Contacts of the helix formed by residues 1086 - 1094 (chain C) in PDB entry 5YS0
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 SER1086 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1084C ASP* 3.2 24.8 + - - -
1085C THR* 1.3 75.2 - - - +
1087C TYR* 1.3 65.0 + - - +
1089C LYS* 3.1 5.9 + - - +
1090C LYS* 3.0 28.1 + - - +
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Residues in contact with TYR1087 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079C LEU* 3.3 49.1 - - + +
1080C LEU* 4.2 4.0 - - + -
1084C ASP 4.4 3.3 + - - +
1085C THR 3.5 0.2 - - - -
1086C SER* 1.3 82.1 + - - +
1088C ILE* 1.3 53.4 + - - +
1090C LYS* 3.7 16.3 - - + +
1091C ILE* 2.8 65.3 + - + +
1216C ASP 2.8 22.5 + - - -
1217C LEU* 3.8 19.3 - - + -
1219C LYS 4.9 0.2 + - - -
1220C ILE* 3.1 39.8 - - + +
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Residues in contact with ILE1088 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079C LEU 4.0 2.8 + - - +
1080C LEU* 3.2 52.3 - - + +
1081C TYR* 5.1 6.5 - - + -
1085C THR* 3.6 19.0 + - - +
1087C TYR* 1.3 77.8 - - - +
1089C LYS* 1.3 58.2 + - - +
1091C ILE* 4.2 10.3 - - + -
1092C ILE* 3.2 36.1 - - + +
1103C ILE* 3.6 23.0 - - + +
1111C ARG* 3.7 21.5 - - - +
1134C GLU* 5.1 4.7 - - - +
1213C LEU* 6.0 2.9 - - + -
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Residues in contact with LYS1089 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085C THR 3.4 15.3 + - - +
1086C SER* 3.1 7.7 + - - +
1088C ILE* 1.3 77.5 - - - +
1090C LYS* 1.3 60.4 + - - +
1091C ILE 3.3 0.4 - - - -
1092C ILE* 3.9 3.6 - - - +
1093C GLU* 3.0 37.6 + - - +
1100C VAL* 2.9 50.3 + - + +
1101C CYS 3.0 17.4 + - - -
1102C ASP* 3.9 14.1 + - - +
1103C ILE* 4.0 15.3 - - + -
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Residues in contact with LYS1090 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086C SER* 3.0 15.8 + - - +
1087C TYR* 3.8 18.8 - - + +
1089C LYS* 1.3 77.9 - - - +
1091C ILE* 1.3 71.4 + - + +
1093C GLU* 3.2 22.7 - - - +
1094C ASN* 3.0 28.0 + - - +
1216C ASP* 3.2 26.7 - - - +
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Residues in contact with ILE1091 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080C LEU* 4.4 11.9 - - + -
1087C TYR* 2.8 53.0 + - + +
1088C ILE* 4.5 8.1 - - + -
1090C LYS* 1.3 78.7 - - + +
1092C ILE* 1.3 66.6 + - + +
1094C ASN* 3.1 21.4 + - - +
1213C LEU* 4.2 36.6 - - + +
1216C ASP* 3.3 48.2 - - + +
1217C LEU* 5.4 1.3 - - + -
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Residues in contact with ILE1092 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088C ILE* 3.2 34.1 + - + +
1089C LYS* 3.6 3.3 + - - +
1091C ILE* 1.3 79.4 - - + +
1093C GLU* 1.3 60.9 + - - +
1094C ASN 2.8 18.2 - - - +
1096C ASN 3.6 10.7 + - - -
1097C ASN* 3.5 25.2 + - - +
1100C VAL* 3.9 22.9 - - + -
1103C ILE* 5.6 4.7 - - + -
1113C ILE* 4.6 11.2 - - + -
1115C TYR* 4.6 20.9 - - + +
1132C VAL* 6.3 0.2 - - + -
1149C GLN* 6.2 2.0 - - - +
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Residues in contact with GLU1093 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089C LYS* 3.0 27.2 + - + +
1090C LYS* 3.2 30.9 - - + +
1092C ILE* 1.3 76.3 - - + +
1094C ASN* 1.3 58.7 + - - +
1096C ASN* 4.2 9.2 - - - -
1097C ASN 3.9 20.6 + - - +
1098C PHE* 6.0 0.2 - - - -
1100C VAL* 5.1 9.6 - - + +
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Residues in contact with ASN1094 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090C LYS* 3.0 19.3 + - - +
1091C ILE 3.2 15.5 - - - +
1092C ILE 2.8 16.7 + - - +
1093C GLU* 1.3 80.7 - - - +
1096C ASN* 3.2 30.9 + - - -
1212C GLN* 4.2 21.1 - - - +
1216C ASP* 2.7 40.3 + - + +
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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