Contacts of the helix formed by residues 623 - 642 (chain E) in PDB entry 3RCW
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 ASN 623 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E LEU* 3.5 13.0 - - - +
571E LEU* 4.9 1.8 - - - -
621E TYR* 3.3 5.1 - - - +
622E LYS* 1.3 86.7 + - - +
624E LEU* 1.3 65.5 + - - +
625E HIS* 3.2 15.2 + - - +
626E GLU* 2.9 46.7 + - - +
627E PHE* 3.5 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 624 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E LEU* 4.3 7.2 - - + +
570E LEU* 6.3 0.2 - - + -
571E LEU* 4.1 23.6 - - + -
574E VAL* 5.7 0.2 - - + -
623E ASN* 1.3 71.2 - - - +
625E HIS* 1.3 64.2 + - - +
627E PHE* 2.8 16.9 + - + +
628E GLU* 2.8 41.0 + - + +
663E LEU* 4.1 11.7 - - + +
666E ALA* 3.8 20.9 - - + +
667E ARG* 3.4 44.2 - - + +
670E VAL* 4.3 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 625 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623E ASN* 3.2 13.4 + - - +
624E LEU* 1.3 79.0 - - - +
626E GLU* 1.3 63.3 + - + +
628E GLU* 3.4 10.9 + - - +
629E GLU* 2.9 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 626 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615E ARG* 3.5 22.8 + - - +
620E GLY 3.6 2.3 - - - +
621E TYR* 3.8 16.4 - - + -
622E LYS* 2.9 49.2 + - - +
623E ASN* 2.9 27.1 + - - +
625E HIS* 1.3 78.7 - - + +
627E PHE* 1.3 69.6 + - - +
629E GLU* 3.2 12.6 + - - +
630E ASP* 3.2 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 627 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E LEU* 3.6 55.0 - - + -
574E VAL* 3.6 19.1 - - + -
575E LEU* 3.8 26.7 - - + -
578E LEU* 3.9 12.1 - - + -
612E MET* 3.6 24.7 - - + +
616E LEU* 4.5 4.7 - - + -
621E TYR* 3.7 36.2 - + + -
623E ASN 3.5 3.7 + - - +
624E LEU* 2.8 14.4 + - + +
626E GLU* 1.3 72.0 - - - +
628E GLU* 1.3 66.9 + - - +
630E ASP* 2.8 18.4 + - - +
631E PHE* 2.9 10.4 + - + -
663E LEU* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 628 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624E LEU* 2.8 38.9 + - + +
625E HIS* 3.6 11.5 + - - +
627E PHE* 1.3 78.8 - - - +
629E GLU* 1.3 57.8 + - - +
631E PHE* 3.0 9.9 + - - +
632E ASP* 2.8 44.7 + - - +
663E LEU* 4.0 37.9 - - + +
667E ARG* 5.4 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 629 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615E ARG* 6.1 0.9 - - - +
625E HIS* 2.9 39.1 + - + +
626E GLU* 3.4 12.5 - - - +
627E PHE 3.1 0.4 + - - -
628E GLU* 1.3 75.9 - - - +
630E ASP* 1.3 59.6 + - - +
632E ASP* 3.3 9.5 + - - +
633E LEU* 3.1 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 630 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605E HIS* 4.8 2.8 + - - -
607E MET* 3.5 30.4 - - + +
612E MET* 3.9 13.2 - - + -
615E ARG* 3.2 33.5 + - - +
621E TYR* 2.5 28.8 + - - +
626E GLU 3.2 4.8 + - - +
627E PHE 2.8 10.9 + - - +
629E GLU* 1.3 76.7 - - - +
631E PHE* 1.3 64.5 + - - +
633E LEU* 3.2 23.1 + - - +
634E ILE* 3.2 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 631 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578E LEU* 3.7 25.4 - - + -
609E PHE* 4.2 14.1 - + - -
612E MET* 4.0 9.1 - - + -
627E PHE* 2.9 12.7 + - + +
628E GLU* 3.0 11.6 + - - +
630E ASP* 1.3 76.1 - - - +
632E ASP* 1.3 68.0 + - - +
634E ILE* 2.9 27.4 + - + +
635E ILE* 3.1 34.2 + - + +
655E LEU* 3.5 46.9 - - + -
656E ARG* 4.4 7.6 - - + -
659E GLY* 4.1 12.1 - - - -
660E GLY* 4.9 0.4 - - - -
663E LEU* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 632 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628E GLU* 2.8 32.9 + - - +
629E GLU* 3.7 7.8 + - - +
631E PHE* 1.3 88.7 - - - +
633E LEU* 1.3 54.2 + - + +
635E ILE* 4.3 7.3 - - - +
636E ASP* 2.5 56.4 + - - +
656E ARG* 5.8 3.3 - - - +
