Contacts of the helix formed by residues 1129 - 1148 (chain W) in PDB entry 6G0L
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 ALA1129 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059W ALA* 3.5 5.3 - - - +
1062W CYS* 3.3 22.7 - - - -
1063W VAL* 3.7 3.8 - - + -
1117W VAL* 3.6 21.9 + - + +
1119W PHE* 2.8 34.5 - - + -
1127W LEU 3.3 1.0 + - - -
1128W ASN* 1.3 71.1 - - - +
1130W GLU* 1.3 61.4 + - - +
1132W LEU* 3.2 19.4 - - - +
1133W LEU* 3.4 15.6 - - - +
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Residues in contact with GLU1130 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063W VAL* 4.2 23.1 - - + +
1117W VAL* 4.9 12.6 + - + +
1128W ASN 3.6 0.2 - - - -
1129W ALA* 1.3 77.0 - - - +
1131W SER* 1.3 61.9 + - - +
1133W LEU* 4.6 6.6 - - - +
1134W SER* 2.9 48.8 + - - +
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Residues in contact with SER1131 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018W TYR* 4.7 1.3 - - - -
1022W LEU* 3.8 14.8 - - - +
1128W ASN* 3.7 29.1 + - - +
1129W ALA 3.4 0.6 - - - -
1130W GLU* 1.3 79.2 - - - +
1132W LEU* 1.3 57.9 + - - +
1134W SER* 2.9 19.8 + - - -
1135W ARG* 3.5 29.9 + - - +
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Residues in contact with LEU1132 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018W TYR* 4.7 14.8 + - + -
1021W ILE* 5.2 12.1 - - + -
1022W LEU* 4.0 14.7 - - + +
1055W MET* 4.2 14.8 - - + +
1056W MET* 3.7 15.0 - - + -
1059W ALA* 3.2 36.6 - - + -
1119W PHE* 3.7 11.4 - - + -
1127W LEU* 5.7 0.4 - - + -
1128W ASN 3.3 17.3 + - - +
1129W ALA 3.2 10.5 - - - +
1131W SER* 1.3 75.6 - - - +
1133W LEU* 1.3 94.3 + - + +
1135W ARG* 4.8 0.5 - - - +
1136W VAL* 3.0 33.9 + - - +
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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
----------------------------------------------------------
1056W MET* 3.3 42.7 - - + +
1059W ALA* 4.2 2.5 - - + -
1060W LYS* 3.7 40.4 - - + +
1063W VAL* 3.7 18.2 - - + -
1129W ALA 3.4 13.0 + - - +
1130W GLU* 3.3 10.8 + - - +
1132W LEU* 1.3 90.9 - - + +
1134W SER* 1.3 62.6 + - - +
1136W VAL* 4.1 1.2 - - - +
1137W GLU* 3.6 27.2 + - - +
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Residues in contact with SER1134 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130W GLU* 2.9 29.5 + - - +
1131W SER* 2.9 23.0 + - - -
1132W LEU 3.3 0.2 - - - -
1133W LEU* 1.3 78.7 - - - +
1135W ARG* 1.3 64.0 + - - +
1137W GLU* 4.0 2.6 + - - +
1138W ASP* 3.2 35.2 + - - +
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Residues in contact with ARG1135 (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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1021W ILE 5.5 0.7 - - - +
1022W LEU* 3.4 43.5 + - + +
1131W SER* 3.5 35.4 + - - +
1132W LEU 4.8 0.7 - - - +
1134W SER* 1.3 80.7 + - - +
1136W VAL* 1.3 67.6 + - + +
1137W GLU 3.2 1.8 - - - -
1138W ASP* 4.4 6.3 - - + +
1139W LEU* 3.1 34.8 + - + +
1191W TYR* 3.9 38.8 + - - -
1257W ASP* 3.7 33.2 + - - +
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Residues in contact with VAL1136 (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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1021W ILE* 3.7 28.7 - - + +
1025W GLY* 4.4 5.2 - - - -
1026W ASN* 4.7 9.0 - - + +
1052W TYR* 4.5 13.0 - - - +
1056W MET* 3.5 28.3 - - + -
1132W LEU 3.0 24.0 + - - +
1133W LEU 4.1 1.6 - - - +
1134W SER 3.6 0.2 - - - -
1135W ARG* 1.3 75.4 - - - +
1137W GLU* 1.4 69.8 + - - +
1139W LEU* 3.2 25.7 - - - +
1140W LYS* 3.3 22.2 + - - +
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Residues in contact with GLU1137 (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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1056W MET* 5.4 5.9 - - + +
1133W LEU 3.6 16.8 + - - +
1134W SER* 4.3 2.9 - - - +
1135W ARG 3.2 0.4 - - - -
1136W VAL* 1.4 81.9 - - + +
1138W ASP* 1.3 61.0 + - - +
1140W LYS* 2.7 44.6 + - - +
1141W TYR* 3.0 28.6 + - - +
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Residues in contact with ASP1138 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134W SER* 3.2 23.2 + - - +
1135W ARG* 3.4 7.9 + - + +
1137W GLU* 1.3 75.4 - - - +
1139W LEU* 1.3 65.1 + - - +
1141W TYR* 3.3 9.4 + - - +
1142W LEU* 3.2 17.2 + - - +
1257W ASP* 4.7 8.1 - - - +
1260W LEU* 3.2 43.9 - - + +
