Contacts of the helix formed by residues 602 - 619 (chain B) in PDB entry 2XP0
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 TYR 602 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B PHE* 5.9 0.2 - - - -
530B TYR* 4.1 20.2 - + + -
531B GLY 5.7 0.4 - - - +
532B CYS* 3.9 14.5 + - + +
539B LEU* 4.2 13.1 - - + +
540B ASN 4.0 17.5 - - - +
541B LEU* 3.7 32.9 + - + +
601B CYS* 1.3 73.0 - - - +
603B CYS* 1.3 77.0 + - - +
605B GLY 3.8 0.2 - - - -
606B LEU* 2.8 63.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B CYS* 3.4 9.2 - - - -
602B TYR* 1.3 98.5 - - - +
604B CYS* 1.3 65.6 + - - +
606B LEU* 3.7 5.7 - - - +
607B ARG* 3.2 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B CYS* 3.8 10.1 - - - -
512B VAL* 3.8 7.0 - - + -
513B CYS* 3.7 15.3 - - - -
600B LEU* 4.2 12.8 - - + +
601B CYS* 3.4 6.4 - - - +
602B TYR 3.4 0.6 - - - -
603B CYS* 1.3 77.1 - - - +
605B GLY* 1.3 65.2 + - - +
607B ARG* 3.4 36.8 + - - +
608B SER* 3.3 22.3 + - - -
994B ZN 2.3 34.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PHE* 3.5 10.6 - - - -
539B LEU* 3.5 25.4 - - - -
541B LEU* 4.5 1.3 - - - -
600B LEU* 3.8 16.2 - - - +
601B CYS 2.9 10.7 + - - -
604B CYS* 1.3 73.8 - - - +
606B LEU* 1.3 59.6 + - - +
608B SER 3.4 0.7 + - - -
609B PHE* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B LEU* 4.2 18.7 - - + +
545B CYS* 5.0 9.6 - - + +
602B TYR* 2.8 51.4 + - + +
603B CYS* 3.7 5.8 - - - +
604B CYS 3.3 0.2 - - - -
605B GLY* 1.3 76.2 - - - +
607B ARG* 1.3 58.6 + - - +
609B PHE* 3.4 23.6 - - + +
610B ARG* 3.0 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B VAL* 3.7 17.0 - - - +
590B SER* 5.4 4.8 + - - +
591B ASP* 5.5 4.4 + - - +
603B CYS* 3.2 11.1 + - - +
604B CYS* 3.4 44.6 + - - +
605B GLY 3.2 0.4 - - - -
606B LEU* 1.3 81.8 - - - +
608B SER* 1.3 64.2 + - - +
610B ARG* 3.6 8.4 + - - +
611B GLU* 3.4 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PHE* 3.6 26.7 - - - -
589B LEU* 3.6 26.4 - - - +
591B ASP* 5.4 4.0 + - - +
594B VAL* 4.3 12.2 - - - +
600B LEU* 5.1 1.6 - - - +
604B CYS 3.3 11.4 + - - -
605B GLY* 4.1 1.6 - - - -
607B ARG* 1.3 78.4 + - - +
609B PHE* 1.3 60.7 + - - +
611B GLU* 3.2 8.6 + - - +
612B LEU* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PHE* 3.7 8.8 - - + -
541B LEU* 3.4 23.6 - - + -
545B CYS* 3.9 34.1 - - + -
546B LEU* 4.2 4.5 - - + -
549B VAL* 3.7 23.3 - - + -
571B TRP* 4.0 16.8 - + - -
574B MET* 3.9 20.0 - - + -
575B LEU* 4.0 26.2 - - + -
605B GLY 2.8 19.5 + - - +
606B LEU* 3.4 15.3 - - + +
608B SER* 1.3 76.9 - - - +
610B ARG* 1.3 59.3 + - + +
612B LEU* 3.3 5.2 + - + +
613B THR* 2.8 47.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B CYS 5.3 2.2 + - - -
547B ASP 3.8 8.9 + - - -
548B GLY 3.1 34.1 + - - -
549B VAL* 3.7 32.2 + - + +
550B LEU* 5.4 0.3 - - - +
551B ASN* 4.3 3.4 - - - +
552B ASN* 3.3 32.3 + - - +
606B LEU* 3.0 42.4 + - + +
607B ARG* 3.8 7.2 - - - +
608B SER 3.3 0.2 - - - -
609B PHE* 1.3 76.8 - - - +
611B GLU* 1.3 61.7 + - + +
613B THR* 3.4 6.6 + - - -
614B TYR* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B LEU 4.9 0.7 - - - +
589B LEU* 3.5 17.2 - - + +
590B SER* 2.7 52.1 + - - -
591B ASP 4.7 0.2 + - - -