663E LEU* 5.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 633 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605E HIS* 3.1 59.9 - - + +
607E MET* 3.8 11.4 - - + -
629E GLU* 3.1 21.0 + - + +
630E ASP* 3.3 24.0 - - - +
632E ASP* 1.3 78.9 - - + +
634E ILE* 1.3 60.6 + - - +
636E ASP* 4.6 6.1 - - + +
637E ASN* 2.9 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 634 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587E PHE* 3.5 37.6 - - + -
607E MET* 3.1 49.6 - - + +
608E ASP* 3.2 20.9 - - - +
609E PHE* 4.0 6.5 - - + +
612E MET* 4.2 8.3 - - - -
630E ASP 3.2 13.5 + - - +
631E PHE* 2.9 20.9 + - + +
633E LEU* 1.3 77.3 - - - +
635E ILE* 1.3 64.9 + - - +
637E ASN* 4.3 1.4 - - - +
638E CYS* 3.5 19.8 + - - +
655E LEU* 4.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 635 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587E PHE* 5.6 0.7 - - + -
631E PHE* 3.1 41.3 + - + +
632E ASP* 3.7 9.2 - - - +
634E ILE* 1.3 81.5 - - + +
636E ASP* 1.3 73.1 + - - +
638E CYS* 3.6 1.9 + - - +
639E MET* 3.1 33.1 + - + +
652E ALA* 3.4 28.4 - - - +
655E LEU* 3.7 15.9 - - + -
656E ARG* 3.5 46.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 636 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632E ASP* 2.5 43.6 + - - +
633E LEU* 4.7 6.3 - - + +
635E ILE* 1.3 80.1 - - - +
637E ASN* 1.3 62.8 + - - +
639E MET* 3.2 15.6 + - - +
640E LYS* 2.8 32.1 + - - +
656E ARG* 5.7 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 637 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599E TYR* 3.8 12.0 + - - +
603E ILE* 3.6 31.8 - - + +
605E HIS* 2.7 35.6 + - - +
606E PRO* 3.7 6.7 - - - +
607E MET 4.1 4.0 + - - +
633E LEU* 2.9 34.5 + - - +
634E ILE* 4.3 1.8 - - - +
636E ASP* 1.3 76.9 - - - +
638E CYS* 1.3 57.7 + - - +
640E LYS* 2.9 8.8 + - - +
641E TYR* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 638 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586E ILE* 5.6 0.2 - - - -
587E PHE* 3.8 21.1 - - + -
599E TYR* 4.8 3.8 + - - -
634E ILE 3.5 16.3 + - - +
635E ILE 3.9 3.4 - - - +
636E ASP 3.4 0.2 - - - -
637E ASN* 1.3 79.2 - - - +
639E MET* 1.3 62.2 + - - +
641E TYR* 3.3 3.9 + - - -
642E ASN* 3.1 34.6 + - - +
648E PHE* 3.4 44.4 - - - -
649E TYR* 4.7 0.4 - - - -
652E ALA* 3.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 639 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635E ILE* 3.1 34.3 + - + +
636E ASP* 3.2 15.2 + - - +
638E CYS* 1.3 74.8 - - - +
640E LYS* 1.3 63.5 + - - +
642E ASN 3.3 13.2 - - - +
649E TYR* 3.4 36.2 - - + +
652E ALA* 3.6 15.5 - - + -
653E VAL* 3.8 21.3 - - - -
656E ARG* 3.6 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 640 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602E HIS* 4.1 18.2 + - + -
603E ILE* 4.3 15.7 - - + +
604E LYS* 6.0 3.0 - - - +
636E ASP 2.8 14.7 + - - +
637E ASN* 3.2 11.9 - - - +
639E MET* 1.3 79.7 - - - +
641E TYR* 1.3 60.7 + - - +
642E ASN 4.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 641 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596E VAL* 3.0 22.0 - - + +
598E ASP* 2.7 30.6 + - - -
599E TYR* 4.0 33.4 - + + -
602E HIS* 3.5 40.8 - + + -
603E ILE* 4.5 5.6 - - + -
637E ASN 2.9 18.4 + - - +
638E CYS* 4.2 2.9 - - - +
640E LYS* 1.3 74.1 - - - +
642E ASN* 1.3 83.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 642 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638E CYS* 3.1 18.8 + - - +
639E MET 3.3 17.0 - - - +
640E LYS 4.3 1.8 - - - +
641E TYR* 1.3 104.4 + - - +
643E ALA* 1.3 63.7 + - - +
644E ARG 4.0 0.2 + - - -
646E THR* 3.4 22.0 + - - +
648E PHE* 3.7 33.6 - - - +
649E TYR* 3.3 16.0 - - + +
----------------------------------------------------------
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