Contacts of the helix formed by residues 1130 - 1141 (chain A) in PDB entry 1Y6A
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 THR1130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000A LEU* 3.8 35.7 - - + -
1004A ILE* 5.0 9.2 - - + +
1097A PHE* 4.6 0.8 - - + -
1128A TYR 3.9 0.4 + - - -
1129A THR* 1.3 94.4 + - - +
1131A PRO* 1.4 71.5 - - - +
1132A GLU* 3.2 18.6 + - - +
1133A MET* 3.1 32.5 + - + +
1134A TYR 3.0 8.0 + - - -
1161A LEU* 5.6 0.3 - - - +
1165A ASN* 5.8 0.7 - - - +
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Residues in contact with PRO1131 (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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1129A THR* 4.8 1.1 - - + +
1130A THR* 1.4 88.5 - - - +
1132A GLU* 1.3 69.8 + - - +
1134A TYR* 3.5 7.3 + - + +
1135A GLN* 3.0 28.1 + - - +
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Residues in contact with GLU1132 (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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1130A THR* 3.2 25.1 + - - +
1131A PRO* 1.3 88.7 - - + +
1133A MET* 1.3 57.9 + - - +
1135A GLN* 3.5 7.4 + - - +
1136A THR* 3.0 30.2 + - - -
1157A HIS* 4.7 3.8 + - + +
1161A LEU* 3.9 34.7 - - + +
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Residues in contact with MET1133 (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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1004A ILE* 4.4 14.1 - - + -
1007A SER* 4.5 1.6 - - - +
1093A LEU* 3.8 35.2 - - + -
1097A PHE* 3.6 44.6 - - + -
1129A THR* 3.5 13.5 - - - +
1130A THR* 3.1 22.8 + - - +
1132A GLU* 1.3 74.7 - - - +
1134A TYR* 1.3 63.0 + - - +
1136A THR* 3.3 7.4 + - - -
1137A MET* 3.1 27.9 + - + +
1158A LEU* 3.6 25.8 - - + -
1161A LEU* 3.8 15.7 - - + -
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Residues in contact with TYR1134 (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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1122A ARG* 5.0 0.7 - - - +
1123A MET 2.6 26.7 + - - -
1124A ARG* 3.5 8.7 - - - -
1125A ALA* 3.4 39.0 - - + -
1126A PRO* 4.3 0.2 - - + -
1129A THR* 3.3 14.5 + - + +
1130A THR 3.0 14.3 + - - +
1131A PRO* 3.5 7.6 + - + +
1133A MET* 1.3 72.8 - - - +
1135A GLN* 1.3 65.5 + - - +
1137A MET* 3.0 19.5 + - - +
1138A LEU* 3.0 54.4 + - + +
1141A TRP* 4.4 7.6 - + - -
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Residues in contact with GLN1135 (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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1131A PRO 3.0 18.0 + - - +
1132A GLU* 3.5 9.4 - - - +
1134A TYR* 1.3 77.4 - - - +
1136A THR* 1.3 58.2 + - - +
1138A LEU* 3.3 21.0 + - - +
1139A ASP* 2.9 63.1 + - - +
1157A HIS* 6.4 0.2 - - - +
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Residues in contact with THR1136 (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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1093A LEU* 3.7 17.7 - - + -
1132A GLU 3.0 15.5 + - - -
1133A MET* 3.5 17.4 - - + -
1134A TYR 3.2 0.2 - - - -
1135A GLN* 1.3 78.2 - - - +
1137A MET* 1.3 62.5 + - - +
1139A ASP* 3.3 11.5 + - + +
1140A CYS* 3.0 22.4 + - - -
1154A LEU* 3.7 28.3 - - + -
1157A HIS* 3.3 28.9 + - + -
1158A LEU* 4.8 4.5 - - + -
1161A LEU* 4.5 2.1 - - - +
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Residues in contact with MET1137 (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 GLY* 3.6 19.1 - - - +
1093A LEU* 3.7 32.3 - - + +
1094A TRP* 3.8 27.8 - - - -
1097A PHE* 4.1 9.2 - - + -
1126A PRO* 4.1 9.2 - - + -
1129A THR* 3.7 19.5 - - - +
1133A MET* 3.1 21.5 + - + +
1134A TYR* 3.0 24.3 + - + +
1136A THR* 1.3 76.8 - - - +
1138A LEU* 1.3 62.6 + - - +
1140A CYS* 3.2 7.8 + - - +
1141A TRP* 2.9 45.0 + - + -
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Residues in contact with LEU1138 (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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1122A ARG* 4.2 18.7 + - + -
1134A TYR* 3.0 56.2 + - + +
1135A GLN* 3.5 25.1 - - - +
1137A MET* 1.3 76.9 - - - +
1139A ASP* 1.3 62.5 + - - +
1141A TRP* 3.2 28.3 + - + +
1142A HIS* 3.4 10.7 + - - -
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Residues in contact with ASP1139 (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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1135A GLN* 2.9 46.7 + - - +
1136A THR* 3.5 14.7 + - - +
1137A MET 3.2 0.2 - - - -
1138A LEU* 1.3 73.8 - - - +
1140A CYS* 1.3 63.3 + - - +
1142A HIS* 3.2 22.5 + - - +
1147A GLN 4.5 1.4 - - - +
1148A ARG* 3.6 1.2 - - - -
1149A PRO* 3.3 30.7 - - + +
1157A HIS* 5.8 1.9 + - - -
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Residues in contact with CYS1140 (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 VAL* 3.4 39.0 - - - +
1087A TRP* 3.4 10.0 - - - -
1089A PHE* 4.1 10.3 - - - -
1090A GLY* 3.7 14.1 - - - -
1093A LEU* 4.6 0.4 - - - -
1136A THR* 3.0 20.6 + - - +
1137A MET 3.2 8.0 + - - +
1139A ASP* 1.3 76.3 - - - +
1141A TRP* 1.3 59.1 + - - +
1142A HIS 3.2 0.4 - - - -
1148A ARG* 3.1 24.8 - - - -
1149A PRO* 4.1 2.9 - - - -
1154A LEU* 3.9 26.5 - - - -
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Residues in contact with TRP1141 (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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1087A TRP* 3.1 44.0 + + + -
1090A GLY* 3.3 23.8 - - - -
1091A VAL* 3.2 25.9 - - + +
1094A TRP* 4.1 11.2 - + + -
1104A TYR* 5.2 3.4 - - - -
1122A ARG* 2.9 47.9 + - - +
1123A MET* 3.7 57.4 - - + -
1134A TYR* 4.4 2.9 - + - -
1137A MET* 2.9 38.5 + - + +
1138A LEU* 3.4 24.2 - - + +
1139A ASP 3.2 0.8 - - - -
1140A CYS* 1.3 76.1 - - - +
1142A HIS* 1.3 60.5 + - - -
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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