Contacts of the helix formed by residues 1130 - 1149 (chain W) in PDB entry 5O9G
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 ALA1130 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060W ALA* 3.6 33.7 - - + +
1063W CYS* 5.0 0.2 - - + -
1064W VAL* 3.7 11.9 - - + -
1118W VAL* 3.2 16.1 + - + -
1120W PHE* 3.7 19.7 - - + -
1128W LEU 3.9 0.2 + - - -
1129W ASN* 1.3 74.0 - - - +
1131W GLU* 1.3 64.1 + - - +
1132W SER 3.4 0.7 - - - -
1133W LEU* 3.5 5.3 + - - +
1134W LEU* 3.4 26.3 + - - +
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Residues in contact with GLU1131 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064W VAL* 4.5 13.9 - - + +
1071W ARG* 5.7 2.4 + - - -
1117W ALA* 5.7 3.0 - - - +
1118W VAL* 3.4 32.6 - - + +
1129W ASN* 2.9 11.3 + - - +
1130W ALA* 1.3 77.0 - - - +
1132W SER* 1.3 54.0 + - - +
1134W LEU* 3.5 5.1 + - - +
1135W SER* 2.6 41.0 + - - -
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Residues in contact with SER1132 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I A 5.6 1.0 + - - -
1019W TYR* 5.3 0.9 - - - -
1023W LEU* 4.7 14.7 - - - +
1129W ASN* 2.4 41.3 + - - +
1131W GLU* 1.3 69.2 - - - +
1133W LEU* 1.3 51.2 + - - +
1135W SER* 3.4 7.6 + - - -
1136W ARG* 2.6 49.9 + - - +
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Residues in contact with LEU1133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019W TYR* 3.6 31.0 - - + +
1022W ILE* 3.7 25.1 - - + -
1023W LEU* 3.8 18.8 - - + -
1056W MET* 4.2 21.8 - - + -
1057W MET* 4.4 17.9 - - + -
1060W ALA* 4.5 15.3 - - + -
1120W PHE* 4.8 3.6 - - + -
1129W ASN 3.4 20.0 - - - +
1130W ALA* 3.5 5.4 + - - +
1131W GLU 3.2 0.8 - - - -
1132W SER* 1.3 75.5 - - - +
1134W LEU* 1.3 61.7 + - + +
1136W ARG* 3.2 3.3 + - - +
1137W VAL* 2.9 35.9 + - - +
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Residues in contact with LEU1134 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057W MET* 3.7 24.0 - - + +
1060W ALA* 5.3 3.8 - - + -
1061W LYS* 3.7 37.9 - - + +
1064W VAL* 4.5 22.2 - - + -
1130W ALA 3.4 15.7 + - - +
1131W GLU* 4.1 4.5 - - - +
1133W LEU* 1.3 75.2 - - - +
1135W SER* 1.3 59.1 + - - +
1137W VAL* 3.2 7.3 + - - +
1138W GLU* 2.9 36.1 + - + +
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Residues in contact with SER1135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131W GLU 2.6 24.0 + - - -
1132W SER* 3.4 10.2 + - - -
1134W LEU* 1.3 77.1 - - - +
1136W ARG* 1.3 59.0 + - - +
1138W GLU* 3.9 7.4 - - - +
1139W ASP* 2.9 43.8 + - - +
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Residues in contact with ARG1136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022W ILE* 3.8 16.4 - - + +
1023W LEU* 2.4 49.8 + - + +
1026W GLY* 4.8 1.3 - - - -
1132W SER* 2.6 37.2 + - - +
1133W LEU* 3.5 6.5 - - - +
1134W LEU 3.1 0.2 - - - -
1135W SER* 1.3 76.2 + - - +
1137W VAL* 1.3 60.4 + - + +
1139W ASP* 4.6 6.6 + - - -
1140W LEU* 2.9 64.1 + - + +
1192W TYR* 3.3 41.6 - - - -
1258W ASP* 5.0 9.1 + - - -
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Residues in contact with VAL1137 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022W ILE* 5.3 3.6 - - + -
1026W GLY* 4.7 7.6 - - - -
1027W ASN* 4.6 19.5 - - + +
1053W TYR* 3.9 21.8 - - - +
1057W MET* 4.1 16.2 - - + -
1133W LEU 2.9 20.5 + - - +
1134W LEU* 3.2 6.0 + - + +
1136W ARG* 1.3 76.8 - - + +
1138W GLU* 1.3 60.6 + - - +
1140W LEU* 4.9 2.7 - - - -
1141W LYS* 2.8 48.4 + - + +
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Residues in contact with GLU1138 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134W LEU* 2.9 23.8 + - + +
1135W SER* 3.9 7.0 - - - +
1137W VAL* 1.3 81.4 - - + +
1139W ASP* 1.3 58.0 + - - +
1141W LYS* 3.5 29.3 + - - +
1142W TYR 2.9 23.2 + - - -
1265W ARG* 2.9 43.4 + - - +
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Residues in contact with ASP1139 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135W SER* 2.9 32.5 + - - +
1136W ARG* 4.1 8.8 + - - +
1138W GLU* 1.3 77.3 - - - +
1140W LEU* 1.3 60.2 + - + +
1142W TYR* 3.3 7.6 + - - +
1143W LEU* 2.9 28.5 + - - +
1258W ASP* 5.1 10.0 - - - +
1261W LEU* 3.7 37.7 - - + +
1262W SER* 4.9 2.2 + - - -
