Contacts of the helix formed by residues 604 - 623 (chain A) in PDB entry 2WSC
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 TRP 604 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE* 3.2 41.1 - + - -
548A THR* 3.9 25.6 - - + -
551A VAL* 3.3 31.4 - - + -
552A THR* 3.4 15.9 - - - +
555A ILE* 4.0 7.0 - - + -
600A LEU 3.6 11.3 + - - +
601A GLY 3.8 4.5 + - - +
602A LEU 2.8 3.8 + - - -
603A PHE* 1.3 75.7 - - + +
605A MET* 1.4 53.0 + - - +
606A TYR 2.6 0.5 + - - -
607A ASN* 2.3 42.9 + - + +
608A SER* 3.7 3.1 - - - -
1811A CLA 4.9 0.4 - - + -
1786B CLA 3.4 46.0 - + + +
1787B CLA 2.9 61.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TRP* 4.5 3.4 - - + +
404A GLY 4.4 4.0 - - - +
405A PHE* 3.2 59.2 - - + +
408A VAL* 3.6 21.3 - - + -
552A THR* 4.1 9.1 + - + -
601A GLY 3.2 10.0 + - - +
602A LEU* 2.6 26.7 + - + +
604A TRP* 1.4 72.3 - - - +
606A TYR* 1.4 62.3 + - + +
608A SER* 2.5 40.2 + - - +
609A ILE* 2.7 33.9 + - - -
739A LEU* 5.8 1.8 - - + -
1781A CLA 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TRP* 3.6 8.4 - + + -
602A LEU 3.0 5.6 + - - +
603A PHE 3.9 8.1 - - - +
604A TRP 2.6 3.4 + - - -
605A MET* 1.4 82.6 - - - +
607A ASN* 1.3 55.4 + - - +
610A SER* 2.4 48.5 + - - -
738A TYR* 4.4 10.3 - + - -
739A LEU* 3.4 30.1 - - + -
742A GLY* 2.8 44.3 + - - -
743A ILE* 3.6 23.6 - - + -
1811A CLA 2.9 51.8 + - + -
1786B CLA 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A THR* 4.7 11.9 - - + -
603A PHE 4.7 0.2 - - - +
604A TRP* 2.3 33.7 + - + +
606A TYR* 1.3 73.7 + - - +
608A SER* 1.3 59.5 + - - +
610A SER* 2.7 7.3 + - - -
611A VAL* 2.6 38.1 + - - +
1811A CLA 3.4 45.4 - - + +
1786B CLA 3.1 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A THR* 4.1 21.4 - - - +
549A ILE* 5.6 3.6 - - - -
552A THR* 3.2 17.1 + - - -
604A TRP 3.7 0.5 - - - -
605A MET* 2.5 38.9 + - - +
607A ASN* 1.3 73.8 - - - +
609A ILE* 1.3 62.5 - - - +
611A VAL* 3.7 3.3 - - - +
612A VAL* 3.3 26.6 + - - +
1781A CLA 3.6 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A MET* 2.8 45.3 - - + +
401A TRP* 3.3 32.5 - - + -
403A GLY 4.3 0.9 - - - +
404A GLY* 4.2 14.4 - - - -
605A MET* 2.7 26.8 + - - +
608A SER* 1.3 76.4 - - - +
610A SER* 1.3 55.0 + - - +
612A VAL* 2.8 25.0 + - - -
613A ILE* 3.0 34.2 + - + +
1781A CLA 4.0 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TRP* 3.6 18.7 - - - -
606A TYR* 2.4 42.0 + - - -
607A ASN* 2.7 14.0 + - - -
609A ILE* 1.3 70.6 - - - +
611A VAL* 1.3 54.5 + - - -
613A ILE* 4.3 5.7 - - - +
614A PHE* 3.5 28.9 + - - +
746A THR* 5.9 0.2 - - - -
