Contacts of the helix formed by residues 633 - 651 (chain B) in PDB entry 4KSP
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 633 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ILE* 3.7 22.3 - - - +
631B PRO 4.3 1.0 + - - -
632B TYR* 1.3 75.9 - - - +
634B PHE* 1.3 66.1 + - - +
635B GLN* 3.3 13.4 + - - +
636B SER* 2.9 34.0 + - - -
637B ASP* 3.4 4.5 + - - +
700B ARG* 3.7 32.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 634 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B HIS* 3.3 71.8 - + + +
570B SER* 4.6 16.8 - - - -
572B ILE* 4.0 22.2 - - + +
633B SER* 1.3 73.3 - - - +
635B GLN* 1.3 62.4 + - - +
637B ASP 3.4 0.9 + - - -
638B VAL* 3.1 27.9 + - - +
705B LEU* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B SER* 3.0 17.1 - - - +
634B PHE* 1.3 83.2 + - - +
636B SER* 1.3 61.2 + - - +
638B VAL* 3.5 7.5 + - - +
639B TYR 3.2 8.7 + - - -
700B ARG* 3.3 38.1 + - + +
701B ASP* 4.5 9.5 + - - +
703B ARG* 2.9 45.9 + - + +
704B PRO 4.9 1.3 - - - +
705B LEU* 4.1 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ILE* 4.9 0.3 - - - +
618B TRP 4.8 1.7 - - - +
620B ALA* 4.4 5.7 + - - +
622B GLU* 4.1 6.3 - - - -
623B VAL* 3.9 27.4 - - - -
631B PRO 4.5 0.2 - - - -
632B TYR* 3.6 14.9 - - - +
633B SER* 2.9 39.2 + - - -
635B GLN* 1.3 73.3 - - - +
637B ASP* 1.3 67.7 + - - +
639B TYR* 3.3 4.2 + - - +
640B ALA* 3.1 21.7 + - - +
703B ARG* 4.3 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B MET* 3.7 9.2 - - + +
567B HIS* 3.2 25.0 + - + +
572B ILE* 3.4 11.9 - - - +
573B HIS* 2.7 35.9 + - - +
574B ARG* 3.1 25.5 + - - -
575B ASP 4.7 0.2 + - - -
576B LEU* 3.9 8.9 + - - +
633B SER 3.4 1.4 + - - +
634B PHE 3.5 9.9 - - - +
635B GLN 3.3 0.2 - - - -
636B SER* 1.3 83.8 + - - +
638B VAL* 1.3 60.8 + - - +
640B ALA* 3.3 7.8 + - - +
641B PHE* 2.9 22.5 + - - +
706B PHE* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 638 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B HIS* 4.9 0.2 - - + -
634B PHE 3.1 17.6 + - - +
635B GLN* 3.6 13.0 - - + +
636B SER 3.2 0.6 - - - -
637B ASP* 1.3 74.9 - - - +
639B TYR* 1.3 51.5 - - - +
641B PHE* 3.1 7.2 + - - +
642B GLY* 2.8 31.0 + - - -
695B CYS* 4.0 22.5 - - - +
703B ARG* 4.2 6.3 - - + -
704B PRO* 3.3 28.0 - - + +
705B LEU* 4.5 4.5 - - + -
706B PHE* 3.5 27.8 - - + -
709B ILE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 639 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B LEU 4.6 1.5 + - - -
618B TRP 3.5 15.5 - - - -
619B MET 3.3 19.3 - - - -
620B ALA* 3.5 13.9 - - + -
621B PRO* 3.9 17.3 - - + +
635B GLN 3.2 5.3 + - - +
636B SER 3.5 7.9 - - - +
638B VAL* 1.3 77.0 - - - +
640B ALA* 1.3 58.1 + - - +
642B GLY* 2.8 17.0 + - - -
643B ILE* 2.9 31.3 + - + +
655B TYR* 3.8 18.7 + - - -
668B VAL* 4.1 12.6 - - - +
674B SER* 5.7 0.9 - - - -
675B PRO* 4.6 5.6 - - + +
695B CYS 3.4 21.5 + - - -
696B LEU* 3.5 35.2 - - + +
697B LYS 4.2 6.7 - - - -
698B LYS* 6.0 0.4 - - + -
703B ARG* 3.7 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 640 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B LEU* 3.5 34.8 - - + +
618B TRP* 3.5 23.9 - - + +
636B SER 3.1 9.6 + - - +
637B ASP* 3.6 9.6 - - - +
638B VAL 3.3 0.2 - - - -
639B TYR* 1.3 78.3 - - - +
641B PHE* 1.3 63.5 + - - +
643B ILE* 3.0 6.2 + - - +
644B VAL* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 641 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ALA* 3.9 25.6 - - - -
559B THR* 4.0 22.0 - - + -
560B ALA* 3.9 21.1 - - + -
563B MET* 5.1 0.2 - - + -
576B LEU* 3.8 12.2 - - + +
637B ASP 2.9 14.3 + - - +
638B VAL 3.1 9.6 - - - +
640B ALA* 1.3 74.9 - - - +
642B GLY* 1.3 56.6 + - - +
644B VAL* 3.1 11.6 + - + +
645B LEU* 2.9 61.3 + - + +
648B LEU* 6.3 0.7 - - + -
695B CYS* 4.1 12.8 - - - -
706B PHE* 3.8 24.7 - + + -
709B ILE* 3.7 20.6 - - + -
713B ILE* 4.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 642 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B VAL 2.8 13.5 + - - -
639B TYR 2.8 9.1 + - - -
641B PHE* 1.3 72.1 - - - +
643B ILE* 1.3 60.0 + - - -
