Contacts of the helix formed by residues 603 - 608 (chain A) in PDB entry 4B1H
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 CYS 603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A LYS* 3.1 25.7 + - - +
600A ILE* 3.6 4.7 - - - +
601A ALA 3.2 0.6 - - - -
602A LEU* 1.4 75.3 - - - +
604A LEU* 1.3 64.6 + - - +
605A PRO* 3.3 3.1 - - - -
606A ASN* 2.8 18.0 + - - -
607A ILE* 3.2 31.7 + - + +
1603A BME 2.0 50.7 - - - -
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Residues in contact with LEU 604 (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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502A TYR* 6.0 0.2 - - + -
513A MET* 4.5 7.0 - - - -
514A PRO* 3.7 36.8 - - + -
515A CYS* 3.8 16.8 - - + -
536A TRP* 4.3 3.6 - - + -
601A ALA 3.1 15.7 + - - +
603A CYS* 1.3 75.5 - - - +
605A PRO* 1.3 65.5 - - + +
607A ILE* 4.5 1.6 - - - +
608A CYS* 2.9 60.8 + - + +
632A SER* 3.5 20.8 + - - +
633A LEU* 3.7 18.8 - - + +
636A ASN* 3.7 14.6 - - + +
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Residues in contact with PRO 605 (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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502A TYR* 3.5 43.1 + - + +
515A CYS* 4.2 15.0 - - + -
536A TRP* 3.7 22.4 - - + +
602A LEU 3.5 11.4 - - - +
603A CYS 3.4 4.3 - - - -
604A LEU* 1.3 95.4 - - + +
606A ASN* 1.3 66.4 + - - +
609A THR* 3.6 10.3 - - - +
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Residues in contact with ASN 606 (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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497A PRO* 3.8 9.9 - - - +
500A THR 5.2 1.2 - - - +
602A LEU 5.0 0.5 - - - +
603A CYS* 2.8 12.2 + - - +
605A PRO* 1.3 86.9 - - - +
607A ILE* 1.3 63.2 + - + +
609A THR* 3.7 13.0 - - - +
1603A BME 3.9 31.2 + - - +
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Residues in contact with ILE 607 (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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497A PRO* 3.3 15.6 - - + +
600A ILE* 4.1 13.2 - - + -
603A CYS* 3.4 35.4 - - + +
604A LEU 3.0 3.0 + - - +
606A ASN* 1.3 82.8 - - + +
608A CYS* 1.3 60.6 + - - +
609A THR 3.5 0.7 - - - -
628A GLU* 4.1 25.1 - - + +
629A GLN* 3.0 56.7 + - + +
632A SER* 3.9 25.6 - - - -
1603A BME 5.4 0.9 - - - -
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Residues in contact with CYS 608 (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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483A THR* 6.3 0.9 - - - -
502A TYR* 3.5 19.8 - - - -
513A MET* 4.8 12.2 - - + +
604A LEU* 2.9 43.8 + - + +
607A ILE* 1.3 71.8 - - - +
609A THR* 1.3 60.9 + - - +
610A GLN 3.3 7.9 + - - +
612A ILE* 4.9 4.7 - - + -
625A MET* 6.0 0.7 - - - -
629A GLN* 3.8 32.3 - - - +
633A LEU* 3.7 28.3 - - + -
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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