Contacts of the helix formed by residues 726 - 741 (chain O) in PDB entry 5A31
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 LYS 726 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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688O GLU* 4.9 8.7 - - - +
721O TYR* 3.3 15.3 + - + +
724O LEU* 3.4 37.7 - - + +
725O GLY* 1.3 73.3 - - - +
727O THR* 1.3 64.1 + - - +
728O GLN* 3.2 5.0 + - + -
729O GLU* 3.5 34.5 + - + +
730O ARG* 3.3 19.4 + - - +
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Residues in contact with THR 727 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722O HIS* 5.6 3.8 - - + +
725O GLY* 2.8 21.0 + - - +
726O LYS* 1.3 70.5 - - - +
728O GLN* 1.3 65.2 + - - +
730O ARG* 3.1 36.9 - - - +
731O ASN* 3.1 27.5 + - - +
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Residues in contact with GLN 728 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726O LYS* 3.2 2.9 - - + -
727O THR* 1.3 83.1 + - - +
729O GLU* 1.3 63.3 + - + +
731O ASN* 3.4 19.8 + - - +
732O ARG* 3.8 10.0 + - - +
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Residues in contact with GLU 729 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721O TYR* 3.2 43.2 + - + -
726O LYS* 3.5 29.7 + - + +
727O THR 3.5 0.2 - - - -
728O GLN* 1.3 78.0 - - + +
730O ARG* 1.4 67.3 - - - +
732O ARG* 3.1 10.1 + - - +
733O CYS* 2.9 25.5 + - - -
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Residues in contact with ARG 730 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718O ALA* 4.2 10.4 + - + +
721O TYR* 4.0 19.4 - - + +
722O HIS* 3.5 45.8 + - - +
726O LYS 3.3 9.4 + - - +
727O THR* 3.1 44.7 + - - +
729O GLU* 1.4 75.2 - - - +
731O ASN* 1.3 59.6 + - - +
733O CYS* 2.8 9.2 + - - +
734O ALA* 2.6 38.9 + - + +
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Residues in contact with ASN 731 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727O THR* 3.1 12.9 + - - +
728O GLN* 3.6 16.8 - - - +
729O GLU 3.3 0.4 - - - -
730O ARG* 1.3 82.6 + - - +
732O ARG* 1.3 56.6 + - + +
734O ALA* 3.3 6.5 + - - +
735O MET* 2.7 38.7 + - - +
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Residues in contact with ARG 732 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728O GLN* 3.8 9.3 + - - +
729O GLU* 3.1 10.9 + - - +
731O ASN* 1.3 77.8 - - + +
733O CYS* 1.3 58.7 + - - +
735O MET* 3.5 31.2 - - - +
736O LEU* 2.9 38.1 + - + +
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Residues in contact with CYS 733 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714O VAL* 3.2 18.7 - - + +
717O GLN* 4.9 11.4 - - - -
718O ALA* 4.1 23.3 - - + +
721O TYR* 3.4 33.2 - - - -
729O GLU* 2.9 18.4 + - - -
730O ARG* 2.8 11.4 + - - +
732O ARG* 1.3 72.9 - - - +
734O ALA* 1.3 61.6 + - - +
736O LEU* 3.4 12.9 + - - -
737O PHE* 3.1 17.5 + - - +
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Residues in contact with ALA 734 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718O ALA* 4.4 12.0 - - + +
730O ARG* 2.6 24.0 + - + +
731O ASN* 3.7 5.8 - - - +
733O CYS* 1.3 69.7 - - - +
735O MET* 1.3 59.5 + - - +
737O PHE* 3.1 12.4 + - + +
738O ARG* 2.8 31.6 + - + +
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Residues in contact with MET 735 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731O ASN 2.7 19.8 + - - +
732O ARG* 3.5 39.9 - - + +
734O ALA* 1.3 69.1 - - - +
736O LEU* 1.3 85.5 + - + +
738O ARG* 3.0 11.2 + - - +
739O GLN* 3.0 43.7 + - - +
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Residues in contact with LEU 736 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698O LYS* 4.4 30.5 - - - +
714O VAL* 3.9 11.7 - - + -
717O GLN* 6.1 0.7 - - - +
732O ARG* 2.9 26.7 + - + +
733O CYS* 3.4 18.8 - - + +
735O MET* 1.3 86.1 - - + +
737O PHE* 1.3 62.2 + - - +
739O GLN* 3.4 20.4 - - - +
740O LEU* 3.2 32.7 + - + +
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Residues in contact with PHE 737 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711O ARG* 3.6 37.5 - - + -
714O VAL* 3.8 11.4 - - + +
715O TYR* 3.8 42.2 - + + +
718O ALA* 5.9 0.7 - - + -
733O CYS 3.1 10.1 + - - +
734O ALA* 3.1 15.2 + - + +
736O LEU* 1.3 78.6 - - - +
738O ARG* 1.3 67.6 + - + +
740O LEU* 3.2 6.6 + - - -
741O HIS* 2.8 56.7 + + + +
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Residues in contact with ARG 738 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734O ALA* 2.8 18.7 + - + +
735O MET* 3.0 12.3 + - - +
737O PHE* 1.3 81.2 - - + +
739O GLN* 1.3 64.7 + - - +
741O HIS* 3.3 17.2 + - + +
742O GLN* 3.5 8.5 + - - +
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Residues in contact with GLN 739 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735O MET* 3.0 31.9 + - - +
736O LEU* 3.4 20.3 - - - +
738O ARG* 1.3 76.1 - - - +
740O LEU* 1.3 67.0 + - + +
742O GLN* 3.2 25.4 + - - +
743O GLU 4.6 0.5 + - - -
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Residues in contact with LEU 740 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707O LYS* 4.2 21.6 - - + +
708O GLU* 5.4 1.0 - - - +
710O ILE* 3.8 19.5 - - + -
711O ARG* 3.6 48.3 + - + +
714O VAL* 4.2 16.4 - - + -
736O LEU* 3.2 18.6 + - + +
737O PHE* 3.2 8.1 + - - +
739O GLN* 1.3 86.1 - - + +
741O HIS* 1.3 61.3 + - - +
742O GLN 3.3 0.2 - - - -
743O GLU* 3.3 23.8 + - - +
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Residues in contact with HIS 741 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A TYR* 4.1 22.8 + - - -
711O ARG* 3.5 26.0 + - - +
737O PHE* 2.8 41.8 + + + +
738O ARG* 3.5 14.1 - - + +
739O GLN 3.2 0.2 - - - -
740O LEU* 1.3 74.8 - - - +
742O GLN* 1.3 62.7 + - - +
743O GLU 3.2 10.4 + - - +
745O PRO* 5.0 12.6 - - + +
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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
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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