Contacts of the helix formed by residues 604 - 609 (chain A) in PDB entry 5IJ7
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 604 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A GLU* 3.3 13.0 - - - -
590A ALA* 4.3 13.5 - - + -
597A LYS 5.8 1.3 - - - -
599A VAL* 4.2 7.9 - - - -
601A CYS* 3.6 32.5 - - - -
602A LYS 3.7 0.8 - - - -
603A ASN* 1.3 79.1 - - - +
605A SER* 1.4 63.4 + - - +
607A GLN* 3.1 34.5 - - + +
608A ARG* 3.2 38.5 + - - +
610A SER* 4.9 0.2 - - - -
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Residues in contact with SER 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A GLU* 3.2 4.4 + - - -
602A LYS* 4.2 14.9 + - - -
604A CYS* 1.4 74.9 + - - +
606A ILE* 1.4 57.1 + - - +
608A ARG 3.6 0.2 + - - -
609A GLY* 2.8 29.3 + - - -
610A SER* 3.0 25.4 + - - -
612A LYS* 5.8 0.7 + - - -
637A PHE* 3.4 43.9 - - - +
711A PHE* 5.8 0.8 - - - -
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Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A GLU* 2.8 19.2 + - - +
605A SER* 1.4 70.2 - - - +
607A GLN* 1.4 61.2 + - - +
609A GLY* 3.1 14.4 + - - -
637A PHE* 3.6 27.6 - - + -
640A GLU* 3.8 14.6 - - + +
700A MET* 3.5 32.8 - - + -
702A VAL* 4.0 13.7 - - + -
707A ARG* 3.5 51.4 + - + +
708A ILE 4.4 0.4 - - - -
709A GLY* 3.9 25.1 - - - +
711A PHE* 4.8 0.2 - - + -
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Residues in contact with GLN 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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118A GLN* 5.9 0.2 + - - -
579A GLU* 3.0 24.1 + - - +
580A CYS 2.6 23.8 + - - +
582A PRO* 3.4 30.7 - - - +
590A ALA* 4.6 4.6 + - - +
604A CYS* 3.1 29.4 - - + +
606A ILE* 1.4 76.4 - - - +
608A ARG* 1.3 58.5 + - + +
702A VAL* 3.6 13.1 - - + +
703A ASN* 3.7 12.5 + - - +
707A ARG* 3.6 16.4 + - - +
627S ILE* 3.5 43.7 - - + +
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Residues in contact with ARG 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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589A GLY 3.6 3.8 + - - -
590A ALA* 2.9 28.9 + - - +
592A ASP 2.7 22.2 + - - -
593A HIS 2.8 27.5 + - - -
594A TRP* 3.5 21.9 + - + +
596A SER 3.0 18.2 + - - +
597A LYS* 3.3 27.6 + - + -
599A VAL* 3.5 10.5 - - - +
604A CYS* 3.2 39.0 + - - +
607A GLN* 1.3 79.4 - - + +
609A GLY* 1.3 62.5 + - - +
610A SER* 3.6 15.7 - - - +
627S ILE* 4.5 8.1 - - + -
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Residues in contact with GLY 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 5.3 6.7 + - - -
597A LYS* 3.2 14.3 + - - -
605A SER 2.8 11.4 + - - -
606A ILE 3.1 10.1 + - - -
607A GLN 3.4 0.2 - - - -
608A ARG* 1.3 78.9 - - - +
610A SER* 1.4 49.8 + - - -
611A LYS* 2.8 32.7 + - - +
637A PHE* 4.9 2.7 - - - -
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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