Contacts of the helix formed by residues 1086 - 1101 (chain A) in PDB entry 5V6Y
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 ASN1086 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027A CYS* 3.5 29.7 - - - +
1032A TYR* 4.3 3.6 + - - -
1077A ALA* 4.8 2.2 - - - +
1082A CYS* 4.6 0.6 - - - +
1083A PHE* 3.2 39.5 + - + +
1084A TRP* 4.7 1.6 - - - +
1085A PRO* 1.3 74.6 - - - +
1087A ALA* 1.3 63.2 + - - +
1088A GLU* 2.8 37.1 + - - +
1089A VAL* 3.3 20.0 + - - +
1090A ASP* 3.2 27.5 + - - -
2068A THR* 5.6 1.3 - - - -
2120A THR* 6.0 0.9 - - - -
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Residues in contact with ALA1087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086A ASN* 1.3 76.3 - - - +
1088A GLU* 1.3 61.3 + - + +
1090A ASP* 3.2 11.5 + - - +
1091A ARG* 2.9 27.7 + - - +
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Residues in contact with GLU1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027A CYS 3.2 24.4 + - - +
1028A GLN* 4.3 8.9 - - - -
1029A GLU 4.7 9.4 - - - +
1032A TYR* 3.7 20.0 - - + -
1033A GLY* 4.2 14.9 - - - -
1036A LEU* 4.5 2.0 - - + +
1037A ARG* 5.5 0.2 + - - -
1086A ASN* 2.8 11.0 + - - +
1087A ALA* 1.3 81.0 - - + +
1089A VAL* 1.3 57.9 + - - +
1091A ARG* 3.3 49.9 + - - +
1092A PHE* 2.9 26.6 + - - +
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Residues in contact with VAL1089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032A TYR* 3.6 19.3 - - + +
1036A LEU* 4.6 4.0 - - + -
1073A THR* 4.9 2.0 - - - -
1084A TRP* 4.0 19.5 - - + +
1085A PRO* 3.6 25.6 - - + -
1086A ASN* 3.3 36.6 - - - +
1088A GLU* 1.3 72.1 - - - +
1090A ASP* 1.3 62.9 + - - +
1092A PHE* 4.0 6.5 - - - -
1093A PHE* 3.0 46.5 + - + -
2049A TYR* 3.8 12.6 - - - +
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Residues in contact with ASP1090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086A ASN 3.2 16.1 + - - +
1087A ALA* 3.2 11.9 + - - +
1089A VAL* 1.3 74.8 - - - +
1091A ARG* 1.3 59.1 + - - +
1093A PHE* 3.5 2.1 + - - +
1094A LEU* 3.0 27.7 + - - +
2049A TYR* 2.7 43.2 + - + -
2052A ILE* 5.4 5.1 - - + +
2067A ARG 4.3 3.4 - - - +
2068A THR* 2.5 35.1 + - - -
2069A TRP 3.8 11.7 + - - +
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Residues in contact with ARG1091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030A ALA* 6.3 1.0 - - - +
1033A GLY* 5.6 1.2 - - - -
1037A ARG* 4.7 19.9 - - - +
1087A ALA 2.9 15.6 + - - +
1088A GLU* 3.3 38.7 + - - +
1090A ASP* 1.3 76.1 - - - +
1092A PHE* 1.3 62.7 + - - +
1094A LEU* 3.4 15.7 + - + +
1095A ALA* 3.3 20.6 + - - +
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Residues in contact with PHE1092 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A GLY* 5.1 0.9 - - - -
1036A LEU* 3.7 50.3 - - + -
1037A ARG* 3.8 27.8 - - + +
1041A LEU* 4.1 11.2 - - + -
1069A LEU* 3.7 31.0 - - + -
1073A THR* 3.8 17.5 - - + -
1088A GLU 2.9 18.5 + - - +
1089A VAL* 3.6 4.3 - - - +
1090A ASP 3.2 0.2 - - - -
1091A ARG* 1.3 79.3 - - - +
1093A PHE* 1.3 73.8 + + - +
1095A ALA* 3.2 11.3 + - + +
1096A VAL* 3.0 50.2 + - + +
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Residues in contact with PHE1093 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A TYR* 3.4 36.8 - + - -
1069A LEU* 4.2 16.2 - - + -
1070A ALA* 3.6 23.3 - - + -
1073A THR* 3.9 17.0 - - + -
1084A TRP* 5.0 2.0 - + - -
1089A VAL* 3.0 35.9 + - + +
1092A PHE* 1.3 84.5 - + - +
1094A LEU* 1.3 60.6 + - - +
1095A ALA 3.3 0.2 - - - -
1096A VAL* 3.9 9.4 - - + -
1097A HIS* 2.8 38.4 + + - +
2045A GLN* 3.4 23.8 - - - -