1261W SER* 3.7 23.0 + - - -
1264W ARG* 5.9 2.8 - - - -
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Residues in contact with LEU1139 (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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1021W ILE 4.7 1.8 - - - +
1022W LEU 5.5 2.5 - - - +
1023W LYS 5.6 1.1 - - - +
1024W PHE 3.9 8.7 - - - +
1025W GLY* 3.0 41.1 - - - +
1026W ASN* 4.5 5.8 - - + +
1135W ARG* 3.1 30.0 + - + +
1136W VAL* 3.2 9.0 - - - +
1138W ASP* 1.3 73.4 - - - +
1140W LYS* 1.3 80.4 + - + +
1142W LEU* 3.2 5.9 + - - +
1143W LYS* 2.9 52.6 + - + +
1186W VAL* 6.3 2.9 - - + -
1260W LEU* 4.0 6.7 - - + +
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Residues in contact with LYS1140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026W ASN* 6.0 6.9 - - - +
1136W VAL* 3.3 21.9 + - - +
1137W GLU* 2.7 43.5 + - - +
1139W LEU* 1.3 85.8 - - + +
1141W TYR* 1.4 58.1 - - - +
1143W LYS* 3.6 5.4 + - - +
1144W ASN* 3.0 49.3 + - - +
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Residues in contact with TYR1141 (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 GLU 3.0 12.5 + - - +
1138W ASP* 3.6 11.2 - - - +
1139W LEU 3.2 0.2 - - - -
1140W LYS* 1.4 74.5 - - - +
1142W LEU* 1.3 69.6 + - + +
1144W ASN* 3.3 11.7 + - + +
1145W LEU* 3.1 51.0 + - + +
1260W LEU* 4.9 10.3 - - + -
1263W LEU* 4.1 19.5 + - + +
1264W ARG* 3.5 66.4 - - + +
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Residues in contact with LEU1142 (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 ASP 3.2 13.3 + - - +
1139W LEU* 3.2 8.7 + - - +
1141W TYR* 1.3 80.0 - - + +
1143W LYS* 1.3 67.3 + - - +
1144W ASN 3.4 0.2 + - - -
1145W LEU* 4.2 3.6 - - + +
1146W ILE* 3.2 32.0 + - + +
1157W PHE* 5.7 6.7 - - + -
1183W LEU* 4.0 38.6 - - + +
1184W ILE* 5.5 0.7 - - + -
1187W PHE* 3.2 48.5 - - + -
1260W LEU* 4.1 24.9 - - + -
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Residues in contact with LYS1143 (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 PHE 5.9 1.5 + - - -
1139W LEU* 2.9 37.3 + - + +
1140W LYS* 3.8 6.1 - - - +
1142W LEU* 1.3 76.1 - - - +
1144W ASN* 1.3 59.7 + - - +
1146W ILE* 3.6 1.9 - - - +
1147W ASN* 3.0 30.5 + - - +
1186W VAL* 3.9 7.7 + - - +
1187W PHE* 3.1 68.5 + - + +
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Residues in contact with ASN1144 (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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1140W LYS* 3.0 40.4 + - - +
1141W TYR* 3.5 11.9 - - + +
1142W LEU 3.2 0.4 - - - -
1143W LYS* 1.3 78.7 - - - +
1145W LEU* 1.3 61.2 + - - +
1147W ASN* 3.6 9.4 + - - +
1148W SER* 3.3 23.4 + - - -
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Residues in contact with LEU1145 (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 TYR* 3.1 45.6 + - + +
1142W LEU* 3.6 3.6 + - + +
1144W ASN* 1.3 72.2 - - - +
1146W ILE* 1.3 68.4 + - - +
1148W SER* 3.2 14.3 + - - -
1149W ASN* 2.9 46.0 + - - +
1157W PHE* 3.7 28.7 - - + -
1263W LEU* 6.3 2.7 - - + -
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Residues in contact with ILE1146 (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 LEU* 3.2 14.6 + - + +
1143W LYS 3.6 0.2 - - - +
1145W LEU* 1.3 79.3 - - + +
1147W ASN* 1.3 66.0 + - - +
1149W ASN* 3.2 6.3 - - - -
1150W TYR* 2.7 49.7 + - + +
1151W LYS* 5.8 0.2 - - - -
1154W PRO* 3.4 22.2 - - + +
1157W PHE* 4.2 10.1 - - + -
1184W ILE* 3.0 37.0 - - + -
1187W PHE* 3.1 49.6 - - + -
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Residues in contact with ASN1147 (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 LYS 3.0 19.0 + - - +
1144W ASN* 3.6 10.0 + - - +
1145W LEU 3.3 0.2 - - - -
1146W ILE* 1.3 85.8 - - + +
1148W SER* 1.4 57.8 + - - +
1151W LYS* 3.4 43.9 - - - +
1187W PHE* 5.3 4.9 - - + -
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Residues in contact with SER1148 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144W ASN 3.3 12.4 + - - -
1145W LEU* 3.2 13.4 + - - -
1146W ILE 3.2 0.8 - - - -
1147W ASN* 1.4 78.2 - - - +
1149W ASN* 1.3 59.1 + - - +
1151W LYS* 5.9 0.4 - - - -
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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
------------------------------------------------------------
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