Contacts of the helix formed by residues 1059 - 1073 (chain A) in PDB entry 1SO2
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004A ASP* 4.8 4.9 - - - +
1009A LEU* 3.6 30.5 - - - -
1010A PRO 3.9 7.9 - - - +
1011A GLY* 4.7 3.8 - - - -
1057A ILE* 3.9 10.9 + - + +
1058A PHE* 1.3 75.2 - - - +
1060A GLN* 1.3 66.0 + - - +
1061A LEU* 3.8 16.4 - - - -
1062A MET* 3.2 40.1 + - + +
1063A HIS* 3.2 19.4 + - - -
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Residues in contact with GLN1060 (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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677A TRP* 3.6 24.5 + - + +
678A ASN* 3.5 20.1 + - - +
751A TYR* 5.1 2.3 + - - -
1010A PRO 5.1 1.8 + - - -
1011A GLY* 5.6 0.8 - - - -
1058A PHE* 4.0 29.7 + - + -
1059A CYS* 1.3 71.9 - - - +
1061A LEU* 1.3 66.4 + - + +
1063A HIS* 3.2 5.0 + - - +
1064A HIS* 3.0 49.9 + - + +
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Residues in contact with LEU1061 (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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677A TRP* 3.9 37.7 - - + +
751A TYR* 6.1 1.6 - - + -
752A LEU* 4.7 6.1 - - + -
935A LEU* 4.5 15.9 - - + -
942A ALA* 3.5 34.7 - - + +
1000A CYS* 5.3 6.7 - - + -
1009A LEU* 3.6 27.6 - - + -
1010A PRO* 4.5 10.8 - - + +
1059A CYS* 3.8 19.5 - - - -
1060A GLN* 1.3 75.8 - - + +
1062A MET* 1.3 63.5 + - + +
1064A HIS* 3.2 1.7 + - - +
1065A LEU* 2.8 32.1 + - - +
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Residues in contact with MET1062 (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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1000A CYS* 4.1 21.3 - - - +
1001A ASN* 3.9 22.2 - - - +
1004A ASP* 3.6 26.7 - - + +
1009A LEU* 3.7 18.2 - - + -
1059A CYS* 3.2 33.5 + - + +
1061A LEU* 1.3 79.2 - - - +
1063A HIS* 1.3 64.3 + - - +
1065A LEU* 3.6 12.2 - - + +
1066A THR* 3.2 24.3 + - - -
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Residues in contact with HIS1063 (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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1057A ILE 5.7 1.1 - - - -
1058A PHE* 3.6 37.7 - + + -
1059A CYS 3.2 15.6 + - - +
1060A GLN 3.2 8.6 + - - +
1061A LEU 3.2 0.6 - - - -
1062A MET* 1.3 80.8 - - + +
1064A HIS* 1.3 66.5 + - + +
1066A THR* 3.1 8.1 + - - -
1067A GLU* 2.9 38.8 + - + +
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Residues in contact with HIS1064 (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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677A TRP* 3.9 2.7 - + - -
678A ASN* 2.8 32.0 + - - -
942A ALA 3.2 34.3 - - - +
943A LYS* 3.6 15.3 - - - +
944A VAL* 3.8 20.9 - - + +
945A ARG 5.1 0.4 + - - -
1060A GLN* 3.0 43.9 + - + +
1061A LEU 3.2 1.3 + - - +
1063A HIS* 1.3 75.5 - - + +
1065A LEU* 1.3 54.4 + - - +
1067A GLU* 3.1 19.0 + - - +
1068A ASN* 2.7 41.2 + - - +
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Residues in contact with LEU1065 (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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941A PRO* 3.2 32.5 + - + +
942A ALA* 4.2 4.5 - - + +
992A ILE* 4.4 14.6 - - + +
996A VAL* 3.9 22.7 - - + -
997A GLY* 4.2 17.7 - - - +
1000A CYS* 4.1 26.0 - - + -
1001A ASN* 5.6 2.2 - - - +
1061A LEU 2.8 18.1 + - - +
1062A MET* 3.6 15.9 - - + +
1064A HIS* 1.3 76.4 - - - +
1066A THR* 1.3 61.7 + - - +
1068A ASN* 3.5 1.6 + - - +
1069A HIS* 3.1 25.1 + - + +
