Contacts of the helix formed by residues 1049 - 1064 (chain B) in PDB entry 5DSG
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 ASP1049 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048B LEU* 1.3 76.1 - - - +
1050B ALA* 1.3 56.2 + - - +
1051B VAL* 3.2 21.7 + - + +
1052B ARG* 2.7 48.4 + - - +
1053B ARG* 2.8 35.1 + - - +
1083B TRP* 5.1 0.5 - - - -
1113B GLY 3.9 7.1 - - - +
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Residues in contact with ALA1050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B ASP* 1.3 74.5 - - - +
1051B VAL* 1.3 60.6 + - + +
1053B ARG* 3.4 29.8 + - - +
1054B ALA* 2.9 28.3 + - - +
1115B TRP* 5.2 1.6 - - + -
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Residues in contact with VAL1051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049B ASP* 3.2 7.5 - - - +
1050B ALA* 1.3 78.7 - - + +
1052B ARG* 1.3 58.6 + - - +
1054B ALA* 3.0 6.4 + - - +
1055B ALA 2.9 21.5 + - - -
1109B THR* 3.6 23.5 - - + +
1113B GLY* 3.3 36.1 - - - +
1114B THR* 3.7 11.2 - - - +
1115B TRP* 3.7 37.9 - - + +
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Residues in contact with ARG1052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048B LEU* 4.0 17.4 - - + +
1049B ASP* 2.7 52.0 + - - +
1051B VAL* 1.3 73.4 - - - +
1053B ARG* 1.3 61.3 + - - +
1055B ALA* 3.1 9.7 + - - +
1056B LEU* 2.9 24.8 + - - +
1083B TRP* 3.5 57.2 - - - +
1109B THR 4.0 10.1 - - - +
1110B PHE* 2.9 36.5 + - + +
1111B ARG 3.4 20.2 + - - -
1112B THR 3.7 12.3 + - - -
1113B GLY* 3.8 8.3 - - - -
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Residues in contact with ARG1053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B TYR* 3.2 62.8 + - + +
1046B ASP 5.5 1.4 + - - -
1048B LEU* 2.6 41.1 + - + +
1049B ASP* 2.8 23.4 + - - +
1050B ALA* 3.5 30.5 - - - +
1052B ARG* 1.3 76.5 - - - +
1054B ALA* 1.3 56.9 + - - +
1056B LEU* 3.4 7.0 + - - +
1057B ILE* 2.9 37.1 + - + +
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Residues in contact with ALA1054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B ILE* 3.3 35.3 - - + +
1006B MET* 3.7 3.3 - - - +
1050B ALA 2.9 14.3 + - - +
1051B VAL 3.2 10.8 - - - +
1053B ARG* 1.3 75.4 - - - +
1055B ALA* 1.3 57.2 + - - +
1057B ILE* 4.2 6.1 - - + -
1058B ASN* 2.9 24.8 + - - +
1115B TRP* 3.5 26.5 - - + -
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Residues in contact with ALA1055 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006B MET* 3.8 10.9 - - + +
1051B VAL 2.9 5.6 + - - +
1052B ARG 3.1 9.2 + - - +
1054B ALA* 1.3 76.7 - - - +
1056B LEU* 1.3 59.2 + - - +
1058B ASN* 3.1 4.3 + - - +
1059B MET* 2.9 30.3 + - - +
1106B VAL* 3.9 4.9 - - + +
1109B THR* 3.7 28.3 - - + -
1110B PHE* 3.5 29.2 - - + -
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Residues in contact with LEU1056 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035B ILE* 4.5 7.0 - - + -
1041B LEU* 4.3 10.5 - - + +
1044B VAL* 4.4 11.0 - - + -
1045B TYR* 4.1 42.2 - - + +
1048B LEU* 4.7 3.8 - - + -
1052B ARG 2.9 12.7 + - - +
1053B ARG* 3.6 9.0 - - - +
1055B ALA* 1.3 73.4 - - - +
1057B ILE* 1.3 58.9 + - - +
1059B MET* 3.1 7.3 + - + +
1060B VAL* 2.9 40.4 + - + +
1068B VAL* 3.7 30.1 - - + -
1075B LEU* 4.3 13.9 - - + -
1078B LEU* 5.6 0.9 - - + -
1110B PHE* 3.4 16.9 - - + -
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Residues in contact with ILE1057 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B ILE* 3.9 23.8 - - + -
