Contacts of the helix formed by residues 629 - 647 (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 LEU 629 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A THR* 1.3 81.1 - - - +
630A ALA* 1.3 55.0 + - - +
631A ILE 3.3 3.1 - - - -
632A ILE* 3.1 19.4 + - + -
633A GLU* 2.8 51.9 + - + +
671A SER* 5.8 0.9 - - - +
673A SER* 4.0 24.0 - - - +
676A ILE* 4.2 16.2 - - + -
460C GLU* 4.2 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A GLU* 5.9 0.2 - - - +
586A LYS* 4.1 37.9 - - + +
628A THR* 3.4 18.1 + - - +
629A LEU* 1.3 77.9 - - - +
631A ILE* 1.3 61.3 + - + +
633A GLU* 3.4 8.9 + - - +
634A SER* 3.0 32.7 + - - -
383B TYR* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A GLU* 4.2 18.8 - - + +
585A LEU* 4.2 15.9 - - + -
586A LYS* 3.8 39.7 - - + +
589A LEU* 4.0 18.4 - - + -
619A THR* 4.0 11.7 - - + -
622A TYR* 3.7 55.2 - - + -
624A SER* 5.5 1.7 + - - +
628A THR* 5.2 1.0 + - - +
629A LEU 3.3 0.4 - - - -
630A ALA* 1.3 77.0 - - + +
632A ILE* 1.3 61.3 + - - +
634A SER* 5.8 0.4 - - - -
635A GLY* 2.9 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A THR 3.4 19.5 - - - +
620A LEU* 3.7 12.1 - - - +
621A THR* 5.1 0.9 - - - -
622A TYR* 4.0 24.5 - - + +
624A SER* 5.8 2.0 - - - -
628A THR 5.4 2.5 - - - +
629A LEU* 3.1 27.8 + - + +
631A ILE* 1.3 75.4 - - + +
633A GLU* 1.3 58.4 + - - +
636A GLY* 3.0 27.9 + - - -
668A HIS* 3.6 31.1 - - + +
676A ILE* 3.8 22.6 - - + +
679A ASN* 4.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A TRP* 3.9 11.6 - - + -
629A LEU* 2.8 34.6 + - + +
630A ALA* 3.8 6.9 - - - +
632A ILE* 1.3 77.2 - - - +
634A SER* 1.3 57.5 + - - +
637A GLY* 2.9 24.3 + - - -
673A SER* 2.5 28.0 + - - -
675A THR* 3.8 25.7 + - + +
676A ILE* 3.7 17.7 - - + -
679A ASN* 2.9 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LYS* 4.4 3.1 + - - +
589A LEU* 3.6 25.8 - - - -
590A SER* 3.7 19.8 + - - -
593A TRP* 3.4 24.6 - - - -
630A ALA 3.0 18.7 + - - -
631A ILE* 4.1 2.2 - - - -
633A GLU* 1.3 73.9 - - - +
635A GLY* 1.3 65.3 + - - +
637A GLY* 3.1 1.6 + - - -
638A ILE* 2.9 30.7 + - - +
383B TYR* 4.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU* 4.1 6.8 - - - +
616A LEU* 3.9 10.3 - - - +
619A THR* 3.2 26.5 - - - -
631A ILE 2.9 14.5 + - - -
634A SER* 1.3 74.8 - - - +
636A GLY* 1.3 57.5 + - - +
638A ILE* 3.4 12.8 + - - +
639A LEU* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A THR* 3.9 2.4 + - - -
620A LEU* 3.7 22.6 - - - +
632A ILE 3.0 18.5 + - - -
635A GLY* 1.3 73.7 - - - +
637A GLY* 1.3 59.5 + - - +
639A LEU* 3.7 3.5 - - - +
640A ARG* 2.9 27.5 + - - +
668A HIS* 6.0 0.4 - - - -
679A ASN* 3.5 15.8 - - - +
683A THR* 4.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A TRP* 3.5 26.5 + - - -
633A GLU 2.9 17.8 + - - -
634A SER 3.1 1.3 + - - -
636A GLY* 1.3 74.0 - - - +
638A ILE* 1.3 63.3 + - - +
640A ARG* 3.4 3.9 + - - +
641A ASN* 3.0 28.8 + - - +
679A ASN* 3.2 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU* 3.4 39.3 - - + +
592A LEU* 3.6 31.0 - - + -
593A TRP* 3.5 21.7 - - - +
596A SER* 3.8 13.5 - - - +
606A ILE* 4.3 13.5 - - + -
616A LEU* 3.7 25.1 - - + -
634A SER 2.9 19.8 + - - +
635A GLY* 3.6 7.4 - - - +
637A GLY* 1.3 73.0 - - - +
639A LEU* 1.3 66.3 + - - +
641A ASN* 3.1 3.8 + - - +
642A VAL* 3.0 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 4.9 2.0 - - + -
