Contacts of the helix formed by residues 1058 - 1073 (chain F) in PDB entry 2BT4
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 HIS1058 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658D HIS* 5.2 0.7 - - + -
660D GLY* 3.3 23.9 - - - -
661D GLU* 3.3 10.5 - - + -
664D ASP* 3.2 22.8 + - - -
2402D PO4 2.8 36.6 + - - +
858E HIS* 5.1 0.9 - - + +
1056F SER* 3.1 17.0 + - - +
1057F ASN* 1.3 87.7 - - + +
1059F GLU* 1.3 65.3 + - - +
1061F GLU* 3.2 17.0 + - + -
1062F LEU* 3.2 23.5 + - - +
1083F TYR* 4.0 2.7 - - - -
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Residues in contact with GLU1059 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D GLU* 4.1 1.9 - - - +
2402D PO4 3.8 5.8 + - - +
859E GLU* 3.9 3.8 - - - +
883E TYR* 3.4 32.5 + - - +
1058F HIS* 1.3 70.9 - - - +
1060F GLY* 1.3 61.4 + - - +
1062F LEU* 3.2 7.8 + - - +
1063F VAL* 3.1 25.2 + - - +
1083F TYR* 3.4 29.9 + - + +
1087F SER* 2.7 31.4 + - - +
1088F VAL 4.8 0.2 + - - -
1089F ALA* 3.9 5.0 + - + +
1090F ILE* 4.2 7.1 - - + +
2406F TRS 2.7 46.5 + - - -
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Residues in contact with GLY1060 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2402D PO4 3.2 10.4 + - - -
857E ASN* 3.4 26.0 + - - +
858E HIS* 3.4 19.6 + - - -
883E TYR* 4.3 0.4 + - - -
1059F GLU* 1.3 75.8 - - - +
1061F GLU* 1.3 61.1 + - - +
1063F VAL* 3.4 5.8 + - - +
1064F ASP* 3.0 32.1 + - - +
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Residues in contact with GLU1061 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858E HIS* 3.4 10.7 - - + -
1056F SER* 2.4 32.4 + - - +
1058F HIS* 3.2 19.5 + - + +
1060F GLY* 1.3 73.0 - - - +
1062F LEU* 1.3 65.8 + - - +
1064F ASP* 3.2 10.9 + - - +
1065F TRP* 2.9 66.9 + - + +
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Residues in contact with LEU1062 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012F LEU* 4.2 16.9 - - + +
1013F ASN 3.8 22.7 - - - +
1014F GLY* 3.9 16.4 - - - -
1056F SER* 4.1 11.7 - - - +
1058F HIS 3.2 12.3 + - - +
1059F GLU 3.2 6.5 + - - +
1061F GLU* 1.3 77.2 - - - +
1063F VAL* 1.3 56.3 + - - +
1065F TRP* 3.2 24.5 + - + +
1066F ILE* 2.9 37.9 + - + +
1078F ILE* 5.6 4.9 - - + -
1080F PRO* 5.2 3.1 - - + +
1083F TYR* 3.7 30.1 - - + -
1090F ILE* 3.9 17.5 - - + -
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Residues in contact with VAL1063 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815E PRO* 4.7 1.1 - - + -
816E ASN* 3.6 26.9 - - - +
857E ASN* 3.6 31.2 - - + +
1059F GLU 3.1 17.2 + - - +
1060F GLY* 3.6 9.2 - - - +
1062F LEU* 1.3 73.2 - - - +
1064F ASP* 1.3 64.9 + - - +
1066F ILE* 3.2 5.2 + - - +
1067F HIS* 3.0 25.8 + - + +
1089F ALA* 3.9 29.2 - - + +
1090F ILE* 4.0 13.5 - - + -
1093F ALA* 4.1 8.3 - - + -
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Residues in contact with ASP1064 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857E ASN* 2.7 34.4 + - - +
858E HIS* 3.1 22.6 + - - -
1060F GLY 3.0 14.9 + - - +
1061F GLU* 3.4 11.7 - - + +
1063F VAL* 1.3 74.5 - - - +
1065F TRP* 1.3 66.5 + - + +
1067F HIS* 3.3 10.3 + - - +
1068F GLU* 3.0 25.1 + - - +
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Residues in contact with TRP1065 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010F MET* 3.5 9.5 - - + +
1012F LEU* 3.7 29.8 - - + -
1054F ARG* 3.2 54.6 - - + +
1055F GLN 3.5 22.0 - - - -
1056F SER* 3.6 23.3 - - - -
1061F GLU* 2.9 46.8 + - + +
1062F LEU* 3.6 17.0 - - + +
1063F VAL 3.2 0.2 - - - -
1064F ASP* 1.3 81.7 - - + +
1066F ILE* 1.3 60.1 + - - +
