Contacts of the helix formed by residues 600 - 608 (chain A) in PDB entry 3EA4
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 ASN 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597A ILE 4.1 5.7 + - - +
598A PHE* 5.0 1.2 - - - -
599A PRO* 1.3 73.0 - - - +
601A MET* 1.3 61.3 + - - +
602A LEU* 3.0 32.3 + - - +
603A LEU* 3.1 46.9 + - + +
604A PHE* 3.6 10.1 + - - -
614A ARG* 3.7 19.6 + - - +
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Residues in contact with MET 601 (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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538A ASP* 3.8 36.3 - - + +
541A PHE* 4.0 21.5 - - + -
542A ILE* 4.4 9.0 - - + -
562A LEU* 3.4 27.6 - - + -
564A ASN* 4.2 9.2 - - - +
599A PRO* 3.3 30.6 + - + +
600A ASN* 1.3 71.3 + - - +
602A LEU* 1.3 62.9 + - - +
603A LEU 3.2 0.2 - - - -
604A PHE* 3.2 39.3 + - - +
605A ALA 3.2 9.5 + - - -
614A ARG* 4.5 3.6 - - - +
636A LEU* 3.3 17.9 - - + +
638A ASP* 4.5 7.9 - - - +
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Residues in contact with LEU 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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600A ASN* 3.0 17.6 + - - +
601A MET* 1.3 78.1 - - - +
603A LEU* 1.3 60.7 + - + +
605A ALA* 3.3 4.5 + - - +
606A ALA* 2.9 27.9 + - - +
612A ALA* 3.8 16.1 - - + +
613A ALA* 3.4 37.9 - - - +
614A ARG* 3.8 35.0 - - + +
636A LEU* 4.3 7.0 - - + -
638A ASP* 3.9 14.1 - - + -
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Residues in contact with LEU 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 ASN* 3.1 38.6 + - + +
602A LEU* 1.3 78.7 - - + +
604A PHE* 1.3 58.3 + - - +
606A ALA* 3.7 14.6 - - + +
607A ALA* 2.9 29.1 + - - +
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Residues in contact with PHE 604 (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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541A PHE* 5.0 2.0 - - + -
542A ILE* 3.9 23.1 - - + -
545A VAL* 3.9 35.0 - - + -
548A LEU* 3.8 6.8 - - + +
599A PRO* 3.9 21.8 - - + -
600A ASN 3.6 3.9 + - - -
601A MET* 3.2 45.9 + - - +
603A LEU* 1.3 78.4 - - - +
605A ALA* 1.3 60.7 + - - +
607A ALA* 3.4 19.3 + - + +
608A CYS* 3.5 14.6 + - - -
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Residues in contact with ALA 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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548A LEU* 4.0 12.0 - - + +
601A MET 3.2 2.6 + - - -
602A LEU 3.5 8.7 - - - +
604A PHE* 1.3 77.5 - - - +
606A ALA* 1.3 59.1 + - - +
608A CYS* 3.1 4.8 + - - -
609A GLY 3.1 4.3 + - - -
610A ILE* 2.8 53.5 + - + +
612A ALA* 3.8 15.5 - - + -
636A LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 606 (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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602A LEU 2.9 17.4 + - - +
603A LEU* 3.7 19.3 - - + +
605A ALA* 1.3 75.2 - - - +
607A ALA* 1.3 58.4 + - - +
609A GLY* 2.9 20.8 + - - +
610A ILE 3.9 6.7 + - - +
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Residues in contact with ALA 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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603A LEU 2.9 18.1 + - - +
604A PHE* 3.4 10.8 - - + +
606A ALA* 1.3 75.2 - - - +
608A CYS* 1.3 64.5 + - - +
609A GLY 3.4 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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545A VAL 5.4 1.3 - - - -
546A GLN* 5.5 1.1 - - - -
548A LEU* 3.8 29.6 - - + +
549A ALA* 3.6 30.7 - - - +
552A ARG* 3.1 26.7 - - + +
604A PHE 3.5 11.6 + - - +
605A ALA 3.1 6.2 + - - +
606A ALA 3.1 0.6 - - - -
607A ALA* 1.3 82.6 - - - +
609A GLY* 1.3 62.3 + - - +
610A ILE* 3.3 5.8 + - + +
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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