Contacts of the strand formed by residues 1135 - 1145 (chain R) in PDB entry 1YYL
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 THR1135 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1116Q PHE* 4.7 13.0 - - + -
1128R SER 4.8 0.3 - - - +
1129R LYS* 3.5 11.1 - - - +
1130R SER* 2.8 22.6 + - - +
1131R THR* 2.9 29.3 + - - +
1133R GLY 5.0 0.5 - - - -
1134R GLY* 1.3 75.9 - - - +
1136R ALA* 1.3 59.7 + - - +
1183R THR* 3.1 34.5 - - + +
1184R VAL 3.8 3.9 - - - -
1185R PRO* 4.8 1.2 - - - +
1186R SER* 3.8 1.9 + - - -
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Residues in contact with ALA1136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126R PRO* 4.5 7.4 - - + -
1129R LYS* 3.8 6.5 - - + -
1135R THR* 1.3 75.5 - - - +
1137R ALA* 1.3 60.4 + - - +
1138R LEU* 4.0 15.5 - - + -
1183R THR* 3.3 7.8 - - - +
1184R VAL* 2.8 42.9 + - + +
1186R SER* 3.8 18.8 + - - +
1189R LEU* 4.5 11.9 - - + -
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Residues in contact with ALA1137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116Q PHE* 3.8 24.5 - - + -
1118Q PHE* 3.2 35.2 - - + -
1135Q LEU* 4.4 7.4 - - + -
1126R PRO* 3.6 7.6 - - - +
1129R LYS* 3.2 25.9 - - + +
1136R ALA* 1.3 72.3 - - - +
1138R LEU* 1.3 63.3 + - - +
1182R VAL 3.6 6.1 - - - +
1183R THR* 4.5 5.2 - - - +
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Residues in contact with LEU1138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118Q PHE* 4.7 2.3 - - - -
1124R LEU* 3.6 8.5 - - - -
1126R PRO* 3.2 28.9 - - + -
1136R ALA* 4.0 4.9 - - + -
1137R ALA* 1.3 81.6 - - - +
1139R GLY* 1.3 59.9 + - - +
1154R TRP* 4.3 5.2 - - + -
1181R VAL* 3.3 9.2 - - - +
1182R VAL* 2.9 38.3 + - + +
1184R VAL* 3.9 21.5 - - + -
1189R LEU* 4.6 5.2 - - + -
1194R TYR* 3.4 48.7 - - + -
1211R VAL* 4.0 19.5 - - + +
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Residues in contact with GLY1139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123R PRO 3.5 1.2 - - - -
1124R LEU* 2.6 50.0 + - - -
1138R LEU* 1.3 80.5 - - - +
1140R CYS* 1.3 58.9 - - - -
1154R TRP* 3.6 9.9 - - - -
1180R SER 3.2 12.1 - - - -
1211R VAL* 3.6 12.9 - - - +
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Residues in contact with CYS1140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121R VAL* 3.8 15.5 - - + -
1122R PHE 3.2 6.5 - - - +
1124R LEU* 3.6 4.2 - - - +
1139R GLY* 1.3 77.6 - - - -
1141R LEU* 1.3 61.2 + - - +
1142R VAL* 3.5 8.1 + - + +
1152R VAL* 5.6 0.4 - - + -
1154R TRP* 4.4 2.7 - - + -
1179R SER* 3.3 5.9 - - - -
1180R SER* 3.0 31.4 + - - +
1196R CYS* 2.0 53.2 - - + -
1209R LYS* 4.1 9.2 - - - -
1211R VAL* 4.1 9.2 - - - -
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Residues in contact with LEU1141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124Q GLN* 3.4 33.2 - - - +
1131Q SER* 3.5 18.8 - - - +
1133Q VAL* 4.6 12.8 - - + -
1178Q THR* 5.1 7.6 - - + +
1120R SER 3.2 8.7 - - - +
1121R VAL* 3.5 1.2 - - - -
1122R PHE* 2.8 44.4 + - + +
1124R LEU* 4.1 15.8 - - + +
1140R CYS* 1.3 70.7 - - - +
1142R VAL* 1.3 58.3 + - - +
1143R LYS* 3.4 9.6 + - + -
1177R SER* 4.2 13.9 - - - +
1178R LEU 3.9 6.5 - - - +
1179R SER* 3.3 20.6 - - - +
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Residues in contact with VAL1142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119R PRO* 3.6 23.3 - - + -
1120R SER 3.9 2.7 - - - -
1121R VAL* 4.8 3.4 - - + +
1140R CYS* 4.1 13.0 - - + +
1141R LEU* 1.3 73.4 - - - +
1143R LYS* 1.3 59.0 + - - +
1145R TYR* 4.0 7.6 - - + -
1150R VAL* 4.0 13.0 - - + -
1152R VAL* 4.3 6.5 - - + -
1177R SER* 3.2 2.6 - - - -
1178R LEU* 2.7 60.1 + - + +
1180R SER 5.3 0.9 - - - +
1198R VAL* 3.8 37.5 - - + -
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Residues in contact with LYS1143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124Q GLN* 3.6 23.2 - - - +
1129Q THR* 4.5 15.4 + - - +
1131Q SER* 3.7 16.3 + - - +
1180Q THR* 4.4 15.0 + - - +
1119R PRO* 3.5 2.4 - - - +
1120R SER* 2.9 36.2 + - - -
1122R PHE* 3.9 21.5 - - + -
1141R LEU* 4.3 9.4 - - + -
1142R VAL* 1.3 74.1 - - - +
1144R ASP* 1.3 96.4 + - - +
1145R TYR 3.7 1.1 - - - -
1171R GLN* 3.8 17.0 + - - -
1176R TYR 3.9 0.2 - - - -
1177R SER* 3.1 20.2 - - - +
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Residues in contact with ASP1144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129Q THR* 5.6 0.7 + - - -
1117R LYS* 3.5 19.5 - - - +
1118R GLY 3.1 16.6 - - - +
1120R SER* 4.3 7.3 + - - +
1122R PHE* 5.4 0.7 - - - -
1143R LYS* 1.3 108.1 + - - +
1145R TYR* 1.3 56.0 + - - +
1171R GLN* 3.2 18.8 + - - +
1173R SER* 4.6 2.9 + - - -
1175R LEU* 3.9 30.0 - - + +
1176R TYR 3.0 12.1 + - - -
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Residues in contact with TYR1145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117R LYS* 3.3 9.9 - - - +
1119R PRO* 3.3 43.3 - - + -
1142R VAL* 4.0 16.2 - - + -
1144R ASP* 1.3 71.9 - - - +
1146R PHE* 1.3 61.3 + - - +
1147R PRO 3.3 25.1 - - - -
1148R GLU* 2.8 29.3 + - - -
1149R PRO 4.5 0.2 - - - -
1150R VAL* 3.4 33.8 - - + +
1168R ALA* 3.2 12.5 - - - +
1175R LEU* 4.0 4.1 - - - +
1176R TYR* 2.9 64.1 + - + +
1177R SER* 4.0 3.8 - - - -
1178R LEU* 4.4 3.1 - - + -
1200R HIS* 3.8 8.7 - + + -
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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