1068F GLU* 3.2 11.4 + - - +
1069F ALA* 3.0 23.6 + - - +
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Residues in contact with ILE1066 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012F LEU* 3.6 20.0 - - + -
1062F LEU* 2.9 23.9 + - + +
1063F VAL* 3.2 6.9 + - - +
1065F TRP* 1.3 73.9 - - - +
1067F HIS* 1.3 59.6 + - + +
1069F ALA* 3.2 8.7 + - - +
1070F ARG* 2.8 28.1 + - - +
1076F ILE* 4.4 2.7 - - + -
1078F ILE* 4.4 5.4 - - + -
1090F ILE* 4.0 24.5 - - + -
1093F ALA* 3.5 41.7 - - + +
1094F LEU* 3.8 24.0 - - + -
1097F CYS* 3.7 14.8 - - - -
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Residues in contact with HIS1067 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816E ASN* 2.7 29.7 + - - -
818E ASN* 3.2 39.9 + - - +
819E LEU* 3.7 27.1 - - + +
857E ASN* 3.7 20.4 + - - -
1063F VAL* 3.0 20.6 + - + +
1064F ASP* 3.4 10.1 - - - +
1066F ILE* 1.3 77.6 - - - +
1068F GLU* 1.3 61.5 - - - +
1070F ARG* 3.3 20.7 + - - +
1071F LEU* 3.6 13.9 + - - +
1093F ALA* 4.5 5.4 - - + -
1096F THR* 4.3 7.4 - - - -
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Residues in contact with GLU1068 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010F MET* 4.5 0.9 - - + -
1054F ARG* 2.9 43.6 + - - -
1064F ASP 3.0 12.3 + - - +
1065F TRP* 3.4 14.7 - - - +
1067F HIS* 1.3 74.6 - - - +
1069F ALA* 1.3 65.7 + - - +
1071F LEU* 3.2 2.7 + - - -
1072F ASN* 2.9 46.1 + - - +
1073F HIS* 4.3 9.8 - - + -
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Residues in contact with ALA1069 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010F MET* 3.9 14.3 - - + +
1065F TRP 3.0 12.6 + - - +
1066F ILE* 3.4 9.6 - - - +
1068F GLU* 1.3 76.2 - - - +
1070F ARG* 1.3 65.3 + - - +
1071F LEU 3.1 0.5 + - - -
1073F HIS* 3.1 43.0 + - + +
1076F ILE* 3.9 30.3 - - + -
1100F LEU* 4.3 4.7 - - + +
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Residues in contact with ARG1070 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819E LEU* 3.8 23.5 - - - +
822E GLN* 2.6 49.3 + - - +
823E ARG* 5.5 3.0 - - - +
1066F ILE 2.8 12.9 + - - +
1067F HIS* 3.3 14.8 + - - +
1069F ALA* 1.3 76.2 - - - +
1071F LEU* 1.3 83.6 + - + +
1073F HIS 5.2 1.6 - - - +
1096F THR* 3.0 45.3 + - - +
1097F CYS* 3.9 18.1 - - - +
1098F ASP* 5.4 1.6 + - - +
1100F LEU* 4.5 9.4 - - - +
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Residues in contact with LEU1071 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822E GLN* 5.6 0.2 - - - +
1002F ARG* 3.2 22.3 + - - -
1067F HIS 3.9 12.8 - - - +
1068F GLU* 3.2 2.7 + - - +
1069F ALA 3.0 0.6 - - - -
1070F ARG* 1.3 110.0 - - + +
1072F ASN* 1.3 74.3 + - - +
1073F HIS 3.9 0.9 - - - -
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Residues in contact with ASN1072 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002F ARG* 3.6 18.3 + - - +
1007F ALA* 3.6 15.4 - - - +
1008F PRO* 4.0 6.9 - - - +
1068F GLU* 2.9 39.5 + - + +
1071F LEU* 1.3 94.8 - - - +
1073F HIS* 1.3 75.5 + - + +
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Residues in contact with HIS1073 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002F ARG* 3.7 13.5 - - - +
1007F ALA* 4.2 0.9 - - - -
1008F PRO* 3.3 27.7 - - + +
1010F MET* 3.5 37.4 - - + +
1052F ASP* 2.9 34.8 + - + +
1068F GLU* 4.3 12.3 - - + -
1069F ALA* 3.1 29.6 + - + +
1070F ARG 5.2 1.4 - - - +
1071F LEU 5.3 0.2 - - - -
1072F ASN* 1.3 98.3 - - + +
1074F CYS* 1.3 61.8 + - - +
1075F GLY 3.4 9.2 - - - +
1100F LEU* 3.6 13.2 - - - +
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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