Contacts of the helix formed by residues 624 - 640 (chain A) in PDB entry 2CKH
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 GLN 624 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A MET* 4.3 10.1 - - - +
622A THR* 2.7 25.2 + - - +
623A GLN* 1.3 87.1 - - + +
625A HIS* 1.3 70.8 + - + +
626A MET 3.0 0.9 + - - -
627A PRO* 3.2 23.6 - - + +
628A TYR* 4.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A PHE* 3.3 37.6 - + + -
620A ASN* 4.8 4.3 - - + -
621A PHE* 3.5 37.3 - - + +
622A THR* 3.3 25.6 + - - +
623A GLN 2.8 0.6 + - - +
624A GLN* 1.3 90.3 + - + +
626A MET* 1.3 57.0 + - - +
628A TYR* 3.7 10.1 - - + +
629A PHE* 2.8 40.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ASP* 3.4 25.1 - - - +
604A MET* 3.4 30.7 - - + +
605A PHE* 3.4 48.0 - - + +
608A LYS* 4.5 4.3 - - + -
621A PHE* 3.8 26.5 - - + -
623A GLN* 2.3 46.5 + - - +
624A GLN 3.0 0.8 - - - -
625A HIS* 1.3 64.4 - - + +
627A PRO* 1.4 57.1 - - + +
628A TYR 3.1 1.3 - - - -
629A PHE* 2.9 11.6 + - - +
630A ARG* 2.6 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ASP* 5.0 0.9 - - - +
623A GLN* 3.2 17.0 - - - +
624A GLN* 3.2 20.0 - - - +
626A MET* 1.4 89.7 - - + +
628A TYR* 1.3 58.9 + - - +
630A ARG* 3.3 16.4 - - + +
631A LYS* 3.2 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A PHE* 3.7 25.8 - + + -
421A PRO* 2.9 34.6 + - - +
423A ILE* 4.2 30.5 - - + -
624A GLN 4.3 5.4 - - - +
625A HIS* 3.7 15.9 - - - +
626A MET 3.1 0.2 - - - -
627A PRO* 1.3 77.5 - - - +
629A PHE* 1.3 89.4 + + - +
630A ARG 3.1 0.3 + - - -
631A LYS* 3.2 8.2 + - - +
632A ARG* 2.7 72.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLU* 5.9 0.7 - - - -
420A PHE* 4.5 12.8 - + - -
604A MET* 3.5 6.8 - - + +
608A LYS* 3.4 55.0 - - + +
620A ASN* 5.8 1.3 - - - -
621A PHE* 3.9 35.2 - + + -
625A HIS* 2.8 30.2 + - + +
626A MET* 2.9 14.4 + - - +
628A TYR* 1.3 87.8 - + - +
630A ARG* 1.3 54.1 + - - +
632A ARG* 3.3 33.7 - - + +
633A MET* 2.6 36.4 + - - +
636A GLU* 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PHE* 6.0 0.2 - - - -
460A LEU* 2.6 50.0 + - - +
461A ASN 2.8 20.6 + - - -
462A HIS 3.3 20.9 + - - +
463A LEU* 3.7 4.5 - - - +
464A ASN 2.7 30.7 + - - +
466A LEU* 3.7 14.8 - - - +
600A SER 4.3 5.5 + - - -
601A ASP* 3.0 27.2 + - - +
604A MET* 3.5 25.7 - - + +
626A MET 2.6 19.1 + - - +
627A PRO* 3.3 17.5 - - + +
629A PHE* 1.3 70.3 - - - +
631A LYS* 1.3 70.6 + - + +
633A MET* 3.1 12.0 + - - +
634A VAL* 3.2 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE* 5.2 9.9 - - + -
428A GLU* 3.9 25.1 + - - +
431A ILE* 4.3 28.5 - - + +
435A PHE* 5.3 6.7 - - + -
627A PRO* 3.2 19.7 + - - +
628A TYR* 3.8 7.6 - - - +
630A ARG* 1.3 77.4 - - + +
632A ARG* 1.3 65.9 + - - +
634A VAL* 2.8 29.6 + - - +
635A TRP 3.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLU* 4.2 9.3 + - - -
420A PHE* 4.5 0.8 - - - -
421A PRO* 3.5 17.8 - - - +
422A GLU 6.0 1.1 - - - -
423A ILE* 5.2 8.2 - - + +
427A MET* 6.3 1.6 - - - -
431A ILE* 5.8 0.7 - - - -
608A LYS* 3.3 15.8 - - - +
628A TYR* 2.7 62.3 + - + +
