Contacts of the helix formed by residues 598 - 603 (chain A) in PDB entry 1JZ3
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 598 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 3.1 30.9 + - + +
101A THR* 3.5 8.7 + - - -
102A ASN* 2.8 26.4 + - + +
103A VAL 4.3 2.1 + - - -
104A THR* 5.1 2.4 + - - -
597A ASN* 1.3 77.9 - - - +
599A ARG* 1.3 80.3 + - - +
601A PHE* 3.0 17.0 + - + +
797A GLU* 5.5 2.8 - - - +
800A ARG* 5.9 0.9 + - - -
8506A DMS 3.5 37.2 - - - +
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Residues in contact with ARG 599 (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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100A TYR* 3.4 6.1 - - - -
542A MET* 5.1 5.1 - - - +
588A TYR* 3.4 14.7 - - + +
589A GLY* 2.9 31.2 + - - +
597A ASN* 2.7 18.8 + - - +
598A ASP* 1.3 91.3 + - - +
600A GLN* 1.3 100.7 + - - +
601A PHE* 3.2 6.0 + - - +
602A CYS* 3.7 0.7 - - - -
790A ASP* 5.0 1.0 + - - -
793A ILE* 4.0 7.3 - - - +
794A GLY 3.2 22.8 + - - -
795A VAL* 3.6 11.1 + - - +
796A SER 2.9 27.4 + - - -
797A GLU* 4.1 25.5 + - - +
8506A DMS 5.6 6.3 - - - +
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Residues in contact with GLN 600 (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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542A MET* 3.4 19.7 - - + +
588A TYR* 3.5 23.4 + - + -
598A ASP 3.2 0.2 + - - -
599A ARG* 1.3 119.2 + - - +
601A PHE* 1.3 56.4 + - - +
602A CYS 3.0 6.5 - - - -
603A MET* 2.9 50.2 + - + +
790A ASP* 3.0 22.0 - - - +
793A ILE* 4.8 2.3 - - - +
931A PHE* 3.4 33.2 - - + -
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Residues in contact with PHE 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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100A TYR* 3.2 14.6 - - - +
102A ASN* 3.3 27.8 - - - -
201A ASP* 3.3 2.5 - - - -
540A HIS* 3.9 14.6 - + - -
542A MET* 3.9 21.7 - - + +
598A ASP* 3.0 16.7 + - + +
599A ARG* 4.7 3.3 - - + +
600A GLN* 1.3 79.7 - - - +
602A CYS* 1.3 53.4 + - - +
603A MET 3.2 0.4 - - - -
604A ASN* 3.0 10.0 + - - -
998A SER* 4.8 4.0 - - - -
999A TRP* 3.7 26.7 - + - -
2001A 2DG 3.2 19.3 - - - -
2002A BTB 3.9 3.1 - - - -
3101A NA 2.5 53.6 - - - -
8506A DMS 3.4 32.1 - - + -
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Residues in contact with CYS 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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100A TYR* 3.3 38.5 - - + -
201A ASP* 5.0 0.2 - - - -
203A TRP* 4.2 5.2 - - - +
573A GLN* 2.9 61.6 + - + +
588A TYR* 3.9 19.5 - - - -
589A GLY 4.0 3.1 - - - -
599A ARG 3.7 15.5 - - - -
600A GLN 3.0 2.0 - - - -
601A PHE* 1.3 76.0 - - - +
603A MET* 1.4 62.1 + - - +
604A ASN* 3.7 5.0 + - - -
3101A NA 4.4 2.0 - - - -
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Residues in contact with MET 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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542A MET* 3.5 17.5 - - - +
543A GLY 4.4 2.3 + - - -
572A ASP* 3.5 26.5 - - + +
573A GLN 4.1 2.0 - - - +
574A SER* 3.8 22.7 - - - +
588A TYR* 3.4 32.5 - - + -
600A GLN* 2.9 27.2 + - + +
601A PHE 3.2 0.4 - - - -
602A CYS* 1.4 91.5 - - - +
604A ASN* 1.3 65.1 + - - +
790A ASP* 6.0 0.2 - - - +
930A VAL* 3.5 38.6 - - + -
931A PHE* 4.2 7.9 - - + +
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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