1007B LEU* 5.2 1.1 - - + -
1028B VAL* 4.4 20.9 - - + -
1031B ALA* 4.6 13.2 - - + +
1032B VAL* 3.7 22.2 - - + -
1035B ILE* 3.7 24.7 - - + -
1045B TYR* 4.1 14.6 - - + +
1053B ARG* 2.9 28.0 + - + +
1054B ALA* 3.6 9.0 - - - +
1056B LEU* 1.3 75.8 - - - +
1058B ASN* 1.3 57.9 + - - +
1060B VAL* 3.4 3.4 + - - +
1061B PHE* 2.9 30.1 + - + +
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Residues in contact with ASN1058 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006B MET* 3.4 29.5 - - + +
1007B LEU* 3.8 19.6 - - + +
1010B ASP* 2.8 26.8 + - - -
1054B ALA 2.9 14.3 + - - +
1055B ALA 3.2 9.6 - - - +
1057B ILE* 1.3 77.3 - - - +
1059B MET* 1.3 57.1 + - - +
1061B PHE* 3.1 7.6 + - - +
1062B GLN* 2.9 26.2 + - - +
1102B ARG* 2.7 34.0 + - - +
1106B VAL* 3.9 9.9 - - + +
1118B TYR* 3.9 0.6 + - - -
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Residues in contact with MET1059 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055B ALA 2.9 14.5 + - - +
1056B LEU* 3.1 9.8 + - - +
1058B ASN* 1.3 77.6 - - - +
1060B VAL* 1.3 56.8 + - - +
1062B GLN* 3.2 3.8 + - - -
1063B MET* 2.9 59.8 + - + +
1068B VAL* 3.4 20.2 - - + +
1071B PHE* 3.9 26.2 - - + -
1078B LEU* 6.2 0.4 - - - -
1090B LEU* 4.1 18.2 - - + -
1095B TRP* 4.0 17.3 - - + -
1106B VAL* 3.8 12.6 - - + -
1110B PHE* 3.4 29.2 - - - -
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Residues in contact with VAL1060 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031B ALA* 4.3 27.1 - - + +
1034B GLY* 5.9 0.4 - - - -
1035B ILE* 3.8 23.3 - - + -
1041B LEU* 4.2 13.0 - - + -
1056B LEU* 2.9 23.6 + - + +
1057B ILE 3.8 4.7 - - - +
1059B MET* 1.3 75.5 - - - +
1061B PHE* 1.3 59.7 + - - +
1064B GLY* 2.8 24.3 + - - +
1065B GLU* 3.8 22.9 - - + +
1068B VAL* 3.6 21.3 - - + -
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Residues in contact with PHE1061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B LEU* 3.9 37.2 - - + -
1024B PHE* 4.5 18.6 - + - -
1027B ASP* 3.7 39.0 - - + -
1028B VAL* 4.2 4.7 - - + -
1031B ALA* 4.5 17.9 - - + +
1057B ILE* 2.9 18.6 + - + +
1058B ASN* 3.3 9.9 - - - +
1060B VAL* 1.3 78.9 - - - +
1062B GLN* 1.3 59.4 + - - +
1064B GLY 4.9 0.3 + - - -
1102B ARG* 4.5 6.7 - - - +
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Residues in contact with GLN1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058B ASN* 2.9 11.6 + - - +
1059B MET* 3.2 4.5 + - - +
1061B PHE* 1.3 79.8 - - - +
1063B MET* 1.3 63.9 + - + +
1064B GLY 3.7 0.2 - - - -
1095B TRP* 2.9 32.1 + - - +
1099B THR* 2.9 40.8 + - - +
1102B ARG* 3.2 49.7 + - - +
1106B VAL* 5.4 0.2 - - - +
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Residues in contact with MET1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059B MET* 2.9 59.6 + - + +
1062B GLN* 1.3 85.0 - - + +
1064B GLY* 1.3 65.4 + - - +
1067B GLY* 4.1 16.0 + - - +
1068B VAL* 3.9 6.3 - - + -
1071B PHE* 3.9 12.6 - - + -
1095B TRP* 3.4 46.4 - - + +
1207B PG6 6.0 0.4 - - - -
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Residues in contact with GLY1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060B VAL* 2.8 24.2 + - - -
1061B PHE 4.9 0.4 + - - -
1062B GLN 3.7 0.6 - - - -
1063B MET* 1.3 77.2 - - - +
1065B GLU* 1.3 67.0 + - - -
1066B THR* 3.2 2.9 - - - -
1067B GLY 3.2 1.7 + - - -
1068B VAL* 3.1 24.9 + - - +
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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