Contacts of the helix formed by residues 600 - 610 (chain A) in PDB entry 3A1B
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 ASP 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A ARG* 3.6 7.6 - - - +
599A GLU* 1.3 78.8 + - + +
601A TRP* 1.3 64.0 + - - +
602A PRO* 3.1 7.4 - - - -
603A SER* 3.3 14.9 + - - +
604A ARG* 3.0 53.4 + - - +
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Residues in contact with TRP 601 (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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507A PRO 3.4 22.6 - - - +
508A LEU* 3.9 26.2 - - + +
556A ARG* 5.4 3.4 - - - -
585A MET* 3.5 27.2 + - + +
597A ARG* 3.9 22.0 - - + +
598A ARG* 3.2 28.0 + - + +
599A GLU 4.7 2.5 - - - -
600A ASP* 1.3 75.7 + - - +
602A PRO* 1.4 87.4 - - + +
604A ARG* 3.7 0.4 - - - +
605A LEU* 2.7 53.2 + - + +
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Residues in contact with PRO 602 (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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599A GLU 4.3 3.4 - - - +
600A ASP* 3.1 9.9 - - - -
601A TRP* 1.4 126.6 - - + +
603A SER* 1.3 56.9 + - - +
605A LEU* 3.7 2.9 - - + +
606A GLN* 3.0 34.1 + - - +
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Residues in contact with SER 603 (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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600A ASP* 3.3 23.9 + - - +
602A PRO* 1.3 76.5 - - - +
604A ARG* 1.3 63.9 + - - +
606A GLN* 3.4 11.5 + - - +
607A MET* 2.9 35.2 + - - +
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Residues in contact with ARG 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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505A GLU* 2.7 45.0 + - - +
506A HIS 4.3 2.2 + - - -
507A PRO* 3.6 33.9 - - + +
598A ARG* 3.5 29.0 - - - +
600A ASP* 3.0 49.4 + - - +
603A SER* 1.3 76.2 + - - +
605A LEU* 1.3 57.5 + - - +
607A MET* 3.3 22.7 + - + +
608A PHE* 2.9 30.3 + - - +
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Residues in contact with LEU 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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7A EDO 3.2 27.8 - - - +
507A PRO* 3.9 18.4 - - + +
508A LEU* 3.6 20.6 - - + -
521A PHE* 4.0 14.8 - - + -
556A ARG* 4.2 5.2 - - - +
601A TRP* 2.7 48.0 + - + +
602A PRO* 3.7 4.3 - - + +
604A ARG* 1.3 71.3 - - - +
606A GLN* 1.3 63.2 + - - +
608A PHE* 3.2 6.2 + - - +
609A PHE* 3.1 38.0 + - + -
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Residues in contact with GLN 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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602A PRO* 3.0 20.7 + - + +
603A SER* 3.7 10.2 - - - +
604A ARG 3.3 0.2 - - - -
605A LEU* 1.3 77.2 - - + +
607A MET* 1.3 61.8 + - + +
609A PHE* 3.4 5.1 + - - +
610A ALA* 3.2 24.5 + - - +
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Residues in contact with MET 607 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A LYS* 5.5 0.5 + - - -
603A SER* 2.9 20.5 + - - +
604A ARG* 3.6 30.7 - - + +
606A GLN* 1.3 74.3 - - + +
608A PHE* 1.3 63.3 + - - +
610A ALA* 3.2 22.0 + - - +
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Residues in contact with PHE 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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504A LEU* 3.7 28.5 - - + -
505A GLU 4.8 2.2 - - - -
507A PRO* 3.8 21.3 - - + -
513A MET* 3.7 19.5 - - - -
518A LYS* 3.4 47.9 + - + +
521A PHE* 3.3 27.8 - + + -
522A LEU* 3.7 22.5 - - + +
604A ARG 2.9 17.6 + - - +
605A LEU* 3.3 10.5 - - - +
607A MET* 1.3 77.1 - - - +
609A PHE* 1.3 74.8 + + - +
610A ALA 5.0 1.2 - - - -
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Residues in contact with PHE 609 (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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7A EDO 4.3 7.2 - - - -
521A PHE* 3.9 24.0 - + - -
522A LEU* 3.7 25.3 - - + +
525A ALA* 3.5 34.3 - - + -
526A TYR* 3.6 29.4 - + - +
605A LEU* 3.1 38.6 + - + +
606A GLN* 4.2 4.3 - - - +
607A MET 3.2 0.4 - - - -
608A PHE* 1.3 91.5 - + - +
610A ALA* 1.3 61.0 + - - +
617A EDO 5.1 2.0 - - - -
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Residues in contact with ALA 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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606A GLN 3.2 16.3 + - - +
607A MET* 3.2 15.0 + - - +
608A PHE 5.0 1.6 - - - -
609A PHE* 1.3 80.9 - - - +
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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