3 - - - -
715A HIS* 3.3 28.9 - - + +
716A LYS* 1.3 76.7 - - + +
718A ILE* 1.3 57.3 + - - +
720A MET* 4.9 2.2 - - - -
721A GLY* 2.8 30.1 + - - +
379B SER 4.0 14.8 - - - +
380B TYR* 4.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LEU* 3.7 38.8 - - + +
677A VAL* 3.7 26.5 - - + -
678A SER* 3.7 21.5 - - - +
681A CYS* 4.0 9.4 - - - -
710A LEU* 3.8 22.0 - - + +
713A SER* 3.6 18.6 - - - +
715A HIS* 3.2 27.0 + - + +
717A MET* 1.3 73.2 - - - +
719A ALA* 1.3 55.8 + - - +
722A SER* 2.6 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 719 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LEU 3.6 11.2 + - - -
711A ILE* 3.4 20.7 - - - +
713A SER* 3.6 20.8 - - - +
715A HIS 3.1 10.3 + - - +
716A LYS* 3.7 7.2 - - + +
718A ILE* 1.3 76.6 - - - +
720A MET* 1.3 59.7 + - + +
722A SER* 3.2 2.3 + - - -
723A ALA* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A TRP* 4.4 25.7 - - + -
716A LYS* 2.9 52.7 + - + +
717A MET* 4.4 2.0 - - - +
719A ALA* 1.3 74.3 - - + +
721A GLY* 1.3 57.0 + - - +
723A ALA* 3.3 5.1 + - - +
724A ALA* 2.7 36.9 + - - +
727A ARG* 5.0 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 721 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A CYS* 3.9 18.8 - - - +
682A GLY 4.9 0.2 - - - -
685A TRP* 3.5 24.2 - - - +
717A MET 2.8 18.7 + - - -
720A MET* 1.3 77.1 - - - +
722A SER* 1.3 57.4 + - - +
724A ALA* 3.8 1.4 - - - +
725A ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 722 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A CYS* 3.9 13.1 - - - +
707A LEU* 3.8 27.6 - - - +
710A LEU* 3.4 34.9 - - - -
711A ILE* 3.5 4.1 + - - -
718A ILE 2.6 25.0 + - - -
719A ALA 3.2 5.0 + - - -
721A GLY* 1.3 74.6 - - - +
723A ALA* 1.3 60.0 + - - +
725A ALA* 3.4 1.0 + - - +
726A LEU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A ILE* 3.7 20.4 - - + +
719A ALA 3.0 22.3 + - - +
720A MET* 3.7 5.4 - - - +
722A SER* 1.3 78.6 + - - +
724A ALA* 1.3 57.7 + - - +
726A LEU* 3.3 5.4 + - - +
727A ARG* 2.9 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A TRP* 3.4 40.2 - - + +
720A MET* 2.7 21.4 + - + +
723A ALA* 1.3 71.8 - - - +
725A ALA* 1.3 57.5 + - - +
727A ARG* 3.3 25.5 + - - +
728A ASN* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A LEU* 4.0 15.3 - - + +
685A TRP* 4.1 7.7 - - - +
688A SER* 3.5 20.9 + - - +
707A LEU* 3.9 23.1 - - + -
721A GLY 2.9 18.5 + - - +
722A SER 3.8 2.9 - - - +
724A ALA* 1.3 75.2 - - - +
726A LEU* 1.3 64.6 + - - +
728A ASN* 3.1 6.0 + - - +
729A LEU* 3.1 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A VAL* 4.0 29.6 - - + +
707A LEU* 4.1 10.2 - - + +
708A LYS* 3.9 29.2 - - + +
711A ILE* 4.2 19.3 - - + -
722A SER 2.9 17.9 + - - +
723A ALA* 3.3 4.9 + - - +
725A ALA* 1.3 77.3 - - - +
727A ARG* 1.3 56.2 + - - +
729A LEU* 3.3 5.2 + - + +
730A MET* 3.0 56.3 + - + +
674C LEU* 4.2 16.8 - - + -
715C HIS* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A TRP* 5.8 1.0 - - - -
720A MET* 5.0 5.5 + - - +
723A ALA* 2.9 36.3 + - - +
724A ALA* 3.7 27.9 - - - +
726A LEU* 1.3 72.6 - - - +
728A ASN* 1.3 62.2 + - - +
730A MET* 4.0 6.6 - - - +
731A ALA* 3.0 31.9 + - - +
672C HIS* 3.6 26.6 + - - +
673C SER* 6.1 0.4 - - - +
674C LEU* 4.2 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A TRP* 3.2 24.4 + - - +
688A SER* 3.1 36.8 + - - +
689A ALA* 3.8 16.1 - - - +
690A ARG 5.5 0.2 + - - -
695A GLN* 3.6 19.3 + - - +
724A ALA* 2.9 22.3 + - - +
725A ALA 3.1 7.4 + - - +
727A ARG* 1.3 79.1 - - - +
729A LEU* 1.3 61.0 + - - +
731A ALA* 3.9 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A SER* 4.2 4.7 - - - -
695A GLN* 3.7 42.8 - - + +
698A LEU* 4.0 18.2 - - + -
699A TRP* 2.9 35.0 + - + +
703A ALA* 3.9 27.6 - - + -
704A VAL* 4.2 16.8 - - + -
707A LEU* 4.0 17.7 - - + -
725A ALA 3.1 10.6 + - - +
726A LEU* 3.3 7.4 + - - +
727A ARG 3.2 0.2 - - - -
728A ASN* 1.3 78.8 - - - +
730A MET* 1.3 58.8 + - + +
731A ALA 3.4 0.2 - - - -
714C LYS* 3.5 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A TRP* 3.9 10.3 - - + -
704A VAL* 3.6 38.6 - - + -
726A LEU* 3.0 30.3 + - + +
727A ARG* 3.3 4.2 + - - +
729A LEU* 1.3 76.1 - - - +
731A ALA* 1.3 66.0 + - - +
674C LEU* 3.7 31.6 - - + -
713C SER* 5.2 2.1 + - - +
714C LYS* 3.2 28.4 + - - +
715C HIS* 3.4 45.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ARG 3.0 16.8 + - - +
728A ASN* 4.2 10.3 - - - +
729A LEU 3.4 2.0 - - - -
730A MET* 1.3 82.2 - - - +
714C LYS* 4.1 21.6 - - - +
----------------------------------------------------------
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