Contacts of the helix formed by residues 1014 - 1029 (chain A) in PDB entry 2BOA
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 SER1014 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A MET* 4.1 4.9 - - - +
97A GLU* 4.8 12.3 + - - -
1013A HIS* 1.3 77.9 - - - +
1015A LEU* 1.3 65.5 + - - +
1016A GLU* 3.8 10.6 + - - +
1017A ALA* 3.1 23.1 + - - +
1018A ILE* 3.0 20.4 + - - +
1116A TYR* 4.2 0.7 - - - -
1120A GLN* 3.0 17.5 + - - -
1404B GOL 5.5 0.2 + - - -
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Residues in contact with LEU1015 (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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1013A HIS 3.9 0.6 + - - -
1014A SER* 1.3 71.8 - - - +
1016A GLU* 1.3 56.0 + - - +
1018A ILE* 3.7 6.2 - - + +
1019A TYR* 2.9 79.5 + - + +
1045A ARG* 3.9 18.8 - - - +
1110A VAL* 3.7 34.5 - - + -
1113A PRO* 3.8 15.0 - - + +
1116A TYR* 3.9 11.0 - - + -
1117A VAL* 3.9 24.8 - - + +
1120A GLN* 4.3 0.2 + - - -
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Residues in contact with GLU1016 (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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1014A SER* 3.2 10.1 + - - +
1015A LEU* 1.3 74.7 - - - +
1017A ALA* 1.3 60.2 + - - +
1019A TYR* 4.1 6.9 - - - +
1020A HIS* 3.0 29.5 + - + +
1019B TYR* 5.0 4.8 - - - -
1035B ARG* 2.8 14.9 + - - -
1046B PRO* 4.0 9.9 - - + +
1048B TYR* 2.6 32.7 + - - -
1404B GOL 2.6 41.6 + - - +
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Residues in contact with ALA1017 (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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1001A GLU* 5.0 3.8 - - - +
1007A PHE* 3.8 9.3 - - + -
1013A HIS* 3.8 26.7 - - + -
1014A SER* 3.1 19.5 + - - +
1016A GLU* 1.3 76.6 - - - +
1018A ILE* 1.3 60.9 + - - +
1020A HIS* 3.7 3.4 - - - +
1021A GLU* 2.9 32.1 + - - +
1404B GOL 4.0 14.1 + - - +
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Residues in contact with ILE1018 (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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1007A PHE* 4.9 1.3 - - + -
1013A HIS* 3.8 16.2 - - + +
1014A SER 3.0 15.7 + - - +
1015A LEU* 3.7 6.5 - - - +
1017A ALA* 1.3 72.3 - - - +
1019A TYR* 1.3 68.0 + - + +
1021A GLU* 3.1 6.6 + - - +
1022A MET* 2.9 31.0 + - - +
1076A GLN* 4.5 11.2 - - + -
1077A ALA* 6.3 0.2 - - - -
1080A ILE* 3.9 24.1 - - + +
1109A PRO* 4.1 17.5 - - + -
1110A VAL* 3.8 28.5 - - + -
1116A TYR* 3.6 34.8 - - + +
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Residues in contact with TYR1019 (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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1015A LEU* 2.9 53.4 + - + +
1016A GLU* 4.1 6.7 - - - +
1018A ILE* 1.3 74.7 - - + +
1020A HIS* 1.3 55.3 + - - +
1022A MET* 3.3 15.4 - - - +
1023A ASP 3.0 11.8 + - - -
1035A ARG* 2.5 29.4 + - - +
1045A ARG* 5.2 0.9 - - + -
1046A PRO* 2.6 36.5 + - + -
1047A MET* 4.3 2.1 - - - -
1048A TYR* 3.4 48.9 + + + -
1110A VAL* 4.8 10.1 + - + -
1113A PRO* 3.6 23.6 - - - +
1016B GLU* 5.2 5.8 - - + +
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Residues in contact with HIS1020 (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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1016A GLU 3.0 21.0 + - - +
1017A ALA* 3.7 5.4 - - - +
1019A TYR* 1.3 75.4 - - - +
1021A GLU* 1.3 60.2 + - - +
1023A ASP* 3.1 13.1 + - + +
1024A ASN* 2.8 62.1 + - - -
1035A ARG* 4.4 1.1 - - - +
1020B HIS* 3.4 32.0 + + - -
1404B GOL 3.8 33.3 + - - -
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Residues in contact with GLU1021 (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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1007A PHE* 3.5 47.7 - - + +
1009A TYR* 2.5 36.1 + - + +
1017A ALA 2.9 17.7 + - - +
1018A ILE 3.8 2.9 - - - +
1020A HIS* 1.3 75.1 - - + +
