Contacts of the helix formed by residues 729 - 740 (chain B) in PDB entry 2PZR
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 THR 729 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600B PHE* 3.7 27.8 - - + -
724B LYS* 4.4 0.2 - - - -
728B CYS* 1.3 78.0 - - - +
730B ASN* 1.3 65.1 + - - +
731B GLU* 3.7 8.1 + - - +
732B LEU* 3.3 26.3 + - - +
733B TYR* 3.1 18.5 + - - +
760B ILE* 5.9 0.5 - - - +
802B SO4 3.5 24.9 - - - +
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Residues in contact with ASN 730 (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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724B LYS* 3.2 30.6 - - - +
729B THR* 1.3 71.7 - - - +
731B GLU* 1.3 57.0 + - - +
733B TYR* 3.7 5.7 - - - +
734B MET* 2.9 39.9 + - + +
802B SO4 2.7 38.9 + - - +
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Residues in contact with GLU 731 (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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729B THR* 3.1 8.4 + - - +
730B ASN* 1.3 79.4 - - - +
732B LEU* 1.3 57.6 + - - +
734B MET* 3.4 7.6 + - - +
735B MET* 3.1 26.3 + - + +
759B ARG* 3.1 25.5 + - - +
760B ILE* 3.7 33.8 - - + +
802B SO4 4.0 3.3 + - - +
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Residues in contact with LEU 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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600B PHE* 3.5 30.1 - - + -
604B VAL* 4.1 5.4 - - + -
693B MET* 4.5 3.5 - - - +
697B PHE* 3.4 35.9 - - + -
728B CYS* 3.9 8.1 - - - -
729B THR* 3.3 15.9 + - - +
731B GLU* 1.3 77.1 - - - +
733B TYR* 1.3 63.9 + - - +
735B MET* 3.2 12.9 + - + +
736B MET* 3.1 31.4 + - + +
757B LEU* 4.0 20.6 - - + -
760B ILE* 3.5 31.4 - - + -
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Residues in contact with TYR 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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721B ARG 4.7 0.2 + - - -
722B MET 2.5 24.7 + - - -
723B ASP* 3.6 9.2 + - - -
724B LYS* 3.4 55.9 - - + -
725B PRO* 4.1 8.1 - - + -
728B CYS* 3.9 4.6 - - - -
729B THR 3.1 15.5 + - - +
730B ASN* 3.9 5.8 - - - +
731B GLU 3.2 0.2 - - - -
732B LEU* 1.3 74.5 - - - +
734B MET* 1.3 78.7 + - + +
735B MET 3.0 1.3 - - - -
736B MET* 3.0 10.9 + - - -
737B ARG* 2.9 66.0 + - + +
740B TRP* 4.5 6.5 - + - -
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Residues in contact with MET 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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730B ASN* 2.9 28.4 + - + +
731B GLU* 3.6 7.2 - - - +
733B TYR* 1.3 106.0 - - + +
735B MET* 1.3 59.2 + - - +
737B ARG* 3.6 17.3 + - + +
738B ASP* 3.0 34.9 + - - +
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Residues in contact with MET 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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693B MET* 4.2 13.5 - - - +
731B GLU* 3.1 13.6 + - + +
732B LEU* 3.2 14.1 - - + +
733B TYR 3.0 0.2 - - - -
734B MET* 1.3 76.0 - - - +
736B MET* 1.3 64.7 + - - +
738B ASP* 3.2 19.2 + - - +
739B CYS* 3.3 18.5 + - - -
748B PRO* 5.6 1.6 - - + -
753B LEU* 3.8 29.2 - - + -
756B ASP* 3.6 31.4 - - + -
757B LEU* 3.7 24.2 - - + -
759B ARG* 5.0 2.0 - - - +
760B ILE* 3.7 26.0 - - + -
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Residues in contact with MET 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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690B GLY* 4.3 1.1 - - - +
693B MET* 3.9 32.8 - - + +
694B TRP* 3.9 30.1 - - - -
697B PHE* 3.7 28.7 - - + -
725B PRO* 4.2 3.6 - - + -
728B CYS* 3.6 31.4 - - - -
732B LEU* 3.1 13.6 + - + +
733B TYR* 3.0 20.3 + - + +
735B MET* 1.3 76.6 - - - +
737B ARG* 1.3 62.7 + - - +
739B CYS* 3.0 16.6 + - - +
740B TRP* 3.3 32.9 + - + -
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Residues in contact with ARG 737 (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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719B GLY 4.9 3.6 + - - -
721B ARG* 3.4 32.8 - - - +
733B TYR* 2.9 60.2 + - + +
734B MET* 3.8 20.6 - - + +
736B MET* 1.3 76.6 - - - +
738B ASP* 1.3 63.9 + - - +
740B TRP* 3.3 38.3 + - - +
741B HIS* 3.8 4.0 + - - -
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Residues in contact with ASP 738 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734B MET* 3.0 25.1 + - - +
735B MET* 3.4 12.5 - - - +
736B MET 3.1 0.6 - - - -
737B ARG* 1.3 75.2 - - - +
739B CYS* 1.3 67.2 + - - +
741B HIS* 3.2 34.1 + - - +
746B GLN 5.2 2.5 - - - +
747B ARG* 3.5 9.2 - - - +
748B PRO* 3.7 19.6 - - + +
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Residues in contact with CYS 739 (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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686B VAL* 3.4 25.6 - - - +
687B TRP* 3.4 10.2 - - - -
690B GLY* 3.8 9.4 - - - -
693B MET* 3.5 26.2 - - - -
735B MET 3.4 15.3 - - - -
736B MET 3.0 7.9 + - - +
738B ASP* 1.3 79.9 - - - +
740B TRP* 1.3 59.8 + - + +
747B ARG* 3.0 29.0 + - - -
748B PRO* 4.2 11.7 - - - -
753B LEU* 4.1 21.1 - - - -
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Residues in contact with TRP 740 (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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687B TRP* 3.4 40.3 + + + -
690B GLY* 3.4 23.2 - - - -
691B VAL* 3.4 31.1 - - + +
694B TRP* 4.0 22.2 - + + -
704B TYR* 5.1 4.3 - - - -
721B ARG* 2.8 53.8 + - + +
722B MET* 4.0 32.1 - - + -
733B TYR* 4.5 2.5 - + - -
736B MET* 3.4 26.2 - - + -
737B ARG* 3.3 40.7 + - - +
738B ASP 3.1 1.4 - - - -
739B CYS* 1.3 79.4 - - + +
741B HIS* 1.3 58.9 + - - +
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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
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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