Contacts of the strand formed by residues 1176 - 1185 (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 TYR1176 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1087R THR* 4.8 8.5 - - - +
1110R THR* 4.2 16.5 + - + +
1144R ASP 3.0 22.7 + - - -
1145R TYR* 2.9 47.4 + + + +
1146R PHE* 4.0 24.0 - + - -
1147R PRO* 4.4 0.7 - - + -
1148R GLU* 3.2 46.3 - - + +
1168R ALA* 4.0 9.9 - - + -
1169R VAL 3.5 3.6 - - - -
1170R LEU* 3.7 42.6 - - + +
1171R GLN* 3.6 0.2 + - - -
1175R LEU* 1.3 73.1 - - - +
1177R SER* 1.3 61.7 + - - +
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Residues in contact with SER1177 (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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1141R LEU* 4.2 10.0 - - - +
1142R VAL 3.2 7.6 + - - -
1143R LYS* 3.1 22.8 - - - +
1145R TYR* 4.0 1.3 - - - -
1168R ALA* 4.3 1.1 - - - -
1169R VAL* 3.0 34.2 + - - +
1171R GLN* 3.3 28.3 + - - -
1176R TYR* 1.3 79.8 - - - +
1178R LEU* 1.3 61.6 + - - +
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Residues in contact with LEU1178 (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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1141R LEU* 3.7 2.5 - - - +
1142R VAL* 2.7 62.0 + - + +
1145R TYR* 3.9 8.5 - - + +
1148R GLU* 5.0 1.3 - - - +
1150R VAL* 3.1 33.0 - - + +
1152R VAL* 4.1 12.3 - - + -
1165R THR* 4.2 10.3 - - + -
1166R PHE* 3.6 24.0 - - - +
1167R PRO* 4.4 2.2 - - + +
1168R ALA* 3.7 13.7 - - + +
1169R VAL* 6.1 0.2 - - - -
1177R SER* 1.3 76.9 + - - +
1179R SER* 1.3 73.3 + - - +
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Residues in contact with SER1179 (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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1133Q VAL* 4.5 13.9 - - - +
1176Q SER* 5.5 4.9 - - - -
1178Q THR* 4.8 5.0 + - - -
1124R LEU* 4.6 12.8 - - - -
1140R CYS 3.3 11.0 - - - -
1141R LEU* 3.3 25.1 - - - +
1165R THR* 3.7 0.5 - - - -
1166R PHE* 3.0 41.3 + - - +
1178R LEU* 1.3 80.3 - - - +
1180R SER* 1.3 61.3 + - - +
1181R VAL* 5.0 3.4 - - - -
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Residues in contact with SER1180 (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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1139R GLY* 3.2 4.7 - - - -
1140R CYS* 3.0 34.3 + - - -
1142R VAL* 5.6 0.2 - - - -
1152R VAL* 3.4 27.8 - - - +
1154R TRP* 3.0 27.4 + - - -
1163R VAL* 5.3 0.2 - - - +
1164R HIS 3.4 5.8 + - - -
1165R THR* 2.9 25.8 + - - +
1178R LEU* 4.4 1.0 - - - +
1179R SER* 1.3 76.4 - - - +
1181R VAL* 1.3 63.6 + - - +
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Residues in contact with VAL1181 (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* 4.8 3.8 - - + -
1133Q VAL* 5.6 3.6 - - + -
1135Q LEU* 3.7 39.9 - - + -
1137Q ASN* 4.7 1.3 - - - +
1124R LEU* 4.2 17.3 - - + -
1138R LEU 3.3 12.6 - - - +
1139R GLY* 4.3 0.2 - - - -
1154R TRP* 4.6 1.6 - - - -
1162R GLY 4.5 0.2 - - - -
1163R VAL* 3.3 2.8 - - - +
1164R HIS* 2.6 64.7 + - + +
1166R PHE* 3.8 16.4 - - + -
1179R SER* 5.0 4.0 - - - -
1180R SER* 1.3 82.4 + - - +
1182R VAL* 1.3 60.3 + - - +
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Residues in contact with VAL1182 (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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1135Q LEU* 6.5 0.2 - - - -
1136R ALA 4.0 0.2 - - - +
1137R ALA* 3.6 2.5 - - - +
1138R LEU* 2.9 40.2 + - + +
1154R TRP* 3.8 35.7 - - + -
1159R LEU* 3.8 23.1 - - + -
1161R SER 4.0 2.5 - - - +
1162R GLY 3.5 9.6 - - - +
1163R VAL* 3.3 30.3 - - + -
1181R VAL* 1.3 77.5 - - - +
1183R THR* 1.3 75.1 + - - +
1184R VAL* 4.3 5.4 - - + -
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Residues in contact with THR1183 (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* 5.3 3.2 - - + -
1135Q LEU* 6.0 0.9 - - - +
1137Q ASN* 3.3 28.4 + - - +
1135R THR* 3.1 36.3 - - + +
1136R ALA 3.3 8.5 - - - +
1137R ALA* 4.5 5.9 - - - +
1159R LEU* 5.2 0.3 - - - +
1161R SER 4.4 6.8 - - - +
1162R GLY* 3.5 14.9 + - - -
1182R VAL* 1.3 78.8 - - - +
1184R VAL* 1.3 71.8 + - - +
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Residues in contact with VAL1184 (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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1135R THR* 3.8 2.7 - - - -
1136R ALA* 2.8 35.8 + - + +
1138R LEU* 3.9 24.2 - - + -
1159R LEU* 4.4 7.4 - - + -
1182R VAL* 4.3 15.7 - - + -
1183R THR* 1.3 84.0 - - - +
1185R PRO* 1.3 73.4 - - + +
1189R LEU* 4.7 2.2 - - + -
1194R TYR* 3.3 53.6 - - + +
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Residues in contact with PRO1185 (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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1134R GLY 3.4 8.1 - - - +
1135R THR* 4.8 1.8 - - - +
1184R VAL* 1.3 91.8 - - + +
1186R SER* 1.3 59.7 + - - +
1187R SER* 3.1 12.3 - - - +
1188R SER* 2.8 52.1 + - - +
1189R LEU* 4.0 0.9 + - - +
1194R TYR* 4.4 0.9 - - - +
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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