Contacts of the helix formed by residues 1085 - 1094 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1082A GLY 4.1 10.3 - - - +
1083A ASP 3.6 11.6 + - - +
1084A ASP* 1.3 71.9 + - - +
1086A SER* 1.3 59.0 + - - +
1087A TYR 3.3 1.8 - - - -
1088A ILE* 3.2 11.0 - - - +
1089A LYS* 3.0 29.5 + - - +
1102A ASP* 5.4 2.1 + - - -
1103A ILE* 3.1 40.4 + - - +
1104A PRO 3.7 18.2 - - - +
1105A LYS* 4.0 7.2 - - + +
1111A ARG* 4.2 3.6 - - - +
1118B LYS* 5.8 1.0 + - - -
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Residues in contact with SER1086 (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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1084A ASP* 2.9 25.6 + - - -
1085A THR* 1.3 79.7 + - - +
1087A TYR* 1.3 73.5 + - - +
1089A LYS* 3.9 11.1 - - - +
1090A LYS* 3.2 33.8 + - - +
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Residues in contact with TYR1087 (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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1078A SER 5.1 1.6 - - - -
1079A LEU* 3.2 49.1 - - + +
1080A LEU* 6.1 0.4 - - + -
1084A ASP* 3.3 37.3 + - + -
1085A THR 3.3 0.2 - - - -
1086A SER* 1.3 82.0 - - - +
1088A ILE* 1.3 60.1 + - - +
1090A LYS* 3.1 7.8 + - + +
1091A ILE* 2.8 37.6 + - + +
1220A ILE* 5.0 20.2 - - + -
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Residues in contact with ILE1088 (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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1079A LEU 4.1 2.5 + - - +
1080A LEU* 3.6 41.1 - - + +
1081A TYR* 5.5 4.3 - - + -
1084A ASP 5.3 0.4 + - - -
1085A THR* 3.2 19.0 - - - +
1087A TYR* 1.3 78.4 - - - +
1089A LYS* 1.3 61.2 + - - +
1091A ILE* 4.0 21.3 - - + -
1092A ILE* 2.7 52.5 + - + +
1103A ILE* 3.8 21.8 - - + -
1111A ARG* 4.0 16.2 - - - +
1113A ILE* 5.3 0.7 - - + -
1134A GLU* 5.4 3.1 - - - +
1213A LEU* 4.6 5.4 - - + -
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Residues in contact with LYS1089 (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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1085A THR* 3.0 20.5 + - - +
1086A SER* 3.9 10.1 - - - +
1087A TYR 3.2 0.2 - - - -
1088A ILE* 1.3 78.1 - - - +
1090A LYS* 1.3 64.1 + - - +
1092A ILE* 3.4 2.3 + - - +
1093A GLU* 2.8 63.9 + - - +
1100A VAL* 5.3 3.0 - - + +
1101A CYS 4.9 4.3 - - - +
1102A ASP* 5.1 5.6 - - - +
1103A ILE* 3.7 30.5 - - + +
1093B GLU 3.4 16.4 + - - -
1096B ASN* 5.9 2.9 - - - +
1097B ASN 3.2 26.3 + - - +
1098B PHE* 4.5 14.1 - - + -
1118B LYS* 6.0 0.9 - - - +
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Residues in contact with LYS1090 (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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1086A SER* 3.2 19.8 + - - +
1087A TYR* 3.1 11.5 + - + +
1089A LYS* 1.3 83.3 - - - +
1091A ILE* 1.3 69.1 + - + +
1093A GLU* 3.4 15.7 + - + +
1094A ASN* 3.1 22.9 + - - +
1090B LYS 5.2 1.2 + - - -
1093B GLU* 4.3 9.5 + - - +
1094B ASN* 2.4 44.5 + - - +
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Residues in contact with ILE1091 (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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1080A LEU* 4.7 13.7 - - + -
1087A TYR* 2.8 24.6 + - + +
1088A ILE* 3.5 17.0 - - + +
1090A LYS* 1.3 81.1 - - + +
1092A ILE* 1.3 64.2 + - + +
1094A ASN* 3.0 13.7 + - - +
1095A GLN* 3.2 27.9 - - - +
1213A LEU* 3.6 37.7 - - + +
1216A ASP* 3.5 38.4 - - + +
1217A LEU* 5.6 3.4 - - + +
1220A ILE* 5.4 6.7 - - + -
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Residues in contact with ILE1092 (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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1088A ILE* 2.7 41.6 + - + +
1089A LYS* 4.0 3.6 - - - +
1091A ILE* 1.3 74.6 - - + +
1093A GLU* 1.3 63.2 + - - +
1094A ASN 3.1 0.7 + - - -
1095A GLN* 3.2 14.0 + - - +
1097A ASN* 2.9 32.8 + - - +
1100A VAL* 4.3 16.6 - - + -
1103A ILE* 4.0 7.6 - - + -
1113A ILE* 3.7 37.7 - - + -
1115A TYR* 3.8 31.0 - - + -
1149A GLN* 6.2 2.2 - - - +
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Residues in contact with GLU1093 (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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1089A LYS* 2.8 62.6 + - - +
1090A LYS* 3.7 17.7 - - - +
1091A ILE 3.3 0.2 - - - -
1092A ILE* 1.3 76.2 - - - +
1094A ASN* 1.3 57.6 + - - +
1095A GLN 3.3 1.3 + - - -
1096A ASN* 4.3 3.5 + - - -
1097A ASN 4.0 16.5 + - - +
1100A VAL* 4.2 23.0 - - + +
1089B LYS* 4.7 5.4 - - - -
1090B LYS* 5.3 2.8 + - - -
1093B GLU* 3.2 51.2 - - + +
1097B ASN 4.6 1.4 - - - +
1098B PHE* 5.2 3.1 - - - -
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Residues in contact with ASN1094 (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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1090A LYS 3.1 11.1 + - - +
1091A ILE 3.0 12.5 + - - +
1093A GLU* 1.3 75.1 - - - +
1095A GLN* 1.3 58.3 + - + +
1096A ASN 3.4 6.2 + - - -
1212A GLN* 3.1 23.9 + - - +
1216A ASP* 2.9 36.0 + - - +
1090B LYS* 2.7 32.5 + - - +
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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