Contacts of the helix formed by residues 598 - 603 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B TYR* 2.8 30.2 + - + +
101B THR* 3.6 8.3 + - - -
102B ASN* 2.8 30.1 + - + +
103B VAL 4.3 2.1 + - - -
104B THR* 5.2 2.3 + - - -
597B ASN* 1.3 78.7 - - - +
599B ARG* 1.3 80.1 + - - +
601B PHE* 3.0 17.5 + - - +
8506B DMS 3.6 35.5 + - - +
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Residues in contact with ARG 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.3 7.6 - - - -
588B TYR* 3.4 16.2 - - + +
589B GLY* 3.0 29.6 + - - +
597B ASN* 2.7 23.7 + - - +
598B ASP* 1.3 76.9 - - - +
600B GLN* 1.3 90.1 + - - +
601B PHE* 2.7 48.1 + - - -
602B CYS* 3.7 0.3 - - - -
793B ILE* 4.3 6.2 - - - +
794B GLY 3.5 13.3 + - - -
795B VAL* 3.9 6.5 + - - +
796B SER 3.6 18.8 + - - -
797B GLU* 2.9 25.2 + - - -
8506B DMS 5.3 4.3 - - - +
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Residues in contact with GLN 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B MET* 3.4 21.5 - - + +
588B TYR* 3.5 20.9 + - + -
599B ARG* 1.3 114.9 + - - +
601B PHE* 1.3 56.8 + - - +
602B CYS 3.0 5.6 - - - -
603B MET* 2.8 50.9 + - + +
790B ASP* 3.1 21.6 - - - +
793B ILE* 4.9 5.0 - - - +
931B PHE* 3.5 32.6 - - + -
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Residues in contact with PHE 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.2 12.6 - - - +
102B ASN* 5.5 0.9 - - + +
540B HIS* 4.7 6.3 - + - -
542B MET* 3.4 34.3 - - + -
598B ASP 3.0 15.1 + - - +
599B ARG* 2.7 45.1 - - - -
600B GLN* 1.3 75.6 - - - +
602B CYS* 1.3 50.5 + - - +
603B MET 3.2 2.0 - - - -
604B ASN* 2.8 10.7 + - - -
790B ASP 5.4 1.3 - - - -
794B GLY 3.2 20.4 - - - -
795B VAL* 4.4 0.9 - - + -
998B SER* 3.7 22.7 - - - -
999B TRP* 4.6 5.4 - + - -
2001B 2DG 5.7 1.3 - - - -
3101B NA 2.5 29.7 - - - -
8506B DMS 3.5 45.5 - - + -
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Residues in contact with CYS 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.4 35.6 + - + -
203B TRP* 4.2 6.3 - - - +
571B VAL 4.9 0.3 - - - +
573B GLN* 2.9 65.9 + - + +
588B TYR* 3.9 19.7 - - - -
589B GLY 4.0 2.7 - - - -
599B ARG 3.7 16.6 - - - -
600B GLN 2.8 4.2 + - - -
601B PHE* 1.3 73.8 - - - +
603B MET* 1.3 62.6 + - - +
604B ASN* 3.7 5.3 + - - -
3101B NA 4.4 2.5 - - - -
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Residues in contact with MET 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B MET* 3.4 18.9 - - - +
543B GLY 4.2 2.8 + - - -
572B ASP* 3.4 25.2 - - + +
573B GLN 4.1 0.7 - - - +
574B SER* 3.8 26.7 - - - +
588B TYR* 3.3 33.4 - - + -
600B GLN* 2.8 27.3 + - + +
601B PHE 3.2 0.4 - - - -
602B CYS* 1.3 92.9 - - - +
604B ASN* 1.4 64.6 + - - +
790B ASP* 5.3 0.6 - - - +
930B VAL* 3.6 36.3 - - + -
931B PHE* 4.2 8.3 - - + +
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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