Contacts of the helix formed by residues 1089 - 1103 (chain B) in PDB entry 1Y8Z
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 GLN1089 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041B ASP* 6.0 0.7 - - - +
1062B ALA* 4.0 15.2 - - - +
1087B SER 4.1 0.6 + - - -
1088B VAL* 1.3 77.4 - - - +
1090B GLU* 1.3 67.5 + - - +
1091B ALA* 3.2 9.2 - - + +
1092B THR* 2.8 34.4 + - - +
1093B ILE 3.6 2.6 + - - -
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Residues in contact with GLU1090 (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 VAL 3.9 3.9 + - - +
1089B GLN* 1.3 73.3 - - - +
1091B ALA* 1.3 57.7 + - - +
1092B THR 3.2 0.2 + - - -
1093B ILE* 3.4 12.8 - - - +
1094B ASN* 2.9 58.5 + - - +
1125B LEU* 5.9 1.7 - - - +
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Residues in contact with ALA1091 (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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1062B ALA* 3.8 28.5 - - + +
1089B GLN* 3.0 8.5 + - + +
1090B GLU* 1.3 78.2 - - - +
1092B THR* 1.3 61.2 + - - +
1094B ASN* 4.1 5.1 - - - +
1095B ASN* 2.8 35.1 + - - +
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Residues in contact with THR1092 (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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1008B ALA 5.5 1.8 - - - +
1041B ASP* 2.7 42.1 + - + +
1061B LEU* 3.8 19.1 - - + +
1062B ALA* 3.7 7.3 - - - +
1084B PRO* 4.5 6.7 - - + -
1088B VAL* 3.8 24.9 - - + +
1089B GLN* 2.8 25.9 + - - +
1091B ALA* 1.3 80.7 - - - +
1093B ILE* 1.3 61.8 + - - +
1096B TYR* 3.2 20.4 + - - +
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Residues in contact with ILE1093 (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 PRO* 4.0 7.0 - - + -
1088B VAL* 4.3 5.4 - - + +
1089B GLN 3.6 2.6 + - - +
1090B GLU* 3.4 28.9 - - - +
1092B THR* 1.3 78.2 - - - +
1094B ASN* 1.3 78.2 + - - +
1096B TYR* 3.2 17.1 + - + -
1097B LYS* 3.0 39.0 + - - +
1125B LEU* 3.7 34.8 - - + +
1126B GLY* 3.6 31.4 - - - +
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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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1090B GLU* 2.9 49.4 + - - +
1091B ALA* 4.1 5.8 + - - +
1093B ILE* 1.3 84.7 - - - +
1095B ASN* 1.3 64.6 + - - +
1097B LYS* 3.3 15.8 + - - +
1098B LYS* 3.0 23.0 + - - +
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Residues in contact with ASN1095 (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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1061B LEU* 2.8 32.8 + - + +
1062B ALA 3.3 16.6 + - - -
1065B TYR* 3.5 34.5 - - + +
1091B ALA* 2.8 20.3 + - - +
1092B THR 4.1 1.3 - - - +
1094B ASN* 1.3 78.3 - - - +
1096B TYR* 1.3 60.0 + - - +
1098B LYS* 4.0 14.2 + - - +
1099B LEU* 2.8 30.2 + - - +
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Residues in contact with TYR1096 (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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1006B PHE* 3.9 21.1 - + - -
1008B ALA* 3.5 29.8 - - + -
1061B LEU* 3.8 13.2 - - + +
1080B ILE* 3.7 16.8 - - + +
1083B VAL* 3.5 15.4 - - + +
1084B PRO* 3.7 21.8 - - + -
1092B THR 3.2 14.6 + - - +
1093B ILE* 3.2 18.5 + - + +
1095B ASN* 1.3 78.2 - - - +
1097B LYS* 1.3 64.9 + - + +
1099B LEU* 3.0 22.9 - - + +
1100B LEU* 3.1 32.2 + - + +
1126B GLY 4.1 7.2 - - - -