629A PHE* 3.3 31.6 - - + +
631A LYS* 1.3 73.1 - - - +
633A MET* 1.3 63.2 + - - +
634A VAL 3.2 0.5 + - - -
635A TRP* 3.4 7.1 + - - +
636A GLU* 2.8 64.6 + - - +
643A LEU* 2.8 48.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 4.1 17.0 - - + -
466A LEU* 4.8 0.7 - - - -
470A ILE* 4.1 8.7 - - - -
474A TYR* 3.4 39.3 - - + -
604A MET* 3.3 32.5 - - + +
607A CYS* 3.8 24.5 - - + -
608A LYS* 4.4 9.2 - - + -
629A PHE 2.6 23.7 + - - +
630A ARG 3.1 6.3 + - - +
632A ARG* 1.3 72.6 - - - +
634A VAL* 1.3 51.7 + - - +
636A GLU* 3.0 14.2 + - - +
637A ILE* 2.7 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ILE* 4.4 12.1 - - + -
434A VAL* 4.3 15.0 - - + -
435A PHE* 4.1 16.6 - - + -
457A ILE* 3.8 37.5 - - + -
460A LEU* 3.5 13.2 - - + -
630A ARG 3.2 12.3 - - - +
631A LYS* 2.8 24.4 + - - +
633A MET* 1.3 71.1 - - - +
635A TRP* 1.3 61.7 + - - +
637A ILE* 3.0 10.8 + - - +
638A LEU* 3.0 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A MET* 4.2 44.5 - - + +
430A GLU* 4.2 10.8 + - + -
431A ILE* 5.2 10.2 - - + +
631A LYS 3.7 3.2 + - - +
632A ARG* 3.4 8.8 + - - +
633A MET 3.3 0.2 - - - -
634A VAL* 1.3 75.0 - - - +
636A GLU* 1.3 72.4 + - + +
637A ILE 3.0 1.0 + - - -
638A LEU* 3.2 4.8 + - + +
639A HIS* 3.0 69.9 + + + -
641A LYS* 3.8 22.0 - - + -
643A LEU* 3.7 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A TYR* 4.2 12.8 + - + -
477A MET* 3.4 14.4 - - + +
608A LYS* 4.2 4.3 + - - +
629A PHE 4.6 0.7 - - - +
632A ARG* 2.8 53.7 + - + +
633A MET* 3.0 24.0 + - + +
635A TRP* 1.3 82.0 - - + +
637A ILE* 1.3 58.6 + - - +
640A ARG* 3.1 24.9 + - - -
641A LYS 3.0 24.1 + - - +
642A LEU* 3.4 11.7 - - - +
643A LEU* 3.1 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A SER* 4.0 0.8 + - - +
452A ILE* 4.3 24.9 - - + -
457A ILE* 4.8 5.6 - - + -
460A LEU* 4.5 5.6 - - + -
470A ILE* 4.2 20.0 - - + +
473A PHE* 3.3 50.7 - - + -
474A TYR* 4.4 2.0 - - + -
477A MET* 4.2 15.3 - - + -
633A MET* 2.7 60.5 + - + +
634A VAL* 3.3 9.2 - - - +
635A TRP 3.0 0.2 - - - -
636A GLU* 1.3 71.2 - - - +
638A LEU* 1.3 67.6 + - - +
640A ARG 3.1 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLU* 4.0 22.4 - - + +
431A ILE* 6.3 0.2 - - - -
434A VAL* 4.5 19.1 - - + -
444A LEU* 3.9 44.0 - - + +
445A SER* 3.3 25.7 + - - -
452A ILE* 5.5 0.4 - - + -
457A ILE* 5.0 10.5 - - + -
634A VAL* 3.0 30.3 + - + +
635A TRP* 3.2 2.7 + - - +
637A ILE* 1.3 80.3 - - + +
639A HIS* 1.3 71.3 + - + +
640A ARG* 3.6 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLU* 3.2 25.0 + - - -
635A TRP* 3.0 73.9 + + + +
638A LEU* 1.3 86.6 - - + +
640A ARG* 1.3 76.2 + - - +
641A LYS* 4.2 1.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
447A ALA* 3.7 30.2 - - - +
448A PHE* 5.0 13.3 - - + -
473A PHE* 4.7 9.2 - - + -
477A MET* 3.8 19.5 - - + -
480A GLU* 2.8 40.6 + - - +
636A GLU 3.1 8.6 + - - -
637A ILE 3.1 11.8 + - - +
638A LEU 3.4 1.5 - - - +
639A HIS* 1.3 89.9 - - - +
641A LYS* 1.3 64.4 + - - +
----------------------------------------------------------
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