Contacts of the helix formed by residues 609 - 616 (chain A) in PDB entry 4BHZ
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 LEU 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607A ILE 4.1 0.2 + - - -
608A ASP* 1.3 71.0 - - - +
610A ASN* 1.4 54.9 + - - +
612A TRP* 3.4 3.2 + - + +
613A LEU* 2.9 48.0 + - + +
627A TYR* 4.4 5.4 - - + -
631A MET* 4.5 2.9 - - + -
650A PRO* 3.3 32.9 + - + +
653A PHE* 2.9 27.1 + - + +
654A LEU* 4.6 0.6 - - - +
655A ILE* 4.2 16.6 - - + +
660A LEU* 4.0 33.4 - - + -
723A ILE* 4.0 19.3 - - + -
727A MET* 3.9 22.9 - - + -
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Residues in contact with ASN 610 (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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608A ASP* 2.8 16.1 + - - +
609A LEU* 1.4 71.2 - - - +
611A SER* 1.3 57.2 + - - +
613A LEU* 3.1 6.0 + - - +
614A LYS* 2.8 43.0 + - - +
650A PRO* 3.7 18.5 + - + +
651A ALA* 3.7 17.3 - - + +
683A GLN* 3.6 31.5 - - - +
689A TYR* 5.3 1.5 + - - -
726A TYR* 4.5 12.5 - - - -
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Residues in contact with SER 611 (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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607A ILE* 3.5 21.9 - - - +
608A ASP* 2.6 32.9 + - - -
610A ASN* 1.3 75.4 - - - +
612A TRP* 1.4 59.9 + - - +
614A LYS* 3.9 9.2 - - - +
615A LYS* 3.1 26.3 + - - +
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Residues in contact with TRP 612 (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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607A ILE* 3.6 25.6 - - + +
608A ASP 3.2 18.6 + - - +
609A LEU* 3.6 6.7 - - + +
611A SER* 1.4 76.2 - - - +
613A LEU* 1.4 68.2 + - + +
615A LYS* 3.5 5.7 + - + +
616A LYS* 3.1 60.8 + - + +
619A ILE* 5.2 2.2 - - - +
623A GLU* 3.5 25.2 + - - -
627A TYR* 4.2 10.3 + + - -
655A ILE* 3.5 28.0 - - + -
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Residues in contact with LEU 613 (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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609A LEU* 2.9 41.7 + - + +
610A ASN 3.1 3.6 + - - +
612A TRP* 1.4 78.3 - - + +
614A LYS* 1.3 60.9 + - - +
616A LYS* 2.9 31.9 + - + +
619A ILE* 3.8 35.9 - - + -
650A PRO* 4.2 10.8 - - + -
723A ILE* 5.2 1.1 - - + -
726A TYR* 4.0 37.3 + - + -
727A MET* 3.9 24.0 - - + -
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Residues in contact with LYS 614 (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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610A ASN* 2.8 39.2 + - - +
611A SER* 3.9 8.3 - - - +
613A LEU* 1.3 71.6 - - - +
615A LYS* 1.4 59.2 + - - +
616A LYS 3.7 3.1 + - - +
726A TYR* 4.0 15.3 - - - +
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Residues in contact with LYS 615 (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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607A ILE* 5.6 3.4 - - + -
611A SER 3.1 18.4 + - - +
612A TRP* 3.9 9.4 - - + +
614A LYS* 1.4 76.5 - - - +
616A LYS* 1.3 61.2 + - + +
617A LYS 3.8 1.2 + - - -
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Residues in contact with LYS 616 (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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612A TRP* 3.1 59.1 + - + +
613A LEU* 2.9 23.3 + - + +
614A LYS 4.1 3.0 - - - +
615A LYS* 1.3 78.1 - - - +
617A LYS* 1.3 65.3 + - - +
618A SER 3.8 21.3 - - - +
619A ILE* 4.7 8.7 - - + -
623A GLU* 4.4 12.3 - - - +
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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