616A LEU* 4.4 24.2 - - + +
617A VAL* 4.8 8.5 - - + -
620A LEU* 3.8 36.6 - - + -
635A GLY 2.9 17.1 + - - +
636A GLY* 3.7 5.8 - - - +
638A ILE* 1.3 77.1 - - - +
640A ARG* 1.3 57.1 + - - +
642A VAL* 3.4 7.5 + - + +
643A SER* 2.8 32.7 + - - -
646A ILE* 4.0 24.0 - - + -
656A LEU* 4.6 10.1 - - + -
661A CYS* 3.9 15.9 - - - -
665A LEU* 4.6 2.5 - - + -
683A THR* 4.2 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A TRP* 5.4 4.6 - - - +
636A GLY 2.9 17.4 + - - +
637A GLY* 3.6 5.3 + - - +
638A ILE 3.3 0.2 - - - -
639A LEU* 1.3 74.7 - - - +
641A ASN* 1.3 74.7 + - - +
643A SER* 2.6 21.4 + - - -
678A SER* 3.3 29.9 + - - -
679A ASN* 3.4 37.2 + - - +
682A GLY* 3.7 13.3 - - - -
683A THR* 3.2 26.2 + - - +
686A ASN* 3.9 5.6 + - - +
717A MET* 3.7 26.3 + - - +
379B SER* 3.1 36.3 - - - +
380B TYR* 4.3 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A TRP* 3.2 12.5 + - - -
596A SER* 3.0 37.3 + - - +
597A ALA* 3.5 14.4 - - - +
603A LYS* 2.7 31.1 + - - +
637A GLY 3.0 16.0 + - - +
638A ILE 3.1 3.1 + - - +
640A ARG* 1.3 87.7 + - - +
642A VAL* 1.3 58.0 + - - +
644A SER* 3.1 10.4 + - - -
379B SER* 3.9 4.0 - - - -
380B TYR 3.1 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A SER* 4.4 2.7 - - - -
603A LYS* 3.8 39.5 - - + +
606A ILE* 3.9 25.1 - - + -
607A CYS* 3.9 13.7 - - - -
613A LEU* 4.5 0.4 - - + -
616A LEU* 4.3 13.7 - - + -
638A ILE* 3.0 23.2 + - + +
639A LEU* 3.5 13.7 - - - +
641A ASN* 1.3 71.5 - - - +
643A SER* 1.3 64.3 + - - +
644A SER 3.2 2.7 - - - -
645A LEU* 3.0 8.1 + - - +
646A ILE* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A LEU* 2.8 17.8 + - - -
640A ARG 2.6 18.9 + - - -
641A ASN 3.2 0.2 - - - -
642A VAL* 1.3 78.0 - - - +
644A SER* 1.3 55.2 + - - +
646A ILE* 3.6 12.6 - - - +
647A ALA* 2.9 31.7 + - - +
683A THR* 3.7 29.1 - - - -
686A ASN* 2.8 27.6 + - - +
687A LEU* 4.4 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LYS* 3.2 17.6 + - - +
641A ASN 3.1 17.6 + - - -
643A SER* 1.3 79.8 + - - +
645A LEU* 1.3 58.7 + - - +
647A ALA* 3.9 6.1 - - - +
648A THR* 3.8 16.3 - - - +
686A ASN* 3.3 26.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A THR* 4.4 20.0 - - + +
603A LYS* 3.8 16.2 - - + +
604A ALA* 3.4 44.9 - - + +
607A CYS* 4.5 9.6 - - + -
642A VAL 3.0 8.7 + - - +
644A SER* 1.3 76.4 + - - +
646A ILE* 1.3 68.1 + - - +
647A ALA 3.1 1.6 - - - -
648A THR* 2.9 33.5 + - + +
649A ASN* 3.7 7.4 + - + +
652A HIS* 5.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A CYS* 4.1 14.1 - - - -
613A LEU* 3.8 28.9 - - + -
639A LEU* 4.0 16.8 - - + -
642A VAL* 3.0 24.5 + - + +
643A SER* 3.6 11.7 - - - +
645A LEU* 1.3 77.1 - - - +
647A ALA* 1.3 56.6 + - - +
649A ASN* 2.8 31.6 + - - +
652A HIS* 3.8 25.4 - - + -
653A ARG* 3.7 13.1 - - - +
656A LEU* 3.9 22.4 - - + -
687A LEU* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A SER 2.9 17.0 + - - +
644A SER* 3.9 9.0 - - - +
645A LEU 3.1 0.2 - - - -
646A ILE* 1.3 75.8 - - - +
648A THR* 1.3 59.5 + - + +
649A ASN 3.3 1.6 + - - -
653A ARG* 2.9 36.2 + - - +
686A ASN* 3.4 30.7 - - + +
687A LEU* 4.5 2.9 - - + +
689A ALA* 5.4 0.9 - - + +
690A ARG 5.7 0.7 - - - +
691A ASN* 5.2 0.2 + - - -
----------------------------------------------------------
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