Contacts of the helix formed by residues 655 - 675 (chain A) in PDB entry 5UO5
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 ASP 655 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A MET* 4.2 0.4 - - - -
595A GLY* 4.7 1.3 - - - +
643A LEU* 3.6 34.9 - - + +
647A GLN* 6.0 0.4 - - - +
654A VAL* 1.3 79.0 - - - +
656A HIS* 1.3 59.7 + - - +
657A HIS* 2.9 13.9 + - - +
658A SER* 2.8 33.3 + - - -
659A ALA* 3.0 26.3 + - - +
626B THR* 3.1 24.4 + - - -
627B SER* 3.3 21.2 - - - -
629B LEU* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A MET* 3.8 23.6 - - - +
595A GLY* 5.2 0.8 - - - +
596A THR* 3.5 22.8 + - + +
643A LEU* 5.4 2.0 - - + +
654A VAL 4.0 0.2 + - - -
655A ASP* 1.3 70.8 - - - +
657A HIS* 1.3 74.0 + + - +
660A THR* 2.7 33.6 + - - +
686A PRO* 4.0 13.2 - - + -
688A MET* 4.1 31.7 - - - +
689A SER* 4.2 1.3 - - - -
693A THR* 4.1 18.0 - - + +
629B LEU* 3.6 27.4 - - + +
632B ASP* 2.8 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A ASP* 2.9 9.0 + - - +
656A HIS* 1.3 94.0 + + - +
658A SER* 1.3 65.4 + - - +
660A THR* 3.1 6.9 + - - -
661A GLU* 3.1 26.0 + - - +
692A ILE* 3.9 39.8 + - + -
693A THR* 4.2 5.1 - - + +
694A PRO* 4.8 3.2 - - - +
626B THR* 3.9 35.4 - - + -
629B LEU* 4.1 4.5 - - + -
631B LYS* 4.2 19.1 + - + +
632B ASP* 2.7 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A VAL* 3.8 16.3 - - - +
655A ASP* 2.8 23.5 + - - -
657A HIS* 1.3 76.7 - - - +
659A ALA* 1.3 58.5 + - - +
661A GLU* 3.5 7.2 + - - +
662A SER* 3.0 34.9 + - - -
626B THR* 4.4 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A VAL* 4.0 16.6 - - + +
422A GLY* 6.4 0.4 - - - -
594A MET* 3.6 26.0 - - - -
654A VAL* 3.8 19.4 - - + +
655A ASP 3.0 18.2 + - - +
656A HIS 4.2 0.2 - - - +
658A SER* 1.3 77.6 - - - +
660A THR* 1.3 57.5 + - - +
662A SER* 3.4 6.3 + - - -
663A PHE* 3.0 26.7 + - - +
801A HEM 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A VAL* 4.4 10.8 - - + -
594A MET* 5.2 1.8 - - + -
656A HIS* 2.7 23.7 + - - +
657A HIS 3.1 8.1 + - - -
659A ALA* 1.3 75.7 - - + +
661A GLU* 1.3 65.4 + - - +
663A PHE* 3.3 8.0 + - - +
664A ILE* 3.0 28.2 + - - +
684A ILE 4.6 0.4 - - - +
686A PRO* 3.7 26.2 - - + -
693A THR* 3.5 6.1 - - - -
694A PRO* 3.4 17.6 - - - +
695A VAL* 3.7 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A HIS 3.1 18.4 + - - +
658A SER* 3.8 7.1 - - - +
660A THR* 1.3 75.7 + - - +
662A SER* 1.3 66.8 + - - +
664A ILE* 3.3 5.3 + - - +
665A LYS* 3.2 54.0 + - - +
694A PRO* 3.9 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A VAL 6.0 0.2 - - - -
424A ILE* 3.7 28.9 - - - +
658A SER* 3.0 24.9 + - - -
659A ALA* 3.8 6.1 - - - -
661A GLU* 1.3 77.8 - - - +
663A PHE* 1.3 58.4 + - - +
665A LYS* 3.4 10.2 + - - +
666A HIS* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A CYS 3.6 9.0 - - - -
421A VAL* 3.5 32.9 + - + +
423A ARG* 3.3 37.5 - - - -
424A ILE* 5.6 1.1 - - - -
659A ALA 3.0 18.2 + - - +
660A THR* 3.6 5.4 - - - +
661A GLU 3.2 0.6 - - - -
662A SER* 1.3 77.0 - - - +
664A ILE* 1.3 52.3 + - - +
666A HIS* 3.4 21.3 - + - +
667A MET* 2.7 55.9 + - + +
677A CYS* 4.5 7.6 - - - -
679A ALA* 3.9 12.3 - - + -
684A ILE* 3.9 30.1 - - + -
695A VAL* 3.9 10.3 - - + -
700A MET* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN* 4.6 5.6 - - - +
660A THR 3.0 16.5 + - - +
661A GLU* 3.6 7.6 - - - +
662A SER 3.3 0.2 - - - -
663A PHE* 1.3 76.8 - - - +
665A LYS* 1.3 58.6 + - + +
667A MET* 3.2 25.8 + - + +