1811A CLA 3.1 33.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A VAL* 5.4 2.9 - - + +
544A ILE* 5.3 6.5 - - + -
545A HIS* 4.7 8.3 - - + +
548A THR* 4.8 15.5 - - + +
607A ASN* 2.6 27.0 + - - +
608A SER* 3.7 7.9 - - - +
610A SER* 1.3 72.4 - - - +
612A VAL* 1.3 67.7 + - + +
613A ILE 3.4 0.4 - - - -
614A PHE* 3.5 14.7 - - + +
615A HIS* 3.2 18.7 + - - +
652A TRP* 5.1 1.6 - - + -
1811A CLA 3.8 58.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PHE* 4.7 1.8 - - + -
400A MET* 3.2 36.1 - - + -
545A HIS* 3.2 34.5 - - + +
549A ILE* 6.0 2.0 - - + -
608A SER 3.3 17.3 - - - +
609A ILE* 2.8 11.2 + - - +
611A VAL* 1.3 75.4 - - + +
613A ILE* 1.3 65.0 + - - +
615A HIS* 2.8 22.7 - - - +
616A PHE* 3.1 5.5 + - - +
1781A CLA 4.7 10.8 - - + -
1792A CLA 3.9 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PHE* 4.7 3.1 - - + +
397A THR* 3.0 49.6 - - + +
400A MET* 3.8 7.6 - - + -
401A TRP* 4.6 8.5 - - + +
609A ILE* 3.0 42.0 + - + +
610A SER* 4.3 5.6 - - - +
612A VAL* 1.3 76.9 - - - +
614A PHE* 1.3 69.6 - - + +
615A HIS 2.7 12.0 + - - -
616A PHE* 2.9 20.0 + - - +
617A SER* 3.6 10.9 + - - -
746A THR* 4.8 6.3 - - + -
750A PHE* 3.6 26.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A SER* 3.5 16.3 + - - +
611A VAL* 3.5 17.8 + - + +
612A VAL 3.3 0.6 - - - -
613A ILE* 1.3 85.6 - - + +
615A HIS* 1.3 61.6 + - - +
617A SER* 4.6 1.1 - - - -
618A TRP* 3.6 12.8 + - - +
652A TRP* 3.1 32.2 - + + -
656A PHE* 3.7 26.4 - + - -
657A LEU* 3.6 16.6 - - + -
746A THR* 4.0 13.9 - - + -
749A PHE* 4.1 3.8 - + - -
750A PHE* 6.0 0.4 - + - -
1811A CLA 3.2 86.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ASP* 4.3 11.2 + - - -
541A VAL* 2.7 45.9 - - + +
542A HIS* 4.1 13.4 - + - -
545A HIS* 3.7 11.2 + - - -
611A VAL 3.2 11.0 + - - +
612A VAL* 2.8 17.5 - - - +
613A ILE 2.7 0.4 + - - -
614A PHE* 1.3 78.7 - - - +
616A PHE* 1.4 54.9 + - - -
618A TRP* 3.1 6.2 + - - +
619A LYS* 3.0 31.2 + - - +
642A PHE* 4.6 8.6 - + - -
652A TRP* 4.0 7.2 - + + -
1792A CLA 2.9 55.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.0 47.8 - + + -
392A GLN 4.7 2.2 - - - -
393A LEU* 3.7 17.7 - - + -
396A PHE* 2.8 49.8 - + + -
397A THR* 5.9 0.9 - - + -
612A VAL 3.1 2.2 + - - +
613A ILE* 2.9 11.8 + - - +
615A HIS* 1.4 76.7 + - - +
617A SER* 1.3 59.3 + - - +
619A LYS* 3.6 1.7 - - - +
620A MET* 2.5 49.3 + - + +
625A TRP* 3.2 44.2 - + - -
750A PHE* 5.2 2.0 - + - -
1792A CLA 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 4.9 0.4 - - - -
613A ILE 3.6 7.2 + - - -
614A PHE 4.6 0.2 - - - -
616A PHE* 1.3 86.0 - - - +
618A TRP* 1.3 68.0 + - - +
620A MET* 4.1 3.4 - - - +