645B LEU* 3.3 10.4 + - - +
646B TYR* 3.1 18.2 + - - +
692B MET* 4.1 5.5 - - - +
695B CYS* 3.7 25.4 - - - -
696B LEU* 3.6 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 643 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B LEU 3.4 25.1 - - - +
618B TRP* 3.4 29.8 - - + +
639B TYR* 2.9 35.4 + - + +
640B ALA 3.0 6.9 + - - +
642B GLY* 1.3 73.1 - - - +
644B VAL* 1.3 65.2 + - - +
646B TYR* 3.0 15.6 + - + +
647B GLU* 3.0 13.3 + - - +
654B PRO* 4.1 24.2 - - + -
655B TYR* 4.7 1.8 - - - +
675B PRO* 3.8 21.5 - - + -
696B LEU* 3.5 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 644 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 4.2 16.6 - - + -
559B THR* 5.3 7.0 - - + +
576B LEU* 4.8 3.1 - - + -
577B LYS* 4.1 7.0 - - - +
578B SER* 4.1 12.6 - - - +
581B ILE* 4.1 22.9 - - + -
618B TRP* 3.8 19.3 - - + +
640B ALA 3.0 16.6 + - - +
641B PHE* 3.4 15.0 - - + +
643B ILE* 1.3 74.1 - - - +
645B LEU* 1.3 64.7 + - - +
647B GLU* 3.1 14.6 + - + +
648B LEU* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 645 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ALA* 3.8 24.2 - - + -
641B PHE* 2.9 45.0 + - + +
642B GLY* 3.4 9.9 - - - +
644B VAL* 1.3 76.8 - - - +
646B TYR* 1.3 58.8 + - - +
648B LEU* 3.5 10.0 + - + +
649B MET* 3.2 32.1 + - + +
688B MET* 3.8 24.7 - - - -
691B LEU* 4.2 20.4 - - + -
692B MET* 3.5 29.7 - - + +
695B CYS* 4.4 4.3 - - - -
713B ILE* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 646 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B GLY 3.1 9.3 + - - +
643B ILE* 3.0 19.4 + - + +
645B LEU* 1.3 75.6 - - - +
647B GLU* 1.3 57.5 + - - +
649B MET 3.3 0.3 + - - -
650B THR* 2.7 62.7 + - + +
652B GLN* 3.7 12.3 - - + -
653B LEU 4.1 2.0 - - - -
654B PRO* 3.8 34.5 - - + +
655B TYR 5.3 0.9 + - - -
675B PRO* 3.8 27.1 - - + -
676B ASP* 3.2 36.3 + - - +
677B LEU* 4.2 14.1 - - + -
679B LYS* 3.3 24.1 + - - +
680B VAL* 5.4 0.2 - - + -
692B MET* 3.9 10.7 - - - -
696B LEU* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 647 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 3.9 15.0 - - + +
541B HIS* 2.5 30.6 + - + +
578B SER* 2.6 30.8 + - - -
618B TRP* 2.7 36.3 + - - +
643B ILE* 3.0 15.1 + - + +
644B VAL* 3.1 12.3 + - + +
646B TYR* 1.3 76.4 - - - +
648B LEU* 1.3 56.4 + - - +
651B GLY* 2.7 34.0 + - - -
652B GLN 3.5 19.7 - - - +
653B LEU* 3.9 6.2 - - + +
654B PRO* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 648 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 3.8 36.8 - - + -
540B LEU* 4.1 5.5 - - + +
552B LEU* 3.3 59.1 - - + +
555B ILE* 4.0 14.1 - - + -
556B ALA* 4.1 23.3 - - + +
559B THR* 5.8 0.9 - - - +
641B PHE* 6.3 0.7 - - + -
644B VAL* 3.0 28.4 + - + +
645B LEU* 3.9 9.6 - - + +
647B GLU* 1.3 78.8 - - - +
649B MET* 1.3 75.1 + - + +
650B THR 3.5 0.5 + - - -
651B GLY* 4.0 3.8 + - - -
681B ARG* 5.1 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 649 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B MET* 3.6 29.8 - - - +
552B LEU* 4.3 15.9 - - + +
553B ILE* 5.2 1.8 - - + +
556B ALA* 5.4 0.7 - - + -
645B LEU* 3.2 26.2 + - + +
646B TYR 4.1 1.6 - - - +
648B LEU* 1.3 102.9 - - + +
650B THR* 1.3 58.5 + - - +
680B VAL* 3.5 5.9 - - + -
681B ARG* 3.1 35.6 + - - +
684B CYS* 3.1 34.3 - - + -
688B MET* 3.9 17.7 - - + -
692B MET* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 650 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B TYR* 2.7 49.7 + - + +
649B MET* 1.3 82.3 - - - +
651B GLY* 1.3 58.4 + - - +
652B GLN* 3.0 42.4 + - - +
679B LYS* 3.5 34.7 - - + +
680B VAL* 3.8 8.5 - - + +
681B ARG* 4.6 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 651 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 3.4 30.6 - - - +
541B HIS* 3.5 10.6 + - - -
544B GLU* 5.4 2.4 - - - +
647B GLU 2.7 19.1 + - - -
648B LEU 4.0 3.9 + - - -
649B MET 3.9 0.6 - - - -
650B THR* 1.3 72.8 - - - +
652B GLN* 1.3 60.5 + - - +
681B ARG* 5.6 1.5 - - - +
----------------------------------------------------------
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