Contacts of the strand formed by residues 729 - 736 (chain B) in PDB entry 5ZE3
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 ILE 729 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B LEU* 6.0 0.2 - - - -
711B GLN* 4.1 26.0 - - + +
712B VAL 3.7 3.1 - - - +
713B VAL* 3.9 27.4 - - + -
725B TYR 4.9 3.4 + - - +
726B SER 5.0 2.8 + - - +
727B ASN 3.6 1.1 - - - +
728B ASN* 1.3 79.3 - - + +
730B MET* 1.3 73.5 + - - +
731B LYS* 4.2 15.0 - - + -
748B ILE* 3.4 8.7 - - - +
749B GLY* 3.0 30.9 + - - +
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Residues in contact with MET 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B LEU* 3.6 37.5 - - + -
554B ALA* 3.6 24.0 - - + -
557B VAL* 3.5 29.2 - - + -
710B PHE* 4.2 6.1 - - + -
711B GLN* 3.3 6.8 - - - +
712B VAL* 2.9 48.9 + - + +
729B ILE* 1.3 74.3 - - - +
731B LYS* 1.3 82.3 + - - +
732B CYS* 3.4 25.8 - - - -
746B CYS* 4.2 2.9 - - - -
747B HIS 3.4 11.7 - - - +
748B ILE* 4.5 2.7 - - + +
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Residues in contact with LYS 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B LEU* 6.1 7.0 - - + -
710B PHE 3.2 7.6 - - - +
711B GLN* 4.2 22.0 - - + +
729B ILE* 4.2 15.7 - - + -
730B MET* 1.3 79.7 - - - +
732B CYS* 1.3 62.4 + - - +
745B ASN 3.5 4.3 - - - +
746B CYS* 3.2 1.7 - - - -
747B HIS* 2.8 44.2 + - + +
749B GLY* 5.4 6.4 - - - +
757B GLU* 5.4 6.8 + - - +
760B PHE* 3.7 31.6 - - + -
761B GLU* 4.3 15.6 + - - -
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Residues in contact with CYS 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B VAL* 4.3 2.2 - - - -
709B LEU* 3.7 1.9 - - - -
710B PHE* 2.8 48.9 + - + +
730B MET* 3.4 23.8 - - - -
731B LYS* 1.3 70.7 - - - +
733B ARG* 1.3 59.7 + - - +
743B MET* 4.3 12.3 - - + -
744B TYR 3.9 6.7 - - - +
745B ASN 4.1 2.9 - - - -
746B CYS* 2.0 49.8 - - - -
760B PHE* 3.7 6.3 - - - -
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Residues in contact with ARG 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643B LEU* 5.7 1.3 - - - -
707B ASP* 6.1 2.0 - - - -
708B TYR 4.0 2.7 - - - +
709B LEU* 3.6 19.7 - - + -
732B CYS* 1.3 72.3 - - - +
734B SER* 1.3 59.0 + - - +
744B TYR* 2.8 76.1 + - + +
745B ASN* 3.5 21.6 + - - -
759B LYS 3.3 5.5 + - - -
760B PHE* 1.5 80.3 + - + +
763B PHE* 3.4 45.8 - - - +
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Residues in contact with SER 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640B LEU* 3.9 15.9 - - - +
707B ASP* 3.8 2.9 - - - +
708B TYR* 2.7 48.1 + - - +
710B PHE* 4.5 4.0 - - - +
732B CYS 3.6 0.6 + - - -
733B ARG* 1.3 73.0 - - - +
735B ARG* 1.3 59.3 + - - +
736B TYR 4.2 0.3 + - - -
741B ILE* 4.4 8.7 - - - +
742B TRP 3.1 4.9 - - - -
743B MET* 2.6 43.7 - - - +
744B TYR* 5.2 0.2 - - - -
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Residues in contact with ARG 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706B GLY 3.7 5.2 - - - +
707B ASP* 3.4 30.2 + - - +
734B SER* 1.3 73.3 - - - +
736B TYR* 1.3 66.2 + - - +
737B ASP* 3.5 3.0 + - - -
740B ARG 3.6 3.5 - - - +
741B ILE* 3.7 3.5 - - - -
742B TRP* 3.2 55.2 + - + +
744B TYR* 6.1 5.6 - - + +
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Residues in contact with TYR 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B LEU* 4.0 18.2 - - + -
595B ARG* 3.2 37.0 + - - +
640B LEU* 5.9 1.1 - - + -
700B ILE* 4.4 11.2 - - + -
703B VAL* 3.0 35.2 - - + -
704B PRO* 3.0 25.4 - - + -
705B PRO* 3.1 10.9 - - + +
706B GLY* 2.8 39.2 + - - +
708B TYR* 4.1 10.9 - - + -
734B SER 4.1 1.2 + - - -
735B ARG* 1.3 72.2 - - - +
737B ASP* 1.3 67.4 + - - +
738B GLY* 3.2 32.7 + - - -
739B HIS 4.2 0.2 - - - -
740B ARG 3.8 2.2 - - - -
741B ILE* 3.5 24.6 - - + +
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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
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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) + - + + + + + -
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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