1022A MET* 1.3 60.0 + - - +
1024A ASN* 3.2 18.7 + - - +
1025A ILE* 2.8 38.1 + - + +
1080A ILE* 4.2 4.5 - - + -
1084A ARG* 3.0 19.0 + - - -
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Residues in contact with MET1022 (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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1018A ILE* 2.9 19.6 + - - +
1019A TYR* 3.3 29.6 - - - +
1021A GLU* 1.3 74.2 - - - +
1023A ASP* 1.3 63.5 + - - +
1025A ILE* 3.5 2.3 + - - +
1026A ALA* 3.4 16.8 + - - +
1035A ARG* 3.7 10.3 - - + -
1048A TYR* 3.2 40.2 - - + +
1049A VAL 3.6 18.4 - - - +
1050A LEU* 3.7 33.9 - - + +
1080A ILE* 3.7 15.4 - - + +
1109A PRO* 3.7 24.7 - - + -
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Residues in contact with ASP1023 (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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1019A TYR 3.0 6.1 + - - -
1020A HIS* 3.1 15.7 + - - +
1022A MET* 1.3 76.7 - - - +
1024A ASN* 1.3 61.5 + - - +
1026A ALA* 3.5 6.3 + - - +
1027A ALA* 3.0 28.9 + - - +
1035A ARG* 2.5 49.3 + - - +
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Residues in contact with ASN1024 (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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1020A HIS* 2.8 47.0 + - - +
1021A GLU* 3.2 26.7 + - - +
1023A ASP* 1.3 79.6 - - - +
1025A ILE* 1.3 64.7 + - - +
1027A ALA* 3.8 8.1 - - - +
1028A ASP* 3.0 35.3 + - - +
1084A ARG* 4.5 5.2 - - - +
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Residues in contact with ILE1025 (chain A).
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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1009A TYR* 3.8 14.1 - - - +
1021A GLU 2.8 29.8 + - - +
1022A MET* 3.9 6.3 - - - +
1023A ASP 3.4 0.4 - - - -
1024A ASN* 1.3 73.1 - - - +
1026A ALA* 1.3 57.8 + - - +
1028A ASP* 4.7 0.9 - - - -
1029A PHE* 3.3 32.1 + - - +
1033A ALA* 4.1 6.6 - - + +
1050A LEU* 3.9 16.4 - - + -
1052A PHE* 4.2 0.7 - - + -
1080A ILE* 4.0 12.8 - - + +
1083A ALA* 3.8 26.7 - - + +
1084A ARG* 3.8 37.0 - - + +
1087A VAL* 3.8 26.0 - - + -
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Residues in contact with ALA1026 (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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1022A MET 3.4 10.5 + - - +
1023A ASP* 3.7 10.1 - - - +
1024A ASN 3.2 0.4 - - - -
1025A ILE* 1.3 78.7 - - - +
1027A ALA* 1.3 64.1 + - - +
1030A PRO* 3.2 28.1 - - - +
1033A ALA* 3.6 25.1 - - - +
1034A ARG* 3.8 15.9 - - + -
1035A ARG* 4.1 7.2 - - + +
1050A LEU* 4.2 2.0 - - + -
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Residues in contact with ALA1027 (chain A).
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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1023A ASP* 3.0 22.0 + - - +
1024A ASN* 3.4 11.0 + - - +
1026A ALA* 1.3 77.0 - - - +
1028A ASP* 1.3 65.4 + - - +
1030A PRO* 3.7 12.8 - - - +
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Residues in contact with ASP1028 (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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1024A ASN* 3.0 25.0 + - - +
1025A ILE 4.0 0.4 - - - +
1027A ALA* 1.3 81.8 - - - +
1029A PHE* 1.3 84.1 + - + +
1030A PRO* 3.5 7.3 - - - +
1084A ARG* 3.6 20.8 + - - +
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Residues in contact with PHE1029 (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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1025A ILE 3.3 17.1 + - - +
1026A ALA 3.2 6.6 - - - +
1028A ASP* 1.3 90.6 - - + +
1030A PRO* 1.3 66.4 - - - +
1031A ASP 3.2 2.7 - - - -
1032A LEU* 3.2 18.5 + - + -
1033A ALA* 3.1 21.0 + - - +
1084A ARG* 3.6 25.6 - - - -
1087A VAL* 3.6 46.0 - - + -
1088A SER* 4.8 6.5 - - - -
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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