Contacts of the helix formed by residues 602 - 609 (chain A) in PDB entry 2CG2
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 ARG 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535A LEU* 2.9 22.8 + - - +
536A ALA 4.5 5.1 + - - +
538A MET* 2.8 31.9 + - - +
539A ASP* 4.4 0.2 - - - +
540A THR* 2.9 31.3 + - - +
543A LEU* 3.7 22.2 - - - +
567A LEU* 3.6 19.3 - - + +
569A ASP* 2.8 15.6 + - - +
570A ILE* 3.5 31.7 - - + +
600A ILE 3.5 2.6 + - - -
601A ASP* 1.3 70.9 - - - +
603A ALA* 1.3 52.6 + - - +
605A LEU* 3.0 12.4 + - - +
606A ASN* 2.6 64.4 + - - +
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Residues in contact with ALA 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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569A ASP* 3.0 15.5 + - - +
601A ASP* 4.7 3.1 - - + -
602A ARG* 1.3 76.8 - - - +
604A ASP* 1.3 63.0 + - - +
606A ASN* 3.4 13.6 - - - +
607A ARG* 3.2 29.3 + - - +
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Residues in contact with ASP 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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600A ILE* 3.8 16.4 - - + -
601A ASP* 3.1 26.3 + - + +
603A ALA* 1.3 78.4 - - - +
605A LEU* 1.3 64.9 + - - +
606A ASN 3.2 1.1 - - - -
607A ARG* 2.8 39.6 + - - +
608A LEU* 3.0 22.5 + - - +
618A LEU* 3.7 18.6 - - + +
623A LYS* 3.4 28.0 - - + +
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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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540A THR* 5.1 0.2 - - + -
543A LEU* 4.1 15.5 - - + -
544A PHE* 4.0 31.2 - - + -
547A LEU* 6.1 0.2 - - + -
565A LEU* 4.5 4.9 - - + -
567A LEU* 3.9 21.1 - - + -
600A ILE* 3.6 21.8 - - + +
601A ASP 2.8 13.4 + - - +
602A ARG* 3.5 11.9 - - - +
604A ASP* 1.3 75.2 - - - +
606A ASN* 1.3 62.3 + - - +
608A LEU* 3.1 18.9 + - + +
609A LEU* 3.0 49.8 + - + +
637A PHE* 4.6 11.4 - - + -
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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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532A ALA 6.0 0.4 - - - +
535A LEU* 3.4 32.6 - - + +
536A ALA* 3.8 25.6 + - - +
543A LEU* 4.3 2.4 - - - +
602A ARG* 2.6 61.1 + - - +
603A ALA* 3.4 13.4 - - - +
605A LEU* 1.3 71.7 - - - +
607A ARG* 1.3 61.8 + - + +
609A LEU* 3.2 2.5 + - - -
610A LEU* 3.0 26.5 + - + +
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Residues in contact with ARG 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 ALA 3.2 12.6 + - - +
604A ASP* 2.8 33.3 + - - +
605A LEU 3.4 0.2 - - - -
606A ASN* 1.3 77.7 - - - +
608A LEU* 1.3 62.0 + - - +
610A LEU* 3.1 2.5 + - + +
611A LYS 3.0 4.5 + - - -
612A GLU* 2.9 60.1 + - + +
613A VAL* 3.6 36.8 - - + +
618A LEU* 3.8 11.9 - - - +
621A GLU* 4.2 4.4 + - - -
623A LYS* 3.7 21.8 - - - +
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Residues in contact with LEU 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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600A ILE* 5.2 4.5 - - + -
604A ASP 3.0 13.7 + - - +
605A LEU* 3.1 19.5 + - + +
607A ARG* 1.3 76.5 - - - +
609A LEU* 1.3 60.2 + - + +
611A LYS* 3.1 26.3 + - - +
613A VAL* 3.4 23.2 - - - +
614A SER* 3.9 1.6 - - - -
615A ALA* 3.5 32.1 - - + +
618A LEU* 4.0 14.8 - - + -
624A LEU* 5.2 5.2 - - + -
633A LEU* 5.9 1.1 - - + -
637A PHE* 3.9 31.4 - - + -
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Residues in contact with LEU 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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535A LEU* 4.4 10.3 - - + -
543A LEU* 3.6 40.2 - - + -
547A LEU* 4.6 24.5 - - + -
550A ARG* 5.6 4.9 - - - +
605A LEU* 3.0 38.1 + - + +
606A ASN* 3.2 7.4 + - - +
608A LEU* 1.3 78.4 - - + +
610A LEU* 1.3 60.2 + - - +
611A LYS* 3.2 14.0 + - - +
637A PHE* 4.7 12.8 - - + -
640A LEU* 6.2 0.7 - - + -
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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