Contacts of the helix formed by residues 711 - 729 (chain B) in PDB entry 4YFI
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 GLU 711 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B HIS* 5.4 3.5 + - - +
579B ASN* 6.0 0.2 + - - -
644B ILE* 4.2 20.0 - - - +
645B LYS* 4.0 21.9 + - - +
648B VAL* 5.0 0.9 - - - -
710B PRO* 1.3 76.0 - - - +
712B PHE* 1.3 67.5 + - - +
713B SER* 3.7 17.5 - - - +
714B GLU* 3.0 20.3 + - + +
715B VAL* 3.2 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B ALA* 3.7 23.1 - - + -
574B MET* 3.6 30.3 - - + -
575B GLU* 3.8 22.0 - - + +
578B HIS* 3.4 35.9 + + + +
579B ASN* 5.9 0.9 - - - +
647B ASP 3.9 1.8 - - - -
648B VAL* 3.5 31.8 - - + +
651B TYR* 3.5 50.0 - + + -
711B GLU* 1.3 76.1 + - - +
713B SER* 1.3 62.1 + - - +
715B VAL* 3.2 12.2 + - + +
716B VAL* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B GLU* 3.2 31.8 + - - +
579B ASN* 5.1 6.6 - - - +
711B GLU* 3.7 14.8 - - - +
712B PHE* 1.3 79.4 - - - +
714B GLU* 1.3 62.7 + - - +
716B VAL* 3.5 2.4 + - - +
717B MET* 3.4 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 714 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 4.7 1.9 - - - +
700B ARG* 2.7 43.3 + - - -
710B PRO* 3.7 11.7 - - + +
711B GLU* 3.0 15.4 + - + +
713B SER* 1.3 81.7 + - - +
715B VAL* 1.3 62.9 + - - +
717B MET* 3.5 13.7 + - + +
718B LYS* 3.3 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 715 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B ALA* 3.9 13.9 - - + -
648B VAL* 5.1 5.6 - - + -
651B TYR* 3.7 29.8 - - + -
697B LEU* 4.2 18.8 - - + -
710B PRO* 4.2 22.0 - - + +
711B GLU 3.5 13.9 - - - +
712B PHE* 3.2 22.4 + - + +
714B GLU* 1.3 75.9 - - - +
716B VAL* 1.3 64.4 + - - +
718B LYS* 3.6 1.6 + - - +
719B LEU* 3.1 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B VAL* 5.0 3.8 - - + +
571B ALA* 3.4 39.9 - - + +
572B LYS* 3.8 19.1 - - + +
575B GLU* 3.7 19.7 - - - +
712B PHE 3.1 16.7 + - - +
713B SER 3.9 4.7 - - - +
714B GLU 3.3 0.2 - - - -
715B VAL* 1.3 75.4 - - - +
717B MET* 1.3 61.4 + - + +
719B LEU* 3.5 2.8 + - - +
720B GLU* 2.9 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B SER 3.4 16.3 + - - +
714B GLU* 4.0 13.9 - - + +
715B VAL 3.4 0.4 - - - -
716B VAL* 1.3 75.0 - - + +
718B LYS* 1.3 61.6 + - + +
720B GLU* 3.3 10.7 + - - +
721B GLU* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B PRO* 5.6 6.5 - - + +
697B LEU* 4.0 29.2 - - + -
700B ARG* 4.9 5.8 - - - +
714B GLU* 3.3 41.1 + - + +
717B MET* 1.3 77.8 - - + +
719B LEU* 1.3 58.0 + - - +
721B GLU* 3.4 18.3 + - - +
722B CYS* 3.0 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B LEU* 4.1 22.5 - - + +
567B ALA* 4.0 19.7 - - + +
568B VAL* 3.4 19.2 - - + +
571B ALA* 4.4 1.3 - - + -
651B TYR* 3.0 29.6 - - + +
655B LEU* 4.5 11.7 - - + -
694B ILE* 4.3 17.0 - - + -
697B LEU* 4.2 16.4 - - + -
715B VAL* 3.1 30.9 + - + +
716B VAL 4.0 1.3 - - - +
718B LYS* 1.3 75.7 - - - +
720B GLU* 1.3 60.0 + - - +
722B CYS* 3.4 5.2 + - - +
723B LEU* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 720 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B VAL* 4.1 14.4 - - + -
572B LYS* 3.1 34.1 + - - +
716B VAL* 2.9 34.9 + - - +
717B MET* 3.8 8.1 - - - +
719B LEU* 1.3 74.3 - - - +
721B GLU* 1.3 60.0 + - - +
723B LEU* 3.1 14.8 + - + +
724B CYS* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B MET 2.9 21.3 + - - +
718B LYS* 3.5 21.8 + - - +
720B GLU* 1.3 71.3 - - - +
722B CYS* 1.3 64.0 + - - +
724B CYS* 3.1 12.1 + - + +
725B ASN* 3.0 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B LEU* 4.1 15.3 - - + -
691B PRO* 6.4 0.2 - - - -
693B PRO* 4.0 29.2 - - - -
694B ILE* 4.1 18.8 - - + -
718B LYS* 3.0 27.4 + - - -
719B LEU* 3.6 10.5 - - - +
721B GLU* 1.3 77.4 - - - +
723B LEU* 1.3 62.0 + - - +
725B ASN* 3.5 7.5 + - - +
726B ILE* 3.0 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 723 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B GLN* 4.0 28.3 - - + +
564B LEU* 3.8 28.5 - - + +
565B ILE* 4.1 18.4 - - + +
568B VAL* 5.0 12.1 - - + -
719B LEU 2.8 14.9 + - - +
720B GLU* 3.1 21.0 + - + +
722B CYS* 1.3 77.4 - - - +
724B CYS* 1.3 61.5 + - - +
726B ILE* 4.0 2.3 - - + -
727B GLU* 3.1 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B GLU* 2.8 20.8 + - - -
721B GLU* 3.1 11.2 + - - +
723B LEU* 1.3 75.5 - - - +
725B ASN* 1.3 64.3 + - - +
727B GLU* 3.1 13.0 + - - +
728B LEU* 2.8 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B GLU* 3.0 37.3 + - - +
722B CYS* 4.0 6.5 - - - +
724B CYS* 1.3 81.3 - - - +
726B ILE* 1.3 58.8 + - + +
728B LEU* 3.9 16.0 - - - +
729B MET* 3.1 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B LEU* 3.3 36.8 - - + -
561B GLN* 4.3 33.2 - - + +
564B LEU* 3.3 21.3 - - + -
691B PRO* 5.8 3.1 - - + -
694B ILE* 5.8 2.2 - - + -
722B CYS* 3.0 26.8 + - + +
723B LEU* 4.2 3.4 - - - +
725B ASN* 1.3 77.2 - - + +
727B GLU* 1.3 64.0 + - - +
729B MET* 3.7 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B GLN* 3.2 37.0 + - + +
565B ILE* 5.4 1.2 - - - +
723B LEU* 3.1 35.7 + - - +
724B CYS* 3.1 14.7 + - - +
726B ILE* 1.3 77.7 - - - +
728B LEU* 1.3 65.4 + - + +
729B MET 3.9 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B CYS* 2.8 29.7 + - + +
725B ASN* 4.0 20.2 - - - +
727B GLU* 1.3 74.9 - - + +
729B MET* 1.3 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 729 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B ASN* 3.1 28.0 + - - +
726B ILE* 3.7 22.2 - - + +
727B GLU 3.4 4.5 - - - -
728B LEU* 1.3 80.8 - - + +
----------------------------------------------------------
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