2049A TYR* 3.6 32.7 - + + +
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Residues in contact with LEU1094 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A ASP 3.0 17.7 + - - +
1091A ARG* 3.5 15.7 - - + +
1092A PHE 3.2 0.4 - - - -
1093A PHE* 1.3 77.6 - - - +
1095A ALA* 1.3 57.3 + - - +
1097A HIS* 3.9 2.1 - - - +
1098A GLY* 2.8 26.0 + - - -
1102A ARG* 5.4 1.5 + - - +
2049A TYR* 5.0 4.0 - - + +
2052A ILE* 4.6 14.1 - - + +
2053A MET* 4.0 36.3 - - + +
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Residues in contact with ALA1095 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037A ARG* 6.1 5.4 - - - -
1091A ARG 3.3 8.5 + - - +
1092A PHE* 3.2 11.0 + - + +
1094A LEU* 1.3 76.9 - - - +
1096A VAL* 1.3 66.2 + - + +
1098A GLY* 3.5 2.2 + - - -
1099A ARG* 3.4 26.6 + - - +
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Residues in contact with VAL1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A LEU* 4.2 12.8 - - + -
1044A PHE* 4.0 18.2 - - + -
1066A TYR* 4.8 2.2 - - + -
1069A LEU* 3.7 23.6 - - + -
1092A PHE* 3.0 53.8 + - + +
1093A PHE* 3.7 11.0 - - + +
1094A LEU 3.3 0.2 - - - -
1095A ALA* 1.3 79.0 - - + +
1097A HIS* 1.3 71.5 + - + +
1099A ARG* 4.8 1.1 - - - -
1100A TYR* 3.2 35.2 + - + +
1101A PHE* 4.7 4.7 - - + -
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Residues in contact with HIS1097 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A TYR* 2.8 30.4 + + - -
1093A PHE* 2.8 36.8 + + - +
1094A LEU 4.3 1.3 - - - +
1096A VAL* 1.3 75.5 - - + +
1098A GLY* 1.3 62.0 + - - +
1101A PHE* 3.2 30.6 + + - -
1102A ARG 3.3 4.0 + - - -
2046A TYR* 3.3 50.0 - + - -
2049A TYR* 3.5 21.9 - - + +
2050A GLN* 2.4 29.9 + - - +
2053A MET* 3.2 19.7 - - + +
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Residues in contact with GLY1098 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094A LEU 2.8 20.2 + - - -
1095A ALA* 3.5 4.4 + - - -
1096A VAL 3.2 0.8 - - - -
1097A HIS* 1.3 77.6 - - - +
1099A ARG* 1.3 58.2 + - - +
1100A TYR 3.8 0.2 - - - -
1102A ARG* 3.4 36.9 + - - +
2053A MET* 3.5 14.3 - - - -
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Residues in contact with ARG1099 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A LEU* 6.0 5.8 - - - -
1056A TRP* 4.0 8.8 - - - -
1095A ALA* 3.4 15.9 + - - +
1096A VAL* 3.3 1.0 + - - -
1097A HIS 3.2 0.2 - - - -
1098A GLY* 1.3 80.8 - - - +
1100A TYR* 1.3 92.6 + - + +
1102A ARG* 5.2 1.3 - - - -
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Residues in contact with TYR1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A LEU* 4.7 10.2 - - + +
1044A PHE* 3.6 28.4 - + - -
1045A GLN* 3.5 35.8 + - + +
1048A MET* 3.7 19.5 - - + -
1056A TRP* 3.5 65.0 - + + +
1096A VAL* 3.2 25.3 + - + +
1099A ARG* 1.3 102.6 - - + +
1101A PHE* 1.3 85.4 + - + +
1102A ARG 3.7 2.0 - - - -
1103A SER* 5.6 0.3 + - - -
1104A CYS* 4.2 3.8 - - - -
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Residues in contact with PHE1101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044A PHE* 4.3 13.5 - + - -
1048A MET* 3.7 27.1 - - + -
1056A TRP 3.2 27.6 - - - -
1059A TRP* 5.9 0.4 - + - -
1062A THR* 4.4 11.2 - - - -
1066A TYR* 4.6 11.4 - + + -
1096A VAL* 4.7 6.1 - - + -
1097A HIS* 3.2 28.9 + + - +
1100A TYR* 1.3 94.5 - - + +
1102A ARG* 1.3 62.2 + - - +
1103A SER 3.4 2.5 - - - +
1104A CYS* 3.5 13.2 + - - -
2046A TYR* 3.3 43.7 - + - +
2050A GLN* 2.9 33.5 + - - +
2053A MET* 3.4 1.9 - - - +
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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