Contacts of the helix formed by residues 730 - 745 (chain A) in PDB entry 2PZI
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 730 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A ASP 4.1 8.8 + - - +
728A ALA 2.9 8.7 + - - +
729A PRO* 1.3 84.4 - - + +
731A GLN* 1.3 60.0 + - - +
732A ARG* 4.0 9.9 - - - +
733A HIS* 3.4 21.0 + - - +
734A ARG* 3.1 24.8 + - - +
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Residues in contact with GLN 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A THR* 1.3 70.6 - - - +
732A ARG* 1.3 64.7 + - - +
734A ARG* 3.3 40.9 + - - +
735A TYR* 3.1 35.2 + - + -
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Residues in contact with ARG 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A THR* 3.2 7.9 - - - -
731A GLN* 1.3 79.8 - - - +
733A HIS* 1.3 60.7 + - - +
735A TYR* 3.5 9.6 + - - +
736A THR* 3.3 23.8 + - - +
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Residues in contact with HIS 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A VAL 3.2 14.7 + - - -
434A TYR* 2.9 29.1 - - - -
435A LEU 2.8 18.9 + - - -
436A ASP* 3.8 5.2 - - - +
437A GLY* 3.3 27.4 + - - -
728A ALA* 4.1 4.6 - - + +
730A THR* 3.3 21.3 + - - +
732A ARG* 1.3 77.0 - - - +
734A ARG* 1.3 64.9 + - - +
736A THR* 3.2 21.2 + - + +
737A LEU* 3.0 41.7 + - + +
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Residues in contact with ARG 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A ALA* 3.5 29.7 + - - +
726A ARG* 5.2 4.9 + - - +
728A ALA* 4.0 17.3 + - + +
729A PRO 6.3 0.2 - - - -
730A THR 3.1 11.7 + - - +
731A GLN* 3.4 48.4 + - - +
733A HIS* 1.3 76.0 - - - +
735A TYR* 1.3 60.1 + - + +
737A LEU* 3.3 3.6 + - - +
738A VAL* 2.9 43.4 + - + +
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Residues in contact with TYR 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A GLN* 3.1 26.1 + - + -
732A ARG* 3.5 11.9 - - - +
734A ARG* 1.3 78.3 - - + +
736A THR* 1.3 56.2 + - - +
738A VAL* 3.9 9.4 - - + +
739A ASP* 3.0 30.7 + - - +
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Residues in contact with THR 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A ARG* 3.3 15.1 + - - +
733A HIS* 3.2 32.6 + - + +
735A TYR* 1.3 77.9 - - - +
737A LEU* 1.3 64.2 + - - +
739A ASP* 3.5 5.1 - - - +
740A MET* 3.0 47.7 + - + +
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Residues in contact with LEU 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A TYR* 3.6 23.1 - - + +
721A LEU* 3.7 37.4 - - + +
724A LEU* 3.7 16.2 - - + +
725A ALA* 3.6 33.9 - - + +
728A ALA* 4.0 3.8 - - + -
733A HIS* 3.0 41.2 + - + +
734A ARG 3.8 0.2 - - - +
736A THR* 1.3 72.6 - - - +
738A VAL* 1.3 61.1 + - - +
740A MET* 3.2 14.5 + - - +
741A ALA* 2.8 30.9 + - - +
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Residues in contact with VAL 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ARG* 4.2 16.6 - - + +
725A ALA* 4.0 16.4 - - + -
734A ARG* 2.9 31.0 + - + +
735A TYR* 3.9 10.5 - - + +
737A LEU* 1.3 75.4 - - - +
739A ASP* 1.3 58.5 + - - +
741A ALA* 3.0 9.1 + - - +
742A ASN* 2.9 46.1 + - - +
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Residues in contact with ASP 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A TYR 3.0 19.9 + - - +
736A THR* 3.5 6.5 - - - +
738A VAL* 1.3 76.2 - - - +
740A MET* 1.3 57.6 + - + +
742A ASN* 3.3 12.2 + - - +
743A LYS* 2.8 62.3 + - - +
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Residues in contact with MET 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A TYR* 6.6 0.2 - - - -
721A LEU* 3.7 19.5 - - + +
736A THR* 3.0 38.1 + - + +
737A LEU* 3.5 22.0 - - - +
739A ASP* 1.3 76.2 - - + +
741A ALA* 1.3 61.1 + - - +
743A LYS* 3.5 6.9 + - - +
744A VAL* 3.1 27.5 + - - +
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Residues in contact with ALA 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A GLU* 3.4 9.3 - - + +
721A LEU* 3.8 17.0 - - + +
722A ARG* 3.4 40.8 - - + +
737A LEU 2.8 13.1 + - - +
738A VAL* 3.0 9.8 + - - +
740A MET* 1.3 75.5 - - - +
742A ASN* 1.3 59.2 + - - +
744A VAL* 3.4 2.7 + - - +
745A ARG* 2.9 30.1 + - - +
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Residues in contact with ASN 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722A ARG* 2.7 35.1 + - - +
738A VAL* 2.9 33.1 + - - +
739A ASP* 3.6 14.5 + - - +
741A ALA* 1.3 75.0 - - - +
743A LYS* 1.3 62.5 + - + +
745A ARG* 3.2 42.4 + - - +
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Residues in contact with LYS 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A ARG* 4.1 10.9 + - - -
739A ASP* 2.8 54.0 + - - +
740A MET* 3.8 8.7 - - - +
741A ALA 3.2 0.2 - - - -
742A ASN* 1.3 81.2 - - + +
744A VAL* 1.3 60.5 + - + +
745A ARG 3.7 1.4 + - - +
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Residues in contact with VAL 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LEU* 4.0 24.7 - - + -
714A ARG* 3.2 32.5 + - + +
717A VAL* 3.8 24.5 - - + -
718A GLU* 3.7 28.5 - - + +
721A LEU* 3.9 3.4 - - + -
740A MET 3.1 20.7 + - - +
741A ALA 3.4 5.6 - - - +
743A LYS* 1.3 74.8 - - - +
745A ARG* 1.3 71.4 + - - +
746A PRO* 3.2 1.4 - - - -
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Residues in contact with ARG 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ARG* 3.3 10.4 + - - -
718A GLU* 3.3 29.9 + - - +
722A ARG* 3.3 12.1 - - - +
741A ALA 2.9 15.0 + - - +
742A ASN* 3.2 55.4 + - - +
743A LYS 3.3 3.0 - - - +
744A VAL* 1.3 78.0 - - - +
746A PRO* 1.4 79.1 - - + +
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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