Contacts of the helix formed by residues 729 - 739 (chain B) in PDB entry 3A8P
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 SER 729 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711B LEU* 3.9 11.4 - - - -
727B VAL* 3.3 10.8 + - - -
728B LEU* 1.3 76.3 - - - +
730B VAL* 1.3 64.8 + - - +
731B SER* 3.4 10.0 + - - -
732B SER* 3.0 27.1 + - - -
733B PHE* 3.0 24.8 + - - +
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Residues in contact with VAL 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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708A LYS* 6.1 0.7 - - - +
572B ILE* 4.4 11.0 - - + -
574B GLN* 4.1 20.0 - - + +
687B MET* 4.4 0.9 - - - +
690B PHE* 3.8 18.6 - - + -
707B PRO* 3.5 45.3 - - + +
710B LEU* 3.7 27.8 - - + -
711B LEU* 4.0 14.1 - - + +
729B SER* 1.3 73.4 - - - +
731B SER* 1.3 58.5 + - - +
733B PHE* 3.3 3.4 + - - +
734B HIS* 2.8 28.8 + - + +
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Residues in contact with SER 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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572B ILE* 5.3 0.6 + - - +
574B GLN* 4.2 13.0 - - - +
587B CYS* 3.1 45.9 + - - +
589B SER* 3.5 23.0 + - - -
595B VAL* 3.8 9.3 - - - +
729B SER* 3.2 8.5 + - - -
730B VAL* 1.3 80.5 - - - +
732B SER* 1.3 60.7 + - - +
734B HIS* 3.4 3.5 + - - +
735B ALA* 3.2 18.9 + - - +
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Residues in contact with SER 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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517B VAL* 5.7 0.2 - - - -
525B LEU* 4.4 0.2 - - - +
595B VAL* 4.6 6.0 - - - +
722B LEU* 3.5 22.2 + - - +
725B LEU* 3.9 30.7 - - - -
727B VAL 4.1 2.3 + - - -
728B LEU* 4.0 9.9 - - - +
729B SER* 3.0 30.6 + - - -
731B SER* 1.3 74.0 - - - +
733B PHE* 1.3 62.6 + - - +
735B ALA* 3.2 8.3 + - - +
736B LEU 3.0 22.3 + - - -
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Residues in contact with PHE 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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683B GLU* 3.7 42.4 - - + -
687B MET* 3.3 15.9 - - + -
710B LEU* 3.7 32.3 - - + -
711B LEU* 3.9 14.1 - - + -
713B ALA* 4.3 0.9 - - + -
714B THR* 3.3 45.3 - - + -
718B SER* 4.6 2.5 - - - -
722B LEU* 3.7 15.7 - - + -
728B LEU* 4.3 0.9 - - + -
729B SER 3.0 19.4 + - - +
730B VAL 3.6 2.7 - - - +
732B SER* 1.3 74.5 + - - +
734B HIS* 1.3 65.9 + - - +
736B LEU* 3.2 6.4 + - + +
737B VAL* 3.0 31.9 + - + +
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Residues in contact with HIS 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ASP 3.8 18.0 + - - -
572B ILE* 3.7 23.7 - - + +
589B SER* 2.7 46.2 + - - +
590B ASN 3.5 10.8 - - - -
591B SER* 4.8 0.4 - - - -
687B MET* 3.7 33.1 - - + +
691B ARG* 4.6 6.5 + - - -
730B VAL* 2.8 17.4 + - + +
731B SER 3.5 0.7 - - - +
732B SER 3.2 0.2 - - - -
733B PHE* 1.3 76.8 - - - +
735B ALA* 1.3 58.1 + - - +
737B VAL* 3.3 2.3 + - + -
738B CYS* 2.9 42.6 + - - -
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Residues in contact with ALA 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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517B VAL* 5.2 1.6 - - + -
525B LEU* 3.9 12.9 - - + +
589B SER* 4.9 2.0 - - - -
590B ASN 5.2 1.1 - - - -
593B GLY* 3.5 35.0 - - - +
594B ASP 5.2 0.2 - - - +
595B VAL* 3.9 14.6 - - + -
725B LEU* 5.8 0.2 - - + -
731B SER 3.2 11.3 + - - +
732B SER* 3.2 10.1 + - - +
734B HIS* 1.3 80.9 - - - +
736B LEU* 1.3 56.7 + - - +
738B CYS* 3.4 3.0 + - - +
739B SER* 2.9 29.5 + - - -
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Residues in contact with LEU 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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525B LEU* 3.7 13.6 - - + +
718B SER* 3.5 38.4 - - - +
721B ALA* 4.7 11.4 - - + -
722B LEU* 3.9 24.5 - - + -
732B SER 3.0 12.5 + - - +
733B PHE* 3.5 12.3 - - + +
734B HIS 3.2 0.2 - - - -
735B ALA* 1.3 75.3 - - - +
737B VAL* 1.3 67.1 + - - +
739B SER* 2.5 29.6 + - - +
740B ARG* 3.4 31.7 - - + +
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Residues in contact with VAL 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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683B GLU* 4.4 14.1 - - + -
684B LYS* 3.6 39.8 - - + +
687B MET* 4.3 23.8 - - + -
733B PHE* 3.0 37.8 + - + +
734B HIS* 3.3 4.0 + - + +
736B LEU* 1.3 76.2 - - + +
738B CYS* 1.3 63.7 + - - +
740B ARG* 3.3 30.6 + - - +
741B ASP* 3.6 6.6 + - - +
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Residues in contact with CYS 738 (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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523B ARG* 4.2 0.5 + - - -
590B ASN 3.5 14.8 - - - -
591B SER* 3.5 30.3 - - - +
592B CYS 5.1 1.3 - - - -
593B GLY* 4.1 9.0 - - - +
734B HIS* 2.9 50.4 + - - +
735B ALA 3.6 4.5 - - - +
737B VAL* 1.3 74.1 - - - +
739B SER* 1.3 58.1 + - - +
740B ARG 2.8 11.3 + - - -
741B ASP* 2.9 26.4 + - - +
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Residues in contact with SER 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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519B LEU* 3.8 39.9 - - - +
523B ARG* 3.0 36.5 + - - +
525B LEU* 4.5 4.9 - - - +
735B ALA 2.9 13.7 + - - -
736B LEU* 2.5 34.4 + - - +
738B CYS* 1.3 74.4 - - - +
740B ARG* 1.3 59.0 + - - +
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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