Contacts of the helix formed by residues 1010 - 1025 (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 GLY1010 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008W SER 3.6 3.8 + - - -
1009W ILE* 1.3 72.6 - - - +
1011W GLU* 1.3 65.5 + - - -
1012W SER 3.3 1.6 - - - -
1013W GLU* 2.6 28.2 + - - +
1014W VAL* 3.1 19.8 + - - +
1122W LYS 5.6 0.4 - - - -
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Residues in contact with GLU1011 (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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1010W GLY* 1.3 70.8 - - - -
1012W SER* 1.3 56.0 + - - +
1014W VAL* 2.9 12.3 + - - +
1015W ARG* 2.6 55.9 + - - +
1122W LYS 4.9 2.0 + - - +
1123W GLY* 3.4 37.4 - - - +
1125W LYS* 5.6 1.0 - - - -
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Residues in contact with SER1012 (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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-69I A 4.1 13.6 + - - -
1010W GLY 3.3 1.0 - - - -
1011W GLU* 1.3 83.7 - - - +
1013W GLU* 1.3 55.5 + - - +
1015W ARG* 3.0 13.8 + - - +
1016W ALA* 2.7 33.2 + - - +
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Residues in contact with GLU1013 (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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1008W SER 5.2 0.3 - - - +
1009W ILE* 3.2 20.0 - - + -
1010W GLY* 2.6 35.9 + - - +
1012W SER* 1.3 76.4 + - - +
1014W VAL* 1.3 56.1 + - - +
1016W ALA* 2.9 10.8 + - + +
1017W LEU* 2.7 37.2 + - - +
1040W LEU* 6.4 0.2 - - + -
1041W PRO* 3.2 31.9 - - + +
1043W LYS* 3.0 28.7 + - - +
1048W TYR* 5.2 2.0 - - + -
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Residues in contact with VAL1014 (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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1009W ILE* 3.9 24.7 - - + +
1010W GLY 3.1 20.9 - - - +
1011W GLU* 2.9 12.9 + - - +
1013W GLU* 1.3 76.9 - - - +
1015W ARG* 1.4 59.4 + - - +
1017W LEU* 4.1 4.6 - - - +
1018W TYR* 3.4 24.1 + - - +
1055W MET* 3.8 2.7 - - + +
1121W PHE* 3.3 33.7 - - + +
1122W LYS 4.6 9.2 - - - +
1123W GLY* 4.7 0.2 - - - -
1124W VAL* 3.0 32.9 - - + +
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Residues in contact with ARG1015 (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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-70I C 3.0 40.2 + - - -
-69I A 4.3 19.1 + - - +
1011W GLU* 2.6 50.2 + - - +
1012W SER* 3.1 17.0 - - - +
1014W VAL* 1.4 74.2 - - - +
1016W ALA* 1.3 58.5 + - - +
1018W TYR* 4.0 3.8 + - - +
1019W LYS* 3.8 23.0 + - - +
1123W GLY 3.7 13.8 + - - -
1124W VAL* 4.4 21.1 - - + +
1125W LYS* 3.7 39.0 - - - +
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Residues in contact with ALA1016 (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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1012W SER 2.7 16.0 + - - +
1013W GLU* 2.9 17.4 + - + +
1015W ARG* 1.3 74.3 - - - +
1017W LEU* 1.3 60.2 + - - +
1019W LYS* 3.8 3.2 + - - +
1020W ALA* 3.5 20.4 + - - +
1039W THR* 3.8 30.7 - - + +
1040W LEU* 5.2 4.3 - - + -
1041W PRO* 5.8 0.9 - - + -
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Residues in contact with LEU1017 (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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1009W ILE* 4.8 12.3 - - + -
1013W GLU 2.7 18.1 + - - +
1014W VAL* 4.1 3.8 - - - +
1016W ALA* 1.3 71.5 - - - +
1018W TYR* 1.3 65.3 + - - +
1020W ALA* 3.3 5.9 + - - +
1021W ILE* 3.2 30.0 + - + +
1027W LEU* 3.4 39.9 - - + -
1040W LEU* 5.7 11.9 - - + -
1048W TYR* 4.8 8.7 - - + +
1051W THR* 3.9 24.7 - - - +
1052W TYR* 4.3 15.5 - - + +
1055W MET* 3.9 28.3 - - + -
1121W PHE* 5.1 1.1 - - + -
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Residues in contact with TYR1018 (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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1014W VAL 3.4 14.6 + - - +
