Contacts of the helix formed by residues 1059 - 1071 (chain F) in PDB entry 1SOJ
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 CYS1059 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004F ASP* 3.9 13.7 - - - +
1009F LEU* 3.6 30.1 - - - -
1010F PRO 3.2 23.8 - - - -
1011F GLY* 4.7 1.1 - - - -
1057F ILE* 4.1 9.4 + - + -
1058F PHE* 1.3 76.9 - - - +
1060F GLN* 1.3 70.4 + - - +
1061F LEU* 3.5 1.8 - - - -
1062F MET* 3.1 31.9 + - + +
1063F HIS* 3.2 17.8 + - - -
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Residues in contact with GLN1060 (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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676F ASN* 4.2 9.2 + - - +
677F TRP* 3.5 23.5 + - + +
678F ASN* 3.2 25.8 - - - +
751F TYR* 4.4 7.3 + - - -
1010F PRO 4.9 3.0 + - - -
1011F GLY* 5.2 1.6 - - - -
1058F PHE* 3.8 25.5 + - + -
1059F CYS* 1.3 73.0 - - - +
1061F LEU* 1.3 64.0 + - - +
1062F MET 3.0 1.4 + - - -
1063F HIS* 3.1 11.4 + - - +
1064F HIS* 3.1 30.1 + - + +
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Residues in contact with LEU1061 (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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677F TRP* 3.3 52.4 - - + +
752F LEU* 4.2 7.0 - - + -
935F LEU* 4.7 6.5 - - + -
942F ALA* 3.5 22.0 - - + +
1000F CYS* 3.9 19.1 - - - -
1009F LEU* 3.6 28.7 - - + -
1010F PRO* 5.6 0.9 - - + +
1059F CYS* 5.5 2.9 - - - -
1060F GLN* 1.3 79.1 - - - +
1062F MET* 1.3 83.5 + - + +
1063F HIS 3.3 0.4 - - - -
1064F HIS* 3.9 1.3 - - - -
1065F LEU* 3.4 20.6 + - - +
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Residues in contact with MET1062 (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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1000F CYS* 3.5 32.8 - - + +
1001F ASN* 4.1 16.8 - - - +
1004F ASP* 3.7 21.3 - - + +
1009F LEU* 3.3 34.3 - - + -
1059F CYS* 3.1 23.9 + - + +
1060F GLN 3.0 0.4 + - - -
1061F LEU* 1.3 85.7 - - + +
1063F HIS* 1.3 67.8 + - + +
1065F LEU* 3.5 16.3 - - - +
1066F THR* 3.4 13.7 + - - -
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Residues in contact with HIS1063 (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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1057F ILE 5.7 0.8 + - - -
1058F PHE* 3.2 40.1 - + + -
1059F CYS 3.6 12.0 + - - -
1060F GLN 3.1 7.2 + - - +
1062F MET* 1.3 83.3 - - + +
1064F HIS* 1.3 66.8 + - - +
1065F LEU 3.0 2.0 - - - -
1066F THR* 2.9 19.8 + - - -
1067F GLU* 2.9 23.8 + - + +
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Residues in contact with HIS1064 (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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677F TRP* 4.1 3.1 - + - -
678F ASN* 2.9 26.1 + - - -
941F PRO 4.0 0.2 - - - -
942F ALA 3.2 27.1 - - - +
943F LYS 3.2 14.3 + - - +
944F VAL* 3.5 31.9 - - + +
945F ARG 5.0 0.8 + - - -
1060F GLN* 3.1 39.2 + - + +
1061F LEU* 4.0 1.6 - - - +
1063F HIS* 1.3 76.4 - - - +
1065F LEU* 1.3 57.1 + - - +
1067F GLU* 3.7 7.3 - - - +
1068F ASN* 2.9 38.0 + - - -
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Residues in contact with LEU1065 (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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941F PRO* 2.8 39.2 + - + +
942F ALA* 4.0 3.8 - - + -
992F ILE* 4.1 15.1 - - + +
996F VAL* 3.5 19.3 - - + -
997F GLY* 4.1 18.6 - - - +
1000F CYS* 3.8 33.9 - - + -
1001F ASN* 5.5 1.6 - - - +
1061F LEU 3.4 9.2 + - - +
1062F MET* 3.5 16.4 - - - +
1064F HIS* 1.3 81.2 - - - +
1066F THR* 1.3 61.2 + - - +
1068F ASN* 4.1 1.0 - - - +
1069F HIS* 3.1 23.4 + - - +
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Residues in contact with THR1066 (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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1062F MET 3.4 12.5 + - - -
1063F HIS* 2.9 12.7 + - - -
1065F LEU* 1.3 77.6 - - - +
1067F GLU* 1.3 73.0 + - - +
1069F HIS* 3.5 16.7 - - - +
1070F LYS* 3.5 21.4 + - - +
1073F LYS* 5.4 0.2 + - - -
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Residues in contact with GLU1067 (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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1063F HIS* 2.9 25.7 + - + +
1064F HIS* 3.7 8.7 - - - +
1066F THR* 1.3 78.5 - - - +
1068F ASN* 1.3 69.3 + - - +
1069F HIS 3.0 1.3 - - - -
1070F LYS* 2.9 55.2 + - - +
1071F ILE* 3.7 6.8 + - - +
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Residues in contact with ASN1068 (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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941F PRO 3.1 23.5 + - - +
943F LYS 2.9 23.4 + - - -
945F ARG* 3.5 25.2 + - - +
948F HIS* 3.2 33.3 - - + +
992F ILE* 4.5 3.1 - - + -
1064F HIS* 2.9 23.3 + - - +
1065F LEU 4.2 0.7 - - - +
1067F GLU* 1.3 77.9 - - - +
1069F HIS* 1.3 62.3 - - - +
1071F ILE* 3.1 17.9 - - - +
1072F TRP* 3.0 22.3 - - - -
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Residues in contact with HIS1069 (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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989F GLU* 3.0 33.0 + - + -
992F ILE* 3.6 33.6 - - + +
993F THR* 2.8 21.7 + - - -
1065F LEU 3.1 19.0 + - - +
1066F THR* 3.5 10.1 - - + +
1067F GLU 3.0 0.2 + - - -
1068F ASN* 1.3 77.4 - - - +
1070F LYS* 1.3 65.1 + - - +
1072F TRP* 3.2 11.4 + - - +
1073F LYS* 2.6 46.6 + - + +
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Residues in contact with LYS1070 (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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1066F THR* 3.6 25.9 - - + +
1067F GLU* 2.9 42.3 + - - +
1069F HIS* 1.3 77.4 - - - +
1071F ILE* 1.3 54.9 + - + +
1072F TRP 2.7 14.0 + - - -
1073F LYS* 3.2 28.2 + - - +
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Residues in contact with ILE1071 (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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945F ARG* 3.1 51.4 - - + +
948F HIS* 4.6 0.4 - - + -
949F LEU* 4.2 19.5 - - + -
1067F GLU 3.7 6.0 + - - +
1068F ASN* 3.1 28.9 - - - +
1070F LYS* 1.3 74.0 - - + +
1072F TRP* 1.3 76.9 + - + +
1073F LYS* 5.4 0.4 - - - -
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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