Contacts of the helix formed by residues 673 - 688 (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 SER 673 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 4.0 14.3 - - - +
633A GLU* 2.5 29.6 + - - -
671A SER* 3.1 11.0 + - - -
672A HIS* 1.3 77.6 - - - +
674A LEU* 1.3 58.3 + - - +
675A THR* 3.5 4.7 + - - -
676A ILE* 3.3 23.5 + - - +
677A VAL* 3.1 29.1 + - - +
460C GLU* 3.8 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A HIS 3.4 7.7 + - - +
673A SER* 1.3 69.8 + - - +
675A THR* 1.3 59.2 + - - +
677A VAL* 3.8 6.9 - - + -
678A SER* 2.8 32.8 + - - -
713A SER* 5.0 3.4 - - - +
714A LYS* 4.8 16.6 - - + +
715A HIS* 4.6 21.3 - - + +
718A ILE* 3.7 25.6 - - + +
458C PHE 5.6 5.8 - - - +
460C GLU* 5.6 0.4 + - - -
386D TYR* 4.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A TRP* 3.6 33.4 - - + -
633A GLU* 3.8 25.7 + - + +
673A SER* 3.2 9.2 + - - -
674A LEU* 1.3 77.9 - - - +
676A ILE* 1.3 57.6 + - - +
678A SER* 3.3 6.4 + - - -
679A ASN* 2.8 38.7 + - - +
715A HIS* 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 4.2 20.0 - - + -
632A ILE* 3.8 24.2 - - + -
633A GLU* 3.7 20.2 - - + -
668A HIS* 3.5 40.7 + - + +
671A SER* 3.5 23.1 - - - +
673A SER* 3.3 23.4 + - - +
675A THR* 1.3 72.9 - - - +
677A VAL* 1.3 66.1 + - - +
679A ASN* 3.2 9.7 + - - +
680A ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A HIS 3.3 22.2 - - - +
669A LEU* 3.7 14.1 - - - +
671A SER 3.3 24.2 - - - +
673A SER 3.1 12.9 + - - +
674A LEU* 3.9 8.3 - - + +
676A ILE* 1.3 73.4 - - - +
678A SER* 1.3 58.6 + - - +
680A ALA* 3.3 3.9 + - - +
681A CYS* 2.9 35.7 + - - -
710A LEU* 4.3 14.6 - - + -
718A ILE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ARG* 3.3 17.6 + - - -
674A LEU 2.8 19.9 + - - -
675A THR* 3.4 6.7 - - - -
677A VAL* 1.3 79.0 - - - +
679A ASN* 1.3 63.7 + - - +
681A CYS* 3.4 3.9 + - - +
682A GLY 3.1 17.8 + - - -
715A HIS* 3.2 27.6 + - - -
717A MET* 3.3 18.6 - - - +
718A ILE* 3.7 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 679 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A TRP* 4.0 8.2 - - - -
632A ILE 4.6 0.6 + - - -
633A GLU* 2.9 34.6 + - - +
636A GLY* 3.5 17.9 - - - +
637A GLY* 3.2 19.0 - - - +
640A ARG* 3.4 27.7 + - - +
668A HIS* 6.2 0.9 - - - +
675A THR* 2.8 33.2 + - - +
676A ILE* 3.6 6.3 - - - +
678A SER* 1.3 71.3 - - - +
680A ALA* 1.3 59.3 + - - +
682A GLY 3.2 1.9 + - - -
683A THR* 2.9 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LEU* 3.7 30.9 - - + +
668A HIS* 3.7 27.1 + - + +
669A LEU* 4.2 7.0 - - + -
676A ILE 2.9 15.9 + - - +
677A VAL 3.7 3.8 - - - +
679A ASN* 1.3 75.5 - - - +
681A CYS* 1.3 56.7 + - - +
683A THR* 3.3 2.1 + - - -
684A LEU* 2.8 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A LEU* 3.8 19.3 - - - -
677A VAL* 2.9 21.9 + - - +
678A SER 3.7 4.5 - - - +
680A ALA* 1.3 74.1 - - - +