668A GLU* 2.9 50.5 + - + +
694A PRO* 3.9 26.5 - - + +
695A VAL* 3.7 16.2 - - + -
698A GLN* 3.9 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE* 4.9 6.3 - - + -
661A GLU* 3.2 44.6 + - + +
662A SER* 3.7 10.1 - - - +
664A ILE* 1.3 79.0 - - + +
666A HIS* 1.3 62.0 + - - +
668A GLU* 3.5 16.1 + - - +
669A ASN* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ARG* 5.3 2.1 + - + -
423A ARG* 3.5 35.5 - - + +
424A ILE* 3.5 38.3 + - + +
426A TRP* 3.9 12.1 - + - -
662A SER 2.8 18.6 + - - +
663A PHE* 3.4 22.9 - + - +
665A LYS* 1.3 77.0 - - - +
667A MET* 1.3 58.5 + - - +
669A ASN* 3.1 10.5 + - - +
670A GLU* 2.9 61.6 + - + +
677A CYS* 4.2 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 6.0 0.2 - - - -
317A LEU* 4.7 4.9 - - + -
663A PHE* 2.7 40.5 + - + +
664A ILE* 3.6 23.3 - - + +
666A HIS* 1.3 73.2 - - - +
668A GLU* 1.3 64.1 + - + +
670A GLU* 3.3 1.6 + - - +
671A TYR* 2.9 56.0 + - + -
677A CYS* 4.1 20.2 - - + +
679A ALA* 4.7 6.3 - - - -
698A GLN* 3.5 38.1 - - + -
699A GLU 4.9 1.8 - - - +
700A MET* 4.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A THR* 5.7 0.2 + - - -
315A VAL* 4.6 17.1 - - - +
317A LEU* 4.3 21.3 - - + -
664A ILE* 2.9 37.9 + - + +
665A LYS* 3.7 17.1 + - - +
667A MET* 1.3 76.3 - - + +
669A ASN* 1.3 62.8 + - - +
671A TYR* 3.3 1.9 + - - +
672A ARG* 2.8 54.2 + - - +
698A GLN* 5.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LYS 3.0 14.7 + - - +
666A HIS* 3.5 13.3 + - - +
668A GLU* 1.3 76.8 - - - +
670A GLU* 1.3 56.8 + - - +
672A ARG* 3.2 12.8 + - - +
673A CYS* 2.8 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ARG* 2.8 56.0 + - - +
426A TRP* 4.2 4.3 + - - -
666A HIS* 2.9 48.7 + - + +
667A MET 3.7 4.5 - - - +
669A ASN* 1.3 78.8 + - + +
671A TYR* 1.3 60.1 + - - +
673A CYS* 3.7 8.5 - - - -
674A ARG* 2.8 41.3 + - - +
675A GLY 3.2 2.4 + - - -
676A GLY 3.3 14.8 - - - +
677A CYS* 3.7 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 3.5 30.4 - - + +
317A LEU* 3.5 39.5 - - + -
318A THR 3.4 22.2 - - - +
319A ASP* 3.6 37.4 + - + +
667A MET* 2.9 52.9 + - + +
668A GLU 3.6 5.2 - - - +
670A GLU* 1.3 74.8 - - - +
672A ARG* 1.3 64.1 + - - +
675A GLY* 3.1 20.1 + - - -
676A GLY* 3.6 8.5 - - - +
677A CYS* 3.7 23.2 + - + -
700A MET* 5.2 1.6 - - - -
701A LEU* 4.5 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 5.3 6.1 - - - +
317A LEU* 3.7 22.4 - - - +
668A GLU* 2.8 53.4 + - - +
669A ASN* 3.2 13.9 + - - +
671A TYR* 1.3 81.5 - - - +
673A CYS* 1.3 62.3 + - + +
675A GLY* 4.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ARG* 3.8 11.9 - - - -
669A ASN* 2.8 35.4 + - - +
670A GLU* 3.7 22.0 - - - -
672A ARG* 1.3 75.4 - - + +
674A ARG* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A THR* 4.9 0.7 + - - -
321A LEU* 3.6 45.3 - - + +
369A GLN* 5.3 3.6 + - - -
412A HIS* 4.0 16.2 - - - -
415A ARG* 3.6 57.5 + - - +
416A ASN* 2.9 32.9 + - - +
670A GLU* 2.8 27.3 + - - +
673A CYS* 1.3 76.6 - - - +
675A GLY* 1.3 60.5 + - - +
676A GLY 3.4 4.4 + - - +
678A PRO* 4.8 5.3 - - - +
705A LEU* 3.9 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A THR 4.3 3.1 - - - -
319A ASP* 3.2 5.2 - - - -
320A THR* 2.6 44.7 + - - -
321A LEU* 2.9 7.2 + - - -
671A TYR* 3.1 18.1 + - - -
672A ARG 4.5 1.2 + - - -
673A CYS 3.8 0.4 - - - -
674A ARG* 1.3 79.2 - - - +
676A GLY* 1.3 57.3 + - - +
----------------------------------------------------------
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