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Residues in contact with THR1066 (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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1062A MET 3.2 11.8 + - - -
1063A HIS* 3.1 11.8 + - - -
1065A LEU* 1.3 75.7 - - - +
1067A GLU* 1.3 70.5 + - + +
1069A HIS* 3.3 18.5 + - - +
1070A LYS* 3.5 29.3 + - + +
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Residues in contact with GLU1067 (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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945A ARG 5.8 0.9 + - - -
1063A HIS* 2.9 23.8 + - + +
1064A HIS* 3.3 31.1 + - - +
1066A THR* 1.3 78.3 - - + +
1068A ASN* 1.3 60.6 + - - +
1070A LYS* 3.0 39.2 + - - +
1071A ILE* 3.8 6.5 + - - +
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Residues in contact with ASN1068 (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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941A PRO* 3.1 26.3 + - + +
943A LYS 2.8 28.3 + - - -
945A ARG* 3.3 27.6 + - - +
948A HIS* 3.5 26.3 - - + +
992A ILE* 4.8 2.0 - - + -
1064A HIS* 2.7 22.3 + - - +
1065A LEU 4.1 1.1 - - - +
1067A GLU* 1.3 76.9 - - - +
1069A HIS* 1.3 61.8 + - - +
1071A ILE* 3.3 18.7 - - - +
1072A TRP* 3.2 23.2 + - - -
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Residues in contact with HIS1069 (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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989A GLU* 3.5 30.5 + - + -
992A ILE* 3.7 32.1 - - + +
993A THR* 3.2 29.3 + - - -
1065A LEU* 3.1 18.3 + - + +
1066A THR* 3.4 11.0 - - - +
1067A GLU 3.1 0.2 - - - -
1068A ASN* 1.3 79.9 - - - +
1070A LYS* 1.3 56.9 + - + +
1071A ILE 3.4 0.2 + - - -
1072A TRP* 3.5 2.9 + - - -
1073A LYS* 3.1 41.2 + - + +
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Residues in contact with LYS1070 (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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454A HG9 4.2 29.4 - - - +
1066A THR* 3.7 33.0 + - + +
1067A GLU* 3.0 20.1 + - - +
1069A HIS* 1.3 74.9 - - + +
1071A ILE* 1.3 68.3 + - - +
1072A TRP 3.1 0.7 + - - -
1073A LYS* 3.6 21.7 + - + +
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Residues in contact with ILE1071 (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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454A HG9 3.2 42.7 - - + +
945A ARG* 3.6 37.7 - - + +
948A HIS* 4.4 3.8 - - + -
949A LEU* 4.3 14.6 - - + -
1067A GLU 4.1 3.6 - - - +
1068A ASN* 3.3 39.0 - - - +
1070A LYS* 1.3 79.6 - - - +
1072A TRP* 1.3 82.5 + - + +
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Residues in contact with TRP1072 (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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453A HG9 4.9 2.2 - - + -
454A HG9 3.9 46.6 + - + -
948A HIS* 3.1 23.0 + - - -
949A LEU* 3.7 28.5 - - + -
952A THR* 4.3 8.5 - - + -
984A LEU* 4.0 32.1 - - + -
985A ALA* 3.7 43.0 - - + +
988A GLN* 3.5 28.6 - - + +
989A GLU* 3.9 18.8 - - + +
992A ILE* 4.2 9.9 - - + -
1068A ASN 3.2 23.0 + - - -
1069A HIS 3.5 3.5 + - - +
1070A LYS 3.1 0.2 - - - -
1071A ILE* 1.3 91.5 - - + +
1073A LYS* 1.3 62.7 + - - +
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Residues in contact with LYS1073 (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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454A HG9 2.9 52.4 + - - -
989A GLU* 3.9 23.6 - - + +
1069A HIS* 3.1 35.6 + - + +
1070A LYS* 3.6 14.9 + - + +
1072A TRP* 1.3 77.2 - - - +
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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