682A GLY* 1.3 60.8 + - - +
684A LEU* 3.4 5.3 + - - +
685A TRP* 2.8 30.0 + - - +
707A LEU* 4.8 1.8 - - - -
710A LEU* 4.8 1.3 - - - -
717A MET 4.4 6.5 - - - +
718A ILE* 3.9 21.1 - - - -
721A GLY* 3.9 12.0 - - - +
722A SER* 3.9 36.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ARG* 3.7 26.2 - - - +
678A SER 3.1 10.7 + - - -
679A ASN 3.2 3.5 + - - -
681A CYS* 1.3 75.6 - - - +
683A THR* 1.3 63.3 + - - +
685A TRP* 3.1 29.9 - - - +
686A ASN* 3.2 15.0 + - - -
717A MET 5.5 0.6 + - - -
721A GLY* 4.9 0.8 - - - -
379B SER 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A GLY 4.3 2.1 + - - -
639A LEU* 4.2 15.8 - - + +
640A ARG* 3.2 19.0 + - - +
643A SER* 3.7 22.9 - - - -
656A LEU* 5.5 0.2 - - + -
665A LEU* 3.6 31.2 - - + +
679A ASN 2.9 19.2 + - - -
680A ALA* 3.3 4.1 + - - -
682A GLY* 1.3 75.7 - - - +
684A LEU* 1.3 56.4 + - - +
686A ASN* 3.3 3.3 + - - +
687A LEU* 3.0 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 4.1 9.6 - - + +
665A LEU* 3.9 31.2 - - + -
666A LEU* 4.0 22.0 - - + -
669A LEU* 4.0 24.9 - - + -
680A ALA 2.8 23.0 + - - +
681A CYS* 3.9 4.0 - - - +
683A THR* 1.3 68.9 - - - +
685A TRP* 1.3 58.3 + - - +
687A LEU* 4.4 2.2 - - - +
688A SER* 2.7 38.3 + - - -
698A LEU* 3.8 33.0 - - + -
707A LEU* 4.3 10.5 - - + -
725A ALA* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A CYS 2.8 14.9 + - - +
682A GLY* 3.1 19.7 - - - +
684A LEU* 1.3 79.1 - - - +
686A ASN* 1.3 69.8 + - - +
688A SER* 3.3 3.6 + - - -
689A ALA* 3.6 5.6 + - + +
717A MET* 5.3 2.5 - - - -
720A MET* 4.4 25.8 - - + -
721A GLY* 3.5 26.7 - - - +
724A ALA* 3.4 31.7 - - + +
725A ALA* 4.1 7.8 - - - +
727A ARG* 5.8 1.1 - - - -
728A ASN* 3.2 23.1 + - - +
379B SER* 5.7 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ARG* 3.9 5.7 + - - +
643A SER* 2.8 40.3 + - - +
644A SER* 3.3 28.0 - - - +
647A ALA* 3.4 19.2 - - + +
653A ARG* 3.6 2.1 + - - -
682A GLY 3.2 12.4 + - - -
683A THR 3.8 1.8 - - - +
685A TRP* 1.3 88.1 + - - +
687A LEU* 1.3 62.3 + - - +
689A ALA* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A SER* 4.4 14.8 - - - +
646A ILE* 4.2 16.2 - - + -
647A ALA* 4.5 4.3 - - - +
653A ARG* 2.8 40.2 + - + +
656A LEU* 3.8 29.8 - - + -
661A CYS* 4.6 1.3 - - - -
662A LEU* 3.9 30.5 - - + -
665A LEU* 3.9 7.6 - - + -
683A THR* 3.0 39.3 + - + +
684A LEU* 4.5 2.2 - - + +
686A ASN* 1.3 77.8 - - - +
688A SER* 1.3 58.9 + - - +
689A ALA 3.2 1.5 - - - +
691A ASN* 4.1 1.7 - - - +
694A ASP* 3.9 11.9 - - - +
698A LEU* 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A LEU 2.7 24.9 + - - -
687A LEU* 1.3 75.3 - - - +
689A ALA* 1.3 53.0 + - - +
695A GLN* 2.7 37.3 + - - +
698A LEU* 3.7 25.9 - - - +
725A ALA* 3.5 12.5 - - - -
728A ASN* 3.1 31.4 + - - +
729A LEU* 4.2 9.2 - - - -
----------------------------------------------------------
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