Contacts of the strand formed by residues 1173 - 1181 (chain Q) 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 TYR1173 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1103Q ARG* 2.9 25.9 + - - -
1105Q GLU* 2.7 40.2 + - - +
1138Q ASN* 3.0 8.4 - - - -
1139Q PHE* 2.8 52.9 + - + +
1140Q TYR* 3.9 13.2 - + - -
1142Q ARG* 3.4 46.2 - - + -
1163Q VAL* 4.5 3.4 - - + -
1164Q THR* 3.8 21.3 - - - -
1165Q GLU 4.2 0.4 - - - -
1166Q GLN* 3.5 36.1 + - + +
1172Q THR* 1.3 77.4 - - - +
1174Q SER* 1.3 62.0 + - - +
1164R HIS* 5.8 1.1 - - - -
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Residues in contact with SER1174 (chain Q).
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* 5.2 0.2 - - - -
1136Q LEU 3.2 8.4 + - - -
1137Q ASN* 3.7 2.8 + - - -
1138Q ASN* 3.2 21.1 + - - -
1139Q PHE* 3.4 2.7 - - - -
1163Q VAL* 3.4 4.0 - - - +
1164Q THR* 2.9 43.3 + - - -
1173Q TYR* 1.3 71.4 + - - +
1175Q LEU* 1.3 60.2 + - - +
1164R HIS* 3.3 28.6 + - - -
1166R PHE* 3.2 18.7 - - - -
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Residues in contact with LEU1175 (chain Q).
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* 3.7 1.9 - - - -
1136Q LEU* 2.9 42.1 + - + +
1139Q PHE* 3.3 15.4 - - + -
1142Q ARG 5.3 2.5 - - - +
1144Q ALA* 4.4 26.7 - - + +
1146Q VAL* 3.8 24.7 - - + -
1161Q GLU* 3.9 24.0 - - + +
1162Q SER 3.3 12.6 - - - +
1163Q VAL* 4.4 16.4 - - + -
1174Q SER* 1.3 74.8 - - - +
1176Q SER* 1.3 88.6 + - - +
1177Q SER 3.9 2.0 - - - +
1166R PHE* 3.5 6.3 - - - -
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Residues in contact with SER1176 (chain Q).
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* 4.7 11.2 - - - -
1134Q CYS 3.2 11.4 - - - -
1135Q LEU* 5.0 2.2 - - - -
1160Q GLN 3.7 1.2 - - - +
1161Q GLU* 3.1 6.2 - - - +
1162Q SER* 3.1 32.7 + - - -
1175Q LEU* 1.3 79.1 - - - +
1177Q SER* 1.3 61.0 + - - +
1178Q THR* 4.0 6.0 + - - -
1166R PHE* 3.7 33.6 - - - +
1179R SER* 5.5 5.2 - - - -
1181R VAL* 6.3 0.4 - - - -
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Residues in contact with SER1177 (chain Q).
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* 3.6 0.2 - - - -
1134Q CYS* 2.9 34.7 + - - -
1146Q VAL* 3.5 29.0 + - - +
1148Q TRP* 2.8 34.0 + - - -
1159Q SER* 4.3 5.7 + - - -
1160Q GLN 3.6 3.4 - - - -
1161Q GLU* 3.7 19.0 + - - +
1175Q LEU* 3.9 3.6 - - - +
1176Q SER* 1.3 71.7 - - - +
1178Q THR* 1.3 59.7 + - - +
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Residues in contact with THR1178 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131Q SER* 4.5 9.0 - - - -
1132Q VAL 3.2 14.4 - - - +
1133Q VAL* 3.8 23.0 - - + +
1159Q SER* 3.1 6.6 - - - -
1160Q GLN* 2.8 41.4 + - - +
1176Q SER* 4.6 7.8 + - - -
1177Q SER* 1.3 73.7 + - - +
1179Q LEU* 1.3 61.4 + - - +
1180Q THR* 3.7 17.2 + - - +
1141R LEU* 5.1 7.0 - - + -
1179R SER* 4.8 5.7 + - - -
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Residues in contact with LEU1179 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130Q ALA 3.8 0.2 - - - +
1131Q SER* 3.4 2.3 - - - -
1132Q VAL* 2.6 59.7 + - + +
1148Q TRP* 3.8 40.2 - - + -
1150Q VAL* 4.1 21.8 - - + -
1155Q GLN* 4.3 13.5 - - + -
1158Q ASN* 3.2 44.9 - - - +
1159Q SER* 4.3 2.9 - - - +
1177Q SER 4.0 1.0 + - - -
1178Q THR* 1.3 71.6 - - - +
1180Q THR* 1.3 59.0 + - - +
1181Q LEU* 4.1 12.1 - - + -
1192Q TYR* 4.3 6.5 - - + -
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Residues in contact with THR1180 (chain Q).
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* 5.4 5.8 - - + -
1130Q ALA 3.6 5.2 - - - +
1131Q SER* 4.2 9.5 + - - +
1158Q ASN* 3.2 20.4 + - - +
1160Q GLN* 5.8 2.4 + - - +
1178Q THR* 3.7 13.8 + - - +
1179Q LEU* 1.3 73.6 - - - +
1181Q LEU* 1.3 83.0 + - - +
1143R LYS* 4.4 19.2 + - - +
1171R GLN* 5.1 6.0 + - - +
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Residues in contact with LEU1181 (chain Q).
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* 3.7 8.1 - - - +
1130Q ALA 2.8 31.9 + - - +
1132Q VAL* 5.6 1.8 - - + -
1150Q VAL* 5.0 6.1 - - + -
1155Q GLN* 5.0 2.2 - - - +
1158Q ASN* 3.2 27.4 - - + +
1179Q LEU* 4.1 16.6 - - + +
1180Q THR* 1.3 93.7 - - - +
1182Q SER* 1.3 67.7 + - - +
1185Q ASP* 4.1 15.5 - - + +
1186Q TYR* 4.2 20.0 - - + +
1189Q HIS* 5.6 1.1 - - + -
1192Q TYR* 4.0 26.9 - - + +
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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