1015W ARG* 4.4 4.9 - - - +
1016W ALA 3.4 0.8 - - - -
1017W LEU* 1.3 78.4 - - - +
1019W LYS* 1.3 77.6 - - + +
1021W ILE* 3.4 8.1 + - + +
1022W LEU* 3.4 46.0 + - + +
1055W MET* 4.5 19.1 - - + -
1124W VAL* 5.1 11.4 - - + -
1127W LEU* 4.3 23.1 - - + -
1128W ASN* 3.0 61.0 + - - +
1131W SER* 4.7 1.4 - - - -
1132W LEU* 4.7 15.5 - - + -
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Residues in contact with LYS1019 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72J A 3.8 9.9 + - - -
73J T 2.5 35.1 + - - -
1015W ARG 3.8 15.8 + - - +
1016W ALA* 3.8 4.4 + - - +
1017W LEU 3.4 0.2 - - - -
1018W TYR* 1.3 95.3 - - + +
1020W ALA* 1.3 64.1 + - - +
1022W LEU* 3.3 24.6 + - - +
1023W LYS* 3.2 22.2 + - - +
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Residues in contact with ALA1020 (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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1016W ALA 3.5 11.8 + - - +
1017W LEU* 3.3 12.0 + - - +
1019W LYS* 1.3 77.7 - - - +
1021W ILE* 1.3 51.6 + - - +
1023W LYS* 3.2 8.0 + - - +
1024W PHE* 2.7 52.3 + - + +
1027W LEU* 4.0 15.0 - - + -
1034W LEU* 4.8 5.2 - - + -
1039W THR* 4.6 15.7 - - + -
1040W LEU* 5.6 1.3 - - + -
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Residues in contact with ILE1021 (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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1017W LEU* 3.2 16.4 + - + +
1018W TYR* 3.6 9.6 - - + +
1019W LYS 3.2 0.2 - - - -
1020W ALA* 1.3 72.9 - - - +
1022W LEU* 1.3 63.2 + - + +
1025W GLY* 2.6 41.3 + - - +
1027W LEU* 3.5 15.3 - - + -
1052W TYR* 3.3 31.4 - - + +
1055W MET* 4.1 26.9 - - + -
1056W MET* 5.8 1.3 - - + +
1132W LEU* 5.0 14.4 - - + +
1135W ARG* 5.5 0.9 - - - +
1136W VAL* 3.7 28.9 - - + +
1139W LEU* 4.7 1.6 - - - +
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Residues in contact with LEU1022 (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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73J T 4.9 2.5 - - - +
1018W TYR* 3.4 40.8 + - + +
1019W LYS* 3.3 33.4 + - + +
1021W ILE* 1.3 78.3 - - + +
1023W LYS* 1.3 58.5 + - - +
1025W GLY 5.0 0.2 + - - -
1131W SER* 3.8 35.0 - - - +
1132W LEU* 4.0 11.7 - - + +
1135W ARG* 3.4 42.3 + - + +
1139W LEU* 5.5 1.9 - - - +
1191W TYR* 4.1 12.2 - - + +
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Residues in contact with LYS1023 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1019W LYS 3.2 11.9 + - - +
1020W ALA* 3.4 11.7 - - - +
1021W ILE 3.1 0.2 - - - -
1022W LEU* 1.3 78.7 - - - +
1024W PHE* 1.3 99.7 + - + +
1025W GLY 3.8 0.2 - - - -
1139W LEU* 5.6 1.2 - - - +
1186W VAL* 5.6 0.2 - - - +
1189W TYR 3.6 14.6 + - - -
1190W GLY* 3.6 3.7 - - - -
1191W TYR* 3.2 45.4 + - - +
1192W GLY 5.2 1.3 - - - -
1193W SER* 4.0 22.8 - - - +
1196W GLN* 5.0 1.4 + - - -
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Residues in contact with PHE1024 (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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1020W ALA* 2.7 27.2 + - + +
1023W LYS* 1.3 124.1 - - + +
1025W GLY* 1.4 64.3 + - - +
1026W ASN 3.7 5.7 + - - +
1027W LEU* 4.9 1.3 - - + -
1030W ILE* 3.6 31.6 - - + -
1034W LEU* 3.6 33.0 - - + -
1039W THR* 6.1 0.2 - - + -
1139W LEU* 3.9 13.4 - - - +
1143W LYS* 5.9 1.9 + - - -
1189W TYR 4.1 8.7 - - - -
1190W GLY* 4.5 6.3 - - - -
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Residues in contact with GLY1025 (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* 2.6 37.8 + - - +
1024W PHE* 1.4 73.1 - - - +
1026W ASN* 1.3 69.7 + - - -
1027W LEU* 2.9 10.4 + - - +
1052W TYR* 3.8 3.8 + - - -
1136W VAL* 4.4 4.9 - - - -
1139W LEU* 3.0 25.9 - - - +
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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