Contacts of the helix formed by residues 1059 - 1071 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004J ASP* 3.5 27.4 - - - -
1009J LEU* 3.9 14.4 - - + -
1010J PRO 3.6 22.0 - - - +
1057J ILE* 4.2 14.8 + - - -
1058J PHE* 1.3 80.1 - - - +
1060J GLN* 1.3 68.3 + - - +
1061J LEU* 3.4 3.1 - - + +
1062J MET* 3.0 32.9 + - + +
1063J HIS* 3.2 16.5 + - - -
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Residues in contact with GLN1060 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A SER* 5.9 4.8 + - - -
676J ASN* 4.2 9.4 + - - +
677J TRP* 3.4 23.6 + - + +
678J ASN* 3.2 26.2 - - - +
751J TYR* 4.4 6.8 + - - -
1010J PRO 4.9 3.2 + - - -
1011J GLY* 5.3 2.0 - - - -
1058J PHE* 3.6 24.2 + - + -
1059J CYS* 1.3 70.6 - - - +
1061J LEU* 1.3 63.9 + - - +
1062J MET 3.0 1.6 + - - -
1063J HIS* 3.1 11.6 + - - +
1064J HIS* 3.1 31.0 + - + +
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Residues in contact with LEU1061 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677J TRP* 3.3 53.6 - - + +
752J LEU* 4.2 8.3 - - + -
935J LEU* 4.7 6.5 - - + -
942J ALA* 3.5 21.1 - - + +
1000J CYS* 4.0 19.5 - - - -
1009J LEU* 3.6 28.7 - - + -
1010J PRO* 5.6 1.3 - - + +
1059J CYS* 5.4 1.8 - - + -
1060J GLN* 1.3 78.5 - - - +
1062J MET* 1.3 84.5 + - + +
1063J HIS 3.3 0.2 - - - -
1064J HIS* 3.9 1.3 - - - -
1065J LEU* 3.4 20.3 + - - +
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Residues in contact with MET1062 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000J CYS* 3.6 32.5 - - + +
1001J ASN* 4.2 15.3 - - - +
1004J ASP* 3.7 21.1 - - + +
1009J LEU* 3.3 34.8 - - + -
1059J CYS* 3.0 23.8 + - + +
1061J LEU* 1.3 88.1 - - + +
1063J HIS* 1.3 68.7 + - + +
1065J LEU* 3.5 15.8 - - - +
1066J THR* 3.4 14.0 + - - -
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Residues in contact with HIS1063 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A TYR* 5.3 6.3 - + - -
668A ASP* 3.9 22.9 + - - -
790A LYS 5.2 1.6 + - - +
1058J PHE* 2.8 45.8 - + + -
1059J CYS 3.6 12.7 + - - -
1060J GLN 3.1 7.2 + - - +
1062J MET* 1.3 84.5 - - + +
1064J HIS* 1.3 66.4 + - - +
1065J LEU 2.9 1.8 - - - -
1066J THR* 2.8 20.5 + - - -
1067J GLU* 2.9 22.8 + - + +
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Residues in contact with HIS1064 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A SER* 5.5 3.6 - - - -
677J TRP* 4.1 2.9 - + - -
678J ASN* 2.9 26.8 + - - -
942J ALA 3.2 27.6 - - - +
943J LYS 3.2 14.8 + - - +
944J VAL* 3.5 30.6 - - + +
945J ARG 5.0 0.6 + - - -
1060J GLN* 3.1 40.2 + - + +
1061J LEU* 4.0 1.1 - - - +
1062J MET 3.5 0.2 - - - -
1063J HIS* 1.3 75.2 - - - +
1065J LEU* 1.3 57.2 + - - +
1067J GLU* 3.7 8.5 - - - +
1068J ASN* 2.9 37.5 + - - +
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Residues in contact with LEU1065 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941J PRO* 2.8 39.9 + - + +
942J ALA* 4.0 3.8 - - + -
992J ILE* 4.1 15.1 - - + +
996J VAL* 3.5 20.0 - - + +
997J GLY* 4.1 19.1 - - - +
1000J CYS* 3.8 33.0 - - + -
1001J ASN* 5.6 1.6 - - - +
1061J LEU 3.4 8.8 + - - +
1062J MET* 3.5 17.0 - - - +
1063J HIS 2.9 0.4 - - - -
1064J HIS* 1.3 81.4 - - - +
1066J THR* 1.3 59.9 + - - +
1068J ASN* 4.2 0.7 - - - +
1069J HIS* 3.1 24.1 + - - +
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Residues in contact with THR1066 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062J MET 3.4 12.8 + - - -
1063J HIS* 2.8 15.6 + - - -
1065J LEU* 1.3 75.1 - - - +
1067J GLU* 1.3 73.2 + - - +
1069J HIS* 3.4 16.2 - - - +
1070J LYS* 3.5 21.4 + - - +
1073J LYS* 5.4 0.2 + - - -
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Residues in contact with GLU1067 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A GLU* 5.8 1.6 - - - +
1063J HIS* 2.9 22.9 + - + +
1064J HIS* 3.7 11.0 - - - +
1066J THR* 1.3 78.7 - - - +
1068J ASN* 1.3 68.2 + - - +
1069J HIS 3.0 1.1 - - - -
1070J LYS* 2.9 53.8 + - - +
1071J ILE* 3.7 6.8 + - - +
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Residues in contact with ASN1068 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941J PRO 3.1 23.1 + - - +
943J LYS 2.9 24.0 + - - -
945J ARG* 3.5 25.5 + - - +
948J HIS* 3.3 31.9 - - + +
992J ILE* 4.5 2.7 - - + -
1064J HIS* 2.9 22.7 + - - +
1065J LEU 4.2 1.1 - - - +
1067J GLU* 1.3 78.5 - - - +
1069J HIS* 1.3 64.0 + - - +
1071J ILE* 3.0 28.1 - - - +
1072J TRP* 3.0 11.4 - - - -
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Residues in contact with HIS1069 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989J GLU* 3.0 33.6 + - + +
992J ILE* 3.5 33.4 - - + +
993J THR* 2.8 21.9 + - - -
1065J LEU 3.1 18.4 + - - +
1066J THR* 3.4 10.5 - - - +
1067J GLU 3.0 0.4 + - - -
1068J ASN* 1.3 78.1 - - - +
1070J LYS* 1.3 65.2 + - - +
1072J TRP* 3.2 12.2 + - - +
1073J LYS* 2.5 47.5 + - + +
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Residues in contact with LYS1070 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A GLU* 3.7 26.2 + - - +
1066J THR* 3.6 24.6 - - - +
1067J GLU* 2.9 44.5 + - - +
1069J HIS* 1.3 77.7 - - - +
1071J ILE* 1.3 55.7 + - + +
1072J TRP 2.7 13.9 + - - -
1073J LYS* 3.1 29.6 + - - +
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Residues in contact with ILE1071 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945J ARG* 3.2 47.8 - - + +
948J HIS* 4.6 0.2 - - + -
949J LEU* 4.2 22.4 - - + -
1067J GLU 4.4 6.1 - - - +
1068J ASN* 3.0 32.9 + - - +
1070J LYS* 1.3 74.9 - - + +
1072J TRP* 1.3 76.4 + - + +
1073J LYS* 5.4 0.2 - - - -
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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