Contacts of the helix formed by residues 985 - 990 (chain A) in PDB entry 5JHN
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 985 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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976A CYS* 3.5 12.1 - - - -
980A CYS* 3.9 19.5 - - - +
982A SER* 3.3 17.3 + - - +
983A SER 3.3 1.1 - - - +
984A ASN* 1.3 73.3 - - - +
986A LEU* 1.3 67.8 + - - +
987A CYS* 3.1 20.1 + - - -
988A GLY* 3.2 13.1 + - - +
989A GLN* 3.0 22.8 + - - +
994A CYS* 6.3 1.3 - - + -
1017A CYS* 4.4 2.0 - - - -
1029A ASN* 4.7 2.5 - - - -
1202A ZN 2.3 34.5 - - - -
1203A ZN 4.3 0.4 - - - -
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Residues in contact with LEU 986 (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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972A GLN* 4.2 9.4 - - + +
973A HIS 3.8 36.6 - - - +
974A CYS* 3.9 8.9 - - - +
975A THR 5.5 0.2 - - - +
984A ASN 3.1 6.1 + - - +
985A CYS* 1.3 73.5 - - - +
987A CYS* 1.3 63.8 + - - +
989A GLN* 3.1 19.6 + - - +
990A LEU* 3.0 51.2 + - + +
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Residues in contact with CYS 987 (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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972A GLN 4.7 4.0 - - - -
973A HIS* 4.0 7.6 - - - -
974A CYS* 3.6 11.0 - - - -
985A CYS* 3.1 3.3 - - - -
986A LEU* 1.3 79.7 - - - +
988A GLY* 1.3 64.8 + - - +
990A LEU* 3.2 22.0 + - - +
991A SER* 4.0 3.1 + - - -
1015A PHE* 3.5 22.2 - - + +
1016A GLU 4.6 3.4 - - - +
1017A CYS* 3.8 3.8 - - - -
1018A ASN* 4.9 0.4 - - - -
1021A CYS* 3.5 10.3 - - - -
1029A ASN* 3.5 17.5 - - - +
1129A GLN* 6.0 0.7 - - - -
1203A ZN 2.3 38.1 - - - -
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Residues in contact with GLY 988 (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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985A CYS* 3.2 15.0 + - - -
987A CYS* 1.3 77.8 - - - +
989A GLN* 1.3 56.2 + - - +
991A SER* 2.9 28.4 + - - -
993A ARG* 3.2 16.4 + - - -
994A CYS* 3.6 28.3 - - - -
1029A ASN* 4.1 4.4 - - - +
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Residues in contact with GLN 989 (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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983A SER 3.0 25.3 + - - +
984A ASN* 3.7 18.1 + - - +
985A CYS 3.0 18.4 + - - +
986A LEU* 3.4 18.9 - - - +
988A GLY* 1.3 75.0 - - - +
990A LEU* 1.3 61.0 + - + +
991A SER 3.0 0.7 - - - -
992A ILE* 2.9 33.3 + - - +
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Residues in contact with LEU 990 (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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972A GLN* 3.7 38.8 - - + +
986A LEU* 3.0 46.3 + - + +
987A CYS* 3.5 12.8 - - + +
988A GLY 3.1 1.0 + - - -
989A GLN* 1.3 79.0 - - + +
991A SER* 1.3 56.0 + - - +
992A ILE 3.5 0.8 + - - -
1013A LEU 4.5 1.0 - - - +
1015A PHE* 3.7 49.2 - - + -
1129A GLN* 4.9 2.2 - - - +
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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