607B ARG* 3.4 21.7 + - + +
608B SER* 3.2 12.8 + - - +
610B ARG* 1.3 77.9 - - + +
612B LEU* 1.3 63.4 + - - +
614B TYR* 3.5 5.7 + - - +
615B GLN* 3.0 29.4 + - - +
639B ARG* 5.7 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PHE* 3.9 12.3 - - + -
575B LEU* 3.7 20.0 - - + -
578B SER* 3.8 31.8 + - - +
579B LEU* 3.6 29.8 - - + -
582B LEU* 4.4 7.4 - - + -
587B PHE* 3.9 20.2 - - + -
588B LEU 4.7 0.2 - - - +
589B LEU* 3.7 22.4 - - + -
608B SER 2.9 17.3 + - - +
609B PHE* 3.8 4.3 - - + +
611B GLU* 1.3 73.9 - - - +
613B THR* 1.3 61.8 + - - +
615B GLN* 3.2 9.3 + - - +
616B TYR* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B VAL* 3.8 22.7 - - + -
550B LEU* 3.9 4.9 - - + -
560B LEU* 3.4 29.3 - - + +
574B MET* 3.5 24.7 - - + +
578B SER* 5.1 0.9 - - - -
609B PHE* 2.8 36.7 + - - -
610B ARG 3.7 3.8 - - - -
611B GLU 3.3 0.2 - - - -
612B LEU* 1.3 74.0 - - - +
614B TYR* 1.3 67.1 + - - +
616B TYR* 3.2 7.5 + - - +
617B ARG* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B LEU* 3.6 21.9 - - + +
551B ASN* 3.7 28.0 - - - -
610B ARG 3.1 13.3 + - - +
611B GLU* 3.8 10.1 - - - +
612B LEU 3.3 0.2 - - - -
613B THR* 1.3 75.3 - - - +
615B GLN* 1.3 60.3 + - + +
617B ARG* 3.2 5.4 + - - +
618B GLN* 2.9 54.9 + - + +
639B ARG* 3.5 44.3 + - + +
655B HIS 4.1 1.6 - - - -
656B ILE* 3.4 24.9 - - + -
657B CYS* 3.0 38.1 + - - -
658B GLU* 4.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B VAL 4.5 1.2 - - - +
587B PHE* 3.2 31.3 - - + +
588B LEU* 2.8 50.0 + - - +
611B GLU* 3.0 26.1 + - - +
612B LEU* 3.2 11.4 + - - +
614B TYR* 1.3 78.1 - - + +
616B TYR* 1.3 65.9 + - - +
618B GLN* 3.4 20.7 + - - +
619B ASN* 2.9 31.0 + - - +
639B ARG* 5.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B LEU* 4.1 8.7 - - + -
563B TYR* 3.7 19.2 - + - -
564B LEU* 3.9 17.8 - - + +
567B ARG* 3.7 22.3 + - - -
569B LEU* 3.8 15.6 - - - +
574B MET* 3.6 31.6 - - + -
577B GLU* 4.5 20.2 - - + -
578B SER* 3.6 20.0 - - - +
587B PHE* 3.6 11.5 - + - -
612B LEU 2.9 13.5 + - - +
613B THR 3.5 8.7 - - - +
615B GLN* 1.3 77.1 - - - +
617B ARG* 1.3 64.3 + - - +
619B ASN* 3.2 13.3 + - - +
620B ILE* 3.5 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B LEU* 3.9 26.1 - - + +
556B GLU* 4.4 8.9 + - - -
559B ILE* 4.7 10.2 - - - +
560B LEU* 4.8 13.5 - - + +
613B THR 2.9 13.3 + - - +
614B TYR 3.2 7.6 + - - +
616B TYR* 1.3 75.8 - - - +
618B GLN* 1.3 70.8 + - - +
620B ILE* 3.0 35.7 + - - +
625B LEU* 3.7 30.3 - - - +
629B VAL* 4.1 17.8 - - - +
630B THR* 5.6 2.0 - - - +
654B ASN* 4.8 3.8 + - - -
656B ILE* 3.9 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B TYR* 2.9 48.4 + - + +
615B GLN* 3.5 26.0 - - - +
617B ARG* 1.3 79.3 + - - +
619B ASN* 1.3 65.8 + - - +
620B ILE 3.3 5.6 + - - +
639B ARG* 4.8 3.9 + - - +
656B ILE* 4.0 17.2 - - + -
657B CYS* 6.2 1.6 - - - +
658B GLU* 4.5 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B VAL* 5.5 4.7 - - - +
587B PHE* 3.6 24.1 - - + -
615B GLN* 2.9 26.5 + - - +
616B TYR* 3.2 6.5 + - - +
617B ARG 3.1 1.2 - - - -
618B GLN* 1.3 86.9 + - - +
620B ILE* 1.3 61.8 + - - +
621B PRO* 3.4 8.8 - - - +
----------------------------------------------------------
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