621A GLN* 2.8 45.9 + - - +
625A TRP* 4.8 1.6 - - - -
656A PHE* 3.7 17.6 - - - -
750A PHE* 3.3 38.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A PHE 3.6 10.7 + - - +
615A HIS 3.1 4.4 + - - +
617A SER* 1.3 81.6 + - - +
619A LYS* 1.3 51.1 + - - +
621A GLN* 4.5 1.8 - - - -
622A SER* 2.7 33.5 + - - -
638A THR* 5.5 2.2 - - + -
641A ASN* 3.2 27.6 + - - +
642A PHE* 3.4 14.2 - + + +
645A SER 3.4 15.0 - - - -
646A SER* 3.6 17.5 - - - -
651A GLY 3.1 19.1 - - - -
652A TRP* 3.4 58.3 - + + -
655A ASP* 2.8 29.6 + - + +
656A PHE* 3.3 32.1 - + + -
660A GLN* 4.5 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ILE* 3.5 35.3 - - - +
533A PRO* 2.6 31.7 + - - +
537A ALA 4.9 0.9 - - - +
538A ASP* 2.9 20.2 + - - +
615A HIS* 3.0 14.9 + - - +
616A PHE 3.6 6.3 - - - +
618A TRP* 1.3 72.4 - - - +
620A MET* 1.3 57.1 + - + +
621A GLN 2.4 19.3 + - - -
622A SER 2.8 2.3 + - - -
623A ASP* 2.7 45.5 + - - +
624A VAL* 5.4 1.6 - - - -
642A PHE* 3.3 31.4 - - + -
1792A CLA 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.4 42.6 - - + +
514A THR* 6.4 1.8 - - + -
529A LEU* 6.1 1.3 - - - -
532A ILE* 4.5 16.8 - - + -
616A PHE* 2.5 37.5 + - + +
617A SER* 3.4 0.8 + - - -
619A LYS* 1.3 68.4 - - + +
621A GLN* 1.3 55.8 + - - +
623A ASP 2.5 18.8 - - - +
624A VAL* 3.3 39.5 - - + -
625A TRP* 2.9 72.1 + - + -
1792A CLA 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A SER* 2.8 32.1 + - - +
618A TRP* 4.5 1.1 - - + -
619A LYS 2.4 14.6 + - - -
620A MET* 1.3 69.5 - - - +
622A SER* 1.3 64.9 + - - +
623A ASP 3.0 1.8 - - - -
625A TRP* 3.1 31.0 - - + +
636A HIS* 3.4 8.0 - - - +
637A ILE* 3.3 41.9 - - + +
638A THR* 3.5 10.7 - - + +
656A PHE* 5.0 0.7 - - - -
660A GLN* 4.0 15.6 - - - +
750A PHE* 5.3 2.8 - - - -
753A ARG* 3.5 30.5 + - - +
754A ILE* 4.0 13.5 - - - +
758A GLY* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A TRP* 2.7 23.6 + - - -
619A LYS 2.8 1.5 + - - -
621A GLN* 1.3 77.7 - - - +
623A ASP* 1.3 71.7 + - - +
636A HIS* 3.7 3.6 + - - +
638A THR* 2.7 32.3 - - - +
640A GLY* 3.2 7.8 + - - -
641A ASN* 3.6 14.8 - - - -
642A PHE* 3.0 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LEU* 5.5 2.0 - - + -
532A ILE* 5.9 0.7 - - - -
533A PRO* 5.5 11.4 - - + -
619A LYS* 2.7 39.5 + - + +
620A MET 2.5 40.2 - - - +
621A GLN* 3.0 1.0 + - - -
622A SER* 1.3 95.3 + - - +
624A VAL* 1.3 64.0 + - + +
625A TRP 3.2 0.2 + - - -
636A HIS* 3.7 15.8 + - + -
640A GLY* 3.7 10.9 - - - -
642A PHE* 4.5 5.0 - - - +
----------------------------------------------------------
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