1130B THR* 2.8 30.9 + - - +
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Residues in contact with LYS1097 (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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1093B ILE* 3.0 44.1 + - + +
1094B ASN* 3.7 15.7 - - - +
1096B TYR* 1.3 75.7 - - + +
1098B LYS* 1.3 66.9 + - - +
1100B LEU* 3.1 20.1 + - - +
1101B ASP* 3.1 13.6 + - - +
1126B GLY* 4.3 4.0 - - - +
1129B GLU* 3.0 45.7 + - + +
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Residues in contact with LYS1098 (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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1065B TYR* 3.2 51.3 + - + +
1094B ASN 3.0 16.9 + - - +
1095B ASN* 3.5 11.3 + - - +
1097B LYS* 1.3 76.8 - - - +
1099B LEU* 1.3 62.1 + - - +
1101B ASP* 3.2 6.0 + - - +
1102B ASN* 2.7 37.7 + - - +
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Residues in contact with LEU1099 (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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1006B PHE* 4.0 30.7 - - + -
1061B LEU* 4.5 5.8 - - + -
1065B TYR* 3.7 26.0 - - + +
1068B ALA* 4.0 17.0 - - + -
1069B LEU* 3.5 38.7 - - + +
1072B VAL* 3.9 15.9 - - + -
1095B ASN 2.8 10.8 + - - +
1096B TYR* 3.0 20.6 - - + +
1098B LYS* 1.3 76.9 - - - +
1100B LEU* 1.3 60.4 + - + +
1102B ASN* 3.2 10.9 + - - -
1103B ILE* 3.2 20.4 + - - +
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Residues in contact with LEU1100 (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 LEU* 5.5 4.5 - - + -
1080B ILE* 3.7 29.8 - - + -
1096B TYR* 3.6 40.8 - - + +
1097B LYS* 3.1 7.9 + - - +
1099B LEU* 1.3 81.2 - - + +
1101B ASP* 1.3 60.5 + - - +
1102B ASN 3.5 0.3 + - - -
1103B ILE* 3.7 19.3 - - + +
1109B VAL* 5.4 0.2 - - + -
1129B GLU* 3.6 41.1 - - + +
1130B THR* 3.7 5.8 - - - +
1133B ARG* 3.8 36.8 - - + -
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Residues in contact with ASP1101 (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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1097B LYS 3.1 11.4 + - - +
1098B LYS* 3.6 11.0 - - - +
1099B LEU 3.2 0.4 - - - -
1100B LEU* 1.3 78.0 - - - +
1102B ASN* 1.3 60.8 + - - +
1103B ILE 3.7 3.1 - - - +
3004B NCO 2.9 52.0 + - - -
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Residues in contact with ASN1102 (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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1065B TYR* 3.3 21.8 + - - +
1069B LEU* 3.9 20.9 - - + +
1073B ASN* 4.2 3.3 - - - +
1098B LYS* 2.7 31.1 + - - +
1099B LEU 3.2 1.2 + - - -
1101B ASP* 1.3 86.3 - - - +
1103B ILE* 1.3 66.2 + - - +
1104B LYS* 3.8 0.9 + - - +
3004B NCO 3.4 28.0 + - - -
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Residues in contact with ILE1103 (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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1069B LEU* 4.5 4.7 - - + -
1072B VAL* 3.8 33.0 - - + +
1073B ASN* 3.3 10.1 - - - +
1078B LEU* 3.9 14.4 - - + -
1099B LEU 3.2 16.2 - - - +
1100B LEU* 3.7 16.5 - - + +
1101B ASP 4.6 3.1 - - - +
1102B ASN* 1.3 81.7 + - - +
1104B LYS* 1.3 68.0 + - - +
1105B PRO* 3.4 5.5 - - - +
1107B ILE* 4.3 11.4 - - + -
1109B VAL* 3.5 31.9 - - + -
1133B ARG* 3.6 22.1 + - + +
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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