1265W ARG* 3.2 24.2 + - - +
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Residues in contact with LEU1140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024W LYS 4.2 6.3 - - - +
1025W PHE* 3.5 39.0 - - - +
1026W GLY* 3.6 6.3 - - - +
1027W ASN 6.0 0.2 - - - +
1136W ARG* 2.9 43.6 + - + +
1137W VAL* 4.5 2.5 - - - +
1139W ASP* 1.3 77.4 - - + +
1141W LYS* 1.3 58.2 + - - +
1143W LEU* 3.3 12.4 + - + +
1144W LYS* 2.9 40.9 + - + +
1187W VAL* 4.4 27.6 - - + +
1191W GLY* 5.5 0.7 - - - -
1192W TYR* 5.0 7.6 - - + +
1261W LEU* 5.6 3.8 - - + -
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Residues in contact with LYS1141 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137W VAL* 2.8 34.6 + - + +
1138W GLU* 3.5 35.3 + - - +
1140W LEU* 1.3 75.8 - - - +
1142W TYR* 1.3 59.2 + - - +
1144W LYS* 3.3 5.2 + - - +
1145W ASN* 2.9 54.6 + - - +
1265W ARG* 5.8 0.7 - - - +
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Residues in contact with TYR1142 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138W GLU 2.9 19.8 + - - +
1139W ASP 3.7 4.5 - - - +
1141W LYS* 1.3 77.3 - - - +
1143W LEU* 1.3 60.3 + - - +
1145W ASN* 4.7 5.8 - - + +
1146W LEU* 2.8 67.9 + - + +
1261W LEU* 5.0 8.3 - - + -
1264W LEU* 3.1 40.8 + - + +
1265W ARG* 3.4 35.0 - - + +
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Residues in contact with LEU1143 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139W ASP 2.9 16.6 + - - +
1140W LEU* 3.6 13.2 - - + +
1141W LYS 3.2 0.2 - - - -
1142W TYR* 1.3 78.3 - - - +
1144W LYS* 1.3 61.8 + - + +
1146W LEU* 4.3 6.7 - - + -
1147W ILE* 2.9 53.8 + - + +
1184W LEU* 4.2 26.0 - - + +
1187W VAL* 3.9 22.7 - - + +
1188W PHE* 3.8 36.3 - - + +
1261W LEU* 4.6 20.2 - - + -
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Residues in contact with LYS1144 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025W PHE 6.0 2.0 - - - -
1031W ILE* 6.0 6.6 - - - +
1140W LEU* 2.9 28.1 + - + +
1141W LYS* 3.9 6.1 - - - +
1143W LEU* 1.3 79.7 - - + +
1145W ASN* 1.3 62.0 + - - +
1148W ASN* 2.9 47.5 + - - +
1187W VAL 5.6 1.6 - - - -
1188W PHE* 2.7 53.5 + - + +
1189W LYS 5.2 1.2 + - - -
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Residues in contact with ASN1145 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141W LYS* 2.9 43.9 + - - +
1142W TYR* 4.4 4.4 - - + +
1144W LYS* 1.3 79.8 - - - +
1146W LEU* 1.3 55.1 + - - +
1148W ASN* 4.8 1.6 - - - -
1149W SER* 2.3 49.4 + - - +
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Residues in contact with LEU1146 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142W TYR* 2.8 57.7 + - + +
1143W LEU* 3.9 9.4 - - + +
1145W ASN* 1.3 78.2 - - - +
1147W ILE* 1.3 65.2 + - + +
1149W SER* 4.6 0.7 - - - -
1150W ASN* 2.9 38.4 + - - +
1158W PHE* 3.9 27.5 - - + -
1160W LEU* 5.7 0.2 - - + -
1184W LEU* 5.8 0.4 - - + -
1264W LEU* 4.3 18.2 - - + -
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Residues in contact with ILE1147 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143W LEU* 2.9 40.3 + - + +
1146W LEU* 1.3 75.9 - - + +
1148W ASN* 1.3 61.1 + - - +
1150W ASN 3.2 0.7 + - - -
1151W TYR* 2.8 48.7 + - + +
1155W PRO* 5.0 9.4 - - + -
1158W PHE* 3.6 46.9 - - + -
1184W LEU* 5.6 5.2 - - + +
1185W ILE* 6.3 2.9 - - + -
1188W PHE* 3.6 40.4 - - + -
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Residues in contact with ASN1148 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144W LYS* 2.9 39.0 + - - +
1145W ASN* 4.7 1.8 - - - +
1147W ILE* 1.3 77.2 - - - +
1149W SER* 1.3 58.5 + - - +
1150W ASN 3.2 1.7 + - - -
1151W TYR 4.3 3.5 - - - +
1152W LYS* 4.0 37.1 + - + +
1188W PHE* 3.2 25.5 - - - -
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Residues in contact with SER1149 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145W ASN* 2.3 35.8 + - - +
1146W LEU* 4.2 3.8 - - - -
1147W ILE 3.2 0.4 - - - -
1148W ASN* 1.3 76.8 - - - +
1150W ASN* 1.3 71.1 + - - +
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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
------------------------------------------------------------
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