Contacts of the helix formed by residues 696 - 713 (chain B) in PDB entry 5YPO
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 696 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B GLU 4.5 3.1 - - - -
661B ILE* 4.0 12.6 - - - +
663B LYS* 6.4 1.1 - - - -
694B GLY 3.4 0.8 - - - -
695B ASP* 1.3 79.0 - - - +
697B PHE* 1.3 65.0 + - - +
698B GLU* 3.4 18.2 + - - +
699B GLU* 3.2 22.7 + - - +
700B ILE* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B THR* 3.3 45.1 - - + -
546B ARG* 3.4 46.7 - - - +
547B ALA* 3.7 28.5 - - + -
550B ASP* 3.4 24.2 - - - -
660B GLU 4.9 0.4 + - - -
661B ILE* 3.6 20.9 - - - +
696B SER* 1.3 73.6 - - - +
698B GLU* 1.3 61.4 + - + +
700B ILE* 3.1 9.9 + - + -
701B TYR* 2.7 56.1 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ARG* 4.2 16.3 + - - -
696B SER* 3.4 20.7 - - - +
697B PHE* 1.3 82.4 + - + +
699B GLU* 1.3 62.6 + - - +
701B TYR* 3.2 5.0 + - - +
702B HIS* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ARG* 4.6 3.9 + - - -
694B GLY* 3.5 14.1 - - - -
695B ASP* 2.9 29.6 + - - +
696B SER* 3.2 19.3 + - - +
697B PHE 3.2 0.2 - - - -
698B GLU* 1.3 78.2 - - - +
700B ILE* 1.3 64.4 + - - +
702B HIS* 3.4 4.4 + - - +
703B LYS* 3.0 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B THR* 4.6 6.3 - - - +
547B ALA* 5.9 0.4 - - + -
650B ILE* 3.6 52.7 - - + -
651B ARG 6.0 0.7 - - - +
657B ASN* 5.9 0.7 - - - +
661B ILE* 3.6 31.4 - - + -
692B VAL* 3.9 11.7 - - + -
693B GLU* 4.0 5.4 - - - -
694B GLY 3.9 23.1 - - - +
696B SER 3.2 13.6 + - - +
697B PHE* 3.1 13.7 + - + +
699B GLU* 1.3 75.6 - - - +
701B TYR* 1.3 60.4 + - - +
703B LYS* 3.2 4.0 + - - +
704B VAL* 2.8 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ALA* 3.9 19.1 - - + -
550B ASP* 3.3 44.9 + - + +
551B LEU* 3.4 19.5 + - + +
554B GLU* 2.6 31.4 + - - +
697B PHE* 2.7 48.6 + + + +
698B GLU* 3.2 5.6 + - - +
700B ILE* 1.3 75.2 - - - +
702B HIS* 1.3 62.3 + - - +
704B VAL* 3.2 7.4 + - + +
705B LYS* 3.0 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B GLU 2.9 17.6 + - - +
699B GLU* 3.8 4.9 - - - +
701B TYR* 1.3 79.1 - - - +
703B LYS* 1.3 70.6 + - - +
705B LYS* 3.3 17.6 + - + +
706B ARG* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ARG* 4.8 4.8 - - - +
692B VAL* 3.8 21.1 - - + -
693B GLU* 2.9 35.7 + - - +
694B GLY* 4.8 0.2 - - - -
699B GLU* 3.0 42.1 + - + +
700B ILE 3.5 7.0 - - - +
702B HIS* 1.3 80.4 - - - +
704B VAL* 1.3 54.3 + - - +
706B ARG* 3.3 6.6 + - - +
707B VAL* 2.7 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B ILE* 4.2 20.0 - - + -
547B ALA* 5.0 6.1 - - + -
551B LEU* 4.2 9.9 - - + -
648B ILE* 4.3 23.3 - - + -
650B ILE* 4.5 10.3 - - + -
692B VAL* 4.4 7.2 - - + -
700B ILE* 2.8 35.9 + - + +
701B TYR* 3.2 12.5 + - + +
703B LYS* 1.3 73.2 - - - +
705B LYS* 1.3 64.4 + - - +
707B VAL* 3.2 7.9 + - - +
708B ILE* 3.0 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 3.7 17.5 - - + -
554B GLU* 2.9 27.5 + - - -
555B PHE* 3.6 30.5 - - + -
701B TYR* 3.0 39.2 + - + +
702B HIS* 3.7 17.0 - - - +
704B VAL* 1.3 77.1 - - - +
706B ARG* 1.3 62.6 + - - +
708B ILE* 3.2 8.7 + - - +
709B GLU* 3.1 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B HIS* 3.0 28.3 + - + +
703B LYS* 3.7 7.2 - - - +
705B LYS* 1.3 76.3 - - - +
707B VAL* 1.3 63.4 + - + +
709B GLU* 3.5 6.2 + - - +
710B ASP* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ILE* 3.9 19.1 - - + -
690B ALA* 3.7 29.4 - - + -
692B VAL* 3.9 20.4 - - + -
703B LYS* 2.7 25.2 + - + +
704B VAL* 3.5 6.1 - - - +
706B ARG* 1.3 73.4 - - + +
708B ILE* 1.3 64.6 + - - +
710B ASP* 3.2 7.7 + - - +
711B LEU* 3.0 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 708 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B ILE* 4.0 28.9 - - + -
551B LEU* 3.9 30.7 - - + -
559B PHE* 4.0 15.9 - - + -
625B HIS* 3.9 20.6 - - + +
646B ILE* 4.5 6.9 - - + +
648B ILE* 3.7 18.2 - - + -
704B VAL* 3.0 22.7 + - + +
705B LYS* 3.2 5.1 + - - +
707B VAL* 1.3 77.1 - - - +
709B GLU* 1.3 62.2 + - - +
711B LEU* 3.9 0.7 - - - +
712B SER* 2.8 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 709 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B LYS 3.1 15.7 + - - +
706B ARG* 3.8 6.7 - - - +
708B ILE* 1.3 77.8 - - - +
710B ASP* 1.3 64.5 + - - +
712B SER* 4.1 4.1 - - - -
713B GLY* 3.4 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 710 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B ARG* 3.0 28.0 + - - +
707B VAL* 3.7 7.8 - - - +
709B GLU* 1.3 79.3 - - - +
711B LEU* 1.3 66.9 + - + +
712B SER 3.5 0.5 + - - -
713B GLY* 3.8 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 711 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ARG* 3.2 31.1 + - - +
646B ILE* 3.8 33.9 - - + -
689B SER* 3.9 29.4 - - - +
690B ALA* 4.7 0.9 - - + -
707B VAL* 3.0 33.2 + - + +
710B ASP* 1.3 79.7 - - + +
712B SER* 1.3 60.9 + - - +
713B GLY 3.5 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ARG* 5.2 5.5 - - - +
625B HIS* 3.1 34.7 + - - -
646B ILE* 3.8 8.1 - - - +
708B ILE 2.8 21.9 + - - -
709B GLU* 3.4 5.4 + - - -
710B ASP 3.3 0.2 - - - -
711B LEU* 1.3 78.7 - - - +
713B GLY* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B GLU 3.4 12.1 + - - -
710B ASP 3.8 7.8 + - - +
711B LEU 3.5 2.5 - - - -
712B SER* 1.3 82.9 - - - +
----------------------------------------------------------
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