Contacts of the helix formed by residues 1085 - 1094 (chain B) 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 THR1085 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079B LEU 5.8 0.7 - - - -
1082B GLY 3.7 16.4 - - - +
1083B ASP 3.7 9.8 + - - +
1084B ASP* 1.3 70.4 + - - +
1086B SER* 1.3 62.6 + - - +
1087B TYR 3.2 2.2 - - - +
1088B ILE* 3.5 9.6 - - - +
1089B LYS* 3.3 23.0 + - - +
1102B ASP* 5.3 1.9 + - - -
1103B ILE* 3.0 41.0 + - - +
1104B PRO 3.7 16.4 - - - +
1105B LYS* 4.3 5.6 - - + -
1111B ARG* 3.7 6.5 - - - +
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Residues in contact with SER1086 (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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1084B ASP* 3.1 16.1 + - - -
1085B THR* 1.3 78.6 - - - +
1087B TYR* 1.3 80.0 + - - +
1089B LYS* 3.5 8.9 + - - +
1090B LYS* 3.3 33.9 + - - +
1193C MET* 4.5 10.0 - - - +
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Residues in contact with TYR1087 (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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1078B SER 5.1 1.3 - - - -
1079B LEU* 3.2 42.8 - - + +
1080B LEU* 6.1 0.4 - - + -
1084B ASP* 3.0 49.9 + - + -
1085B THR 3.2 0.2 - - - -
1086B SER* 1.3 82.7 - - - +
1088B ILE* 1.3 64.2 + - - +
1089B LYS 3.2 0.9 - - - -
1090B LYS* 3.3 9.4 + - - +
1091B ILE* 3.1 26.8 + - - +
1220B ILE* 4.6 16.4 - - + +
1193C MET* 3.2 46.1 - - + +
1194C LEU* 3.1 34.7 + - + -
1195C LYS 3.9 2.1 + - - -
1196C GLY 4.4 1.0 + - - -
1197C THR* 5.3 1.0 + - - -
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Residues in contact with ILE1088 (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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1079B LEU 3.9 3.2 + - - -
1080B LEU* 3.5 43.7 - - + +
1081B TYR* 5.5 4.5 - - + -
1085B THR* 3.5 19.0 - - - +
1087B TYR* 1.3 76.2 - - - +
1089B LYS* 1.3 63.6 + - - +
1091B ILE* 3.6 20.4 - - + -
1092B ILE* 2.9 44.4 + - + +
1103B ILE* 3.6 23.6 - - + -
1111B ARG* 4.0 15.5 - - - +
1113B ILE* 5.8 1.3 - - + -
1134B GLU* 5.5 4.0 - - - +
1213B LEU* 5.1 3.1 - - + -
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Residues in contact with LYS1089 (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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1093A GLU 4.7 6.3 - - - -
1096A ASN* 6.0 1.3 - - - +
1097A ASN 2.6 31.5 + - - +
1098A PHE* 3.3 22.2 - - + +
1085B THR* 3.3 16.7 + - - +
1086B SER* 3.6 9.9 - - - +
1087B TYR 3.2 1.4 - - - -
1088B ILE* 1.3 82.7 - - - +
1090B LYS* 1.3 58.2 + - + +
1092B ILE* 3.4 2.6 + - - +
1093B GLU* 2.8 58.8 + - + +
1100B VAL* 4.7 7.1 + - + +
1101B CYS 4.4 4.9 - - - +
1102B ASP* 5.2 4.3 - - - +
1103B ILE* 3.7 32.8 - - + +
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Residues in contact with LYS1090 (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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1090A LYS* 5.2 1.0 + - - -
1093A GLU 5.3 1.9 + - - -
1094A ASN* 2.7 41.5 + - - +
1086B SER* 3.3 22.4 - - - +
1087B TYR* 3.3 7.9 + - - +
1088B ILE 3.3 0.2 - - - -
1089B LYS* 1.3 74.8 - - + +
1091B ILE* 1.3 66.8 + - + +
1093B GLU* 3.5 16.1 - - - +
1094B ASN* 2.9 25.8 + - - +
1216B ASP* 5.5 0.2 - - - -
1220B ILE* 6.0 4.0 - - + -
1193C MET* 5.5 10.5 - - + -
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Residues in contact with ILE1091 (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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1080B LEU* 4.6 10.1 - - + -
1087B TYR 3.1 17.3 + - - +
1088B ILE* 3.2 23.5 + - + +
1090B LYS* 1.3 75.4 - - - +
1092B ILE* 1.3 66.4 + - + +
1094B ASN* 3.0 13.2 + - - +
1095B GLN* 3.4 29.6 - - - +
1213B LEU* 3.6 34.1 - - + +
1216B ASP* 3.6 36.5 - - + +
1217B LEU* 4.6 1.6 - - + +
1220B ILE* 4.0 18.2 - - + -
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Residues in contact with ILE1092 (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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1088B ILE* 2.9 37.8 + - + +
1089B LYS 3.9 2.7 - - - +
1091B ILE* 1.3 76.0 - - + +
1093B GLU* 1.3 63.9 + - - +
1095B GLN* 3.0 11.8 + - - +
1097B ASN* 2.8 35.7 + - - +
1100B VAL* 3.8 18.4 - - + -
1103B ILE* 4.1 13.5 - - + -
1113B ILE* 3.7 32.8 - - + -
1115B TYR* 3.7 29.8 - - + -
1149B GLN* 6.2 1.6 - - - +
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Residues in contact with GLU1093 (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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1089A LYS* 3.4 19.2 + - - -
1090A LYS* 4.3 7.1 + - - +
1093A GLU* 3.2 49.0 - - + +
1089B LYS* 2.8 57.1 + - - +
1090B LYS* 3.3 20.8 + - - +
1092B ILE* 1.3 74.1 - - - +
1094B ASN* 1.3 58.3 + - - +
1095B GLN 3.3 1.1 + - - -
1096B ASN 4.5 0.9 + - - -
1097B ASN 3.9 10.9 + - - +
1100B VAL* 3.9 23.0 - - + +
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Residues in contact with ASN1094 (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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1090A LYS* 2.4 32.7 + - - +
1090B LYS 2.9 17.0 + - - +
1091B ILE 3.0 4.5 + - - +
1093B GLU* 1.3 77.2 - - - +
1095B GLN* 1.3 59.6 + - + +
1096B ASN* 3.5 4.7 + - - +
1212B GLN* 2.9 23.3 + - - +
1216B ASP* 2.7 38.0 + - - +
1219B LYS* 4.7 5.9 - - - +
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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