Contacts of the helix formed by residues 1083 - 1102 (chain B) in PDB entry 5DHG
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 LYS1083 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078B LEU* 3.0 36.0 + - - +
1081B GLU* 3.5 27.7 - - - +
1082B GLY* 1.3 73.8 - - - +
1084B VAL* 1.3 64.2 + - - +
1085B LYS 3.4 2.9 + - - -
1086B GLU* 3.1 41.6 - - + +
1087B ALA* 3.6 12.6 + - - +
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Residues in contact with VAL1084 (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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1022B ASN 5.2 0.2 - - - -
1023B ALA* 3.7 42.4 - - + +
1026B VAL* 4.3 19.9 - - + +
1079B ALA* 4.2 17.5 - - + +
1082B GLY* 3.0 19.2 + - - +
1083B LYS* 1.3 72.3 - - - +
1085B LYS* 1.3 65.5 + - - +
1087B ALA* 3.1 19.5 + - + +
1088B GLN* 3.3 9.0 + - + +
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Residues in contact with LYS1085 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083B LYS 3.4 0.6 - - - -
1084B VAL* 1.3 80.0 - - - +
1086B GLU* 1.3 58.8 + - - +
1088B GLN* 2.9 36.1 + - - +
1089B ALA* 3.2 4.5 + - - +
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Residues in contact with GLU1086 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078B LEU* 3.7 24.7 - - + +
1083B LYS* 3.1 54.3 - - + +
1085B LYS* 1.3 75.3 - - - +
1087B ALA* 1.3 59.3 + - - +
1088B GLN 3.3 0.2 - - - -
1089B ALA* 3.3 14.6 + - + +
1090B ALA* 3.0 20.3 + - - +
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Residues in contact with ALA1087 (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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1017B ILE* 4.8 1.6 - - - +
1026B VAL* 4.6 12.6 - - + -
1030B LEU* 4.8 3.3 - - + +
1075B ALA* 3.6 27.6 - - + +
1078B LEU* 4.0 10.0 - - + +
1079B ALA* 4.2 9.9 - - + +
1083B LYS 3.6 13.1 + - - +
1084B VAL* 3.1 14.2 + - - +
1086B GLU* 1.3 74.8 - - - +
1088B GLN* 1.3 65.3 + - - +
1090B ALA* 3.1 15.5 + - - +
1091B ALA* 3.2 11.3 + - - +
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Residues in contact with GLN1088 (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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1017B ILE* 3.3 36.1 + - + +
1018B GLU* 3.7 17.4 + - + +
1020B ALA 3.2 26.1 + - - -
1026B VAL* 4.7 11.5 - - + +
1084B VAL* 3.3 9.5 + - + +
1085B LYS* 2.9 19.7 + - - +
1087B ALA* 1.3 79.4 - - - +
1089B ALA* 1.3 58.9 + - - +
1091B ALA* 3.1 18.0 + - - +
1092B GLU* 3.5 4.2 + - - +
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Residues in contact with ALA1089 (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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1085B LYS 3.2 4.5 + - - +
1086B GLU* 3.3 21.1 - - + +
1087B ALA 3.2 0.2 - - - -
1088B GLN* 1.3 79.4 - - - +
1090B ALA* 1.3 61.8 + - - +
1092B GLU* 3.1 19.0 + - - +
1093B GLN* 3.3 9.2 + - - +
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Residues in contact with ALA1090 (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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1071B GLN* 5.1 3.4 - - + +
1075B ALA* 3.7 26.5 - - + +
1078B LEU* 4.8 5.8 - - + -
1086B GLU 3.0 12.4 + - - +
1087B ALA* 3.1 12.1 + - - +
1089B ALA* 1.3 76.0 - - - +
1091B ALA* 1.3 56.5 + - - +
1093B GLN* 2.9 14.2 + - + +
1094B LEU* 2.8 31.3 + - + +
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Residues in contact with ALA1091 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014B LEU* 3.7 20.3 - - + +
1017B ILE* 3.6 31.4 - - + -
1018B GLU* 5.0 7.2 - - + +
1030B LEU* 5.8 1.1 - - + -
1075B ALA* 5.5 0.4 - - - +
1087B ALA 3.2 5.8 + - - +
1088B GLN 3.1 13.9 + - - +
1090B ALA* 1.3 75.1 - - - +
1092B GLU* 1.3 61.8 + - - +
1094B LEU* 3.1 17.3 + - - +
1095B LYS* 3.1 20.3 + - - +
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Residues in contact with GLU1092 (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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1088B GLN 3.5 4.4 + - - +
1089B ALA* 3.1 14.3 + - - +
1091B ALA* 1.3 73.8 - - - +
1093B GLN* 1.3 67.3 + - - +
1095B LYS* 3.2 18.1 + - - +
1096B THR* 3.4 13.0 + - - -
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Residues in contact with GLN1093 (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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1071B GLN* 4.3 11.2 - - + +
1089B ALA 3.3 3.7 + - - +
1090B ALA* 2.9 20.2 + - + +
1092B GLU* 1.3 77.4 - - - +
1094B LEU* 1.3 62.1 + - - +
1096B THR* 3.1 23.2 + - - -
1097B THR* 3.2 9.5 + - - -
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Residues in contact with LEU1094 (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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1014B LEU* 3.9 15.0 - - + -
1030B LEU* 4.3 13.7 - - + -
1033B MET* 3.7 30.5 - - + -
1068B LEU* 3.7 20.2 - - + +
1071B GLN* 3.5 39.0 - - + +
1072B ILE* 3.8 19.7 - - + +
1075B ALA* 5.2 1.3 - - + -
1090B ALA* 2.8 15.3 + - + +
1091B ALA* 3.1 15.7 + - - +
1093B GLN* 1.3 76.6 - - - +
1095B LYS* 1.3 63.1 - - - +
1097B THR* 3.0 5.0 + - - -
1098B ARG* 2.9 22.6 + - - +
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Residues in contact with LYS1095 (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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1014B LEU* 4.0 18.9 - - + +
1091B ALA 3.1 11.3 + - - +
1092B GLU* 3.2 13.0 + - - +
1094B LEU* 1.3 74.9 - - - +
1096B THR* 1.3 63.0 + - - +
1098B ARG* 3.3 6.1 + - - +
1099B ASN* 3.1 23.0 + - - +
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Residues in contact with THR1096 (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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1092B GLU 3.4 8.9 + - - -
1093B GLN* 3.1 13.4 + - - -
1094B LEU 3.1 0.2 - - - -
1095B LYS* 1.3 79.1 - - - +
1097B THR* 1.3 67.0 + - - +
1099B ASN* 3.0 16.4 + - - +
1100B ALA* 3.1 18.0 + - + +
1101B TYR* 6.4 0.4 - - + -
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Residues in contact with THR1097 (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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1064B GLY 4.6 1.6 - - - +
1067B ILE* 4.2 14.3 - - + +
1068B LEU* 4.0 31.0 - - + +
1071B GLN* 2.7 32.5 + - - +
1093B GLN 3.2 4.2 + - - -
1094B LEU 3.0 8.3 + - - -
1096B THR* 1.3 79.2 - - - +
1098B ARG* 1.3 63.3 + - - +
1101B TYR* 3.2 49.6 + - + +
1102B ILE* 4.2 3.1 - - + +
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Residues in contact with ARG1098 (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 TRP* 4.0 18.5 - - + -
1010B LEU* 4.8 19.1 - - + -
1011B ASN* 5.7 2.9 - - - +
1014B LEU* 5.5 2.5 - - + -
1033B MET* 6.4 0.2 - - + -
1068B LEU* 4.7 7.8 - - + +
1094B LEU 2.9 12.0 + - - +
1095B LYS* 3.6 12.3 - - - +
1096B THR 3.1 0.2 - - - -
1097B THR* 1.3 78.6 - - - +
1099B ASN* 1.3 61.0 + - - +
1102B ILE* 3.7 12.8 + - - +
1103B GLN* 3.3 21.3 + - - +
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Residues in contact with ASN1099 (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 TRP* 5.9 0.2 - - - -
1095B LYS 3.1 11.0 + - - +
1096B THR* 3.0 9.8 + - - +
1098B ARG* 1.3 77.8 - - - +
1100B ALA* 1.3 60.9 + - - +
1103B GLN* 3.1 25.2 - - + +
1104B LYS 4.9 0.2 + - - -
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Residues in contact with ALA1100 (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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1096B THR* 3.1 19.7 + - + +
1097B THR* 4.8 0.2 - - - -
1099B ASN* 1.3 81.7 - - - +
1101B TYR* 1.3 83.6 + - + +
1103B GLN 4.7 1.3 + - - -
1104B LYS* 5.1 6.6 + - - +
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Residues in contact with TYR1101 (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 ASP 5.4 0.9 - - - +
1064B GLY* 4.1 24.9 - - - -
1067B ILE* 4.1 28.8 - - + +
1096B THR* 6.4 0.4 - - + -
1097B THR* 3.2 33.3 + - + +
1100B ALA* 1.3 92.0 - - + +
1102B ILE* 1.3 64.8 + - + +
1104B LYS* 5.0 3.8 + - - +
1105B TYR* 3.7 22.0 - - - -
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Residues in contact with ILE1102 (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 LEU* 6.3 2.2 - - + -
1007B TRP* 3.5 27.6 - - + -
1061B PHE* 4.5 13.7 - - + +
1064B GLY* 3.6 35.0 - - - +
1065B PHE* 4.0 32.8 - - + +
1068B LEU* 4.4 20.6 - - + -
1097B THR* 4.2 13.2 - - + +
1098B ARG* 3.7 7.9 + - - +
1101B TYR* 1.3 80.9 - - + +
1103B GLN* 1.3 65.2 + - - +
1104B LYS 3.3 2.5 - - - -
1105B TYR* 3.3 17.1 + - + +
1106B LEU* 3.6 8.0 + - + +
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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