Contacts of the helix formed by residues 1059 - 1073 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004D ASP* 4.5 6.5 - - - +
1009D LEU* 3.6 35.0 - - + -
1010D PRO 4.2 13.7 - - - +
1011D GLY* 5.3 0.9 - - - -
1057D ILE* 3.9 3.9 + - + -
1058D PHE* 1.3 75.3 - - - +
1060D GLN* 1.3 69.0 + - - +
1061D LEU* 4.1 9.0 - - - -
1062D MET* 3.1 32.5 + - + +
1063D HIS* 3.0 24.1 + - - +
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Residues in contact with GLN1060 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676D ASN* 4.7 9.2 + - - +
677D TRP* 3.0 36.5 + - + +
678D ASN* 3.3 20.0 - - - +
751D TYR* 4.9 2.1 + - - -
1010D PRO 5.3 1.8 + - - -
1011D GLY* 5.9 0.4 - - - -
1058D PHE* 3.6 30.1 + - + -
1059D CYS* 1.3 72.0 - - - +
1061D LEU* 1.3 59.8 + - - +
1063D HIS* 2.8 22.1 + - - +
1064D HIS* 3.0 32.5 + - + +
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Residues in contact with LEU1061 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677D TRP* 3.2 50.9 - - + +
752D LEU* 4.4 10.3 - - + -
935D LEU* 5.4 7.4 - - + -
942D ALA* 3.2 29.4 - - + +
1000D CYS* 4.7 9.0 - - - -
1009D LEU* 4.2 18.8 - - + -
1010D PRO* 6.1 0.9 - - + +
1059D CYS* 4.1 10.3 - - - -
1060D GLN* 1.3 79.6 - - - +
1062D MET* 1.3 88.3 + - + +
1064D HIS* 3.8 1.1 - - - -
1065D LEU* 3.1 22.9 + - - +
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Residues in contact with MET1062 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000D CYS* 3.7 32.5 - - + +
1001D ASN* 4.3 14.1 - - - +
1004D ASP* 4.3 13.9 - - - +
1009D LEU* 3.3 29.6 - - + -
1059D CYS* 3.1 25.5 + - + +
1060D GLN 3.0 1.0 - - - -
1061D LEU* 1.3 96.7 - - + +
1063D HIS* 1.3 66.7 + - + +
1065D LEU* 3.4 19.3 - - + +
1066D THR* 3.4 11.4 + - - -
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Residues in contact with HIS1063 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057D ILE 5.7 0.7 - - - -
1058D PHE* 3.1 40.9 - + + -
1059D CYS 3.0 11.3 + - - +
1060D GLN 2.8 9.9 + - - +
1062D MET* 1.3 80.8 - - + +
1064D HIS* 1.3 67.9 + - + +
1066D THR* 2.9 12.3 + - - -
1067D GLU* 2.9 34.0 + - + +
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Residues in contact with HIS1064 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677D TRP* 4.2 1.6 - - - -
678D ASN* 3.0 27.8 + - - -
941D PRO 3.7 1.6 - - - -
942D ALA 3.1 25.1 - - - +
943D LYS* 3.1 27.7 + - - +
944D VAL* 3.7 15.7 + - + -
945D ARG 5.2 1.0 + - - -
1060D GLN* 3.0 36.2 + - + +
1061D LEU* 3.8 2.0 - - - +
1063D HIS* 1.3 75.9 - - + +
1065D LEU* 1.3 58.8 + - - +
1067D GLU* 4.4 8.7 - - - +
1068D ASN* 2.8 37.7 + - - +
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Residues in contact with LEU1065 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941D PRO* 3.1 28.2 + - + +
942D ALA* 4.1 6.7 - - + +
992D ILE* 4.7 11.8 - - + +
996D VAL* 3.4 27.6 - - + -
997D GLY* 3.9 20.2 - - - +
1000D CYS* 3.8 30.3 - - + -
1001D ASN* 5.4 3.1 - - - +
1061D LEU 3.1 11.0 + - - +
1062D MET* 3.4 17.9 - - - +
1064D HIS* 1.3 78.9 - - - +
1066D THR* 1.3 63.0 + - - +
1068D ASN* 4.1 1.2 - - - +
1069D HIS* 3.1 24.1 + - - +
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Residues in contact with THR1066 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062D MET 3.4 9.0 + - - -
1063D HIS* 2.9 14.9 + - - -
1065D LEU* 1.3 77.1 - - - +
1067D GLU* 1.3 79.2 + - - +
1069D HIS* 3.4 7.9 + - - +
1070D LYS* 3.4 32.5 + - - +
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Residues in contact with GLU1067 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063D HIS* 2.9 28.7 + - + +
1064D HIS* 3.7 11.4 - - - +
1066D THR* 1.3 87.1 - - - +
1068D ASN* 1.3 58.7 + - - +
1070D LYS* 2.8 57.7 + - - +
1071D ILE* 3.6 5.6 + - - +
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Residues in contact with ASN1068 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941D PRO* 3.3 24.4 + - + +
943D LYS 3.0 27.1 + - - -
945D ARG* 3.4 26.7 + - - +
948D HIS* 3.5 30.7 - - + +
992D ILE* 4.8 1.3 - - - -
1064D HIS* 2.8 22.8 + - - +
1065D LEU 4.2 0.7 - - - +
1067D GLU* 1.3 76.0 - - - +
1069D HIS* 1.3 62.3 + - - +
1071D ILE* 3.3 19.1 + - - +
1072D TRP* 3.2 22.0 + - - -
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Residues in contact with HIS1069 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989D GLU* 3.6 22.1 + - + -
992D ILE* 3.0 34.0 - - + +
993D THR* 3.1 27.4 + - - -
1065D LEU 3.1 20.4 + - - +
1066D THR* 3.5 9.4 - - - +
1067D GLU 3.0 1.0 + - - -
1068D ASN* 1.3 77.6 - - - +
1070D LYS* 1.3 64.3 + - + +
1072D TRP* 3.0 15.6 + - - +
1073D LYS* 3.1 44.5 + - + +
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Residues in contact with LYS1070 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066D THR* 3.4 25.7 + - + +
1067D GLU* 2.8 37.1 + - - +
1069D HIS* 1.3 79.4 - - + +
1071D ILE* 1.3 59.6 + - - +
1072D TRP 3.3 0.9 + - - -
1073D LYS* 3.7 19.4 + - - +
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Residues in contact with ILE1071 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945D ARG* 3.7 30.7 - - + +
948D HIS* 4.5 3.4 - - + -
949D LEU* 4.3 20.0 - - + -
985D ALA* 5.6 0.3 - - - +
1067D GLU 4.2 2.7 - - - +
1068D ASN* 3.4 37.7 - - - +
1069D HIS 3.1 0.4 + - - -
1070D LYS* 1.3 78.8 - - + +
1072D TRP* 1.3 87.1 + - + +
1073D LYS* 5.0 0.5 - - - +
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Residues in contact with TRP1072 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948D HIS* 3.3 30.5 + - - -
949D LEU* 3.9 22.0 - - + -
952D THR* 4.4 9.2 - - + -
984D LEU* 4.0 31.2 - - + -
985D ALA* 3.4 48.1 - - + +
988D GLN* 3.6 28.8 - - + +
989D GLU* 3.7 18.9 - - + +
992D ILE* 4.3 9.6 - - + +
1068D ASN 3.2 24.1 + - - -
1069D HIS 3.0 5.7 + - - +
1071D ILE* 1.3 95.6 - - + +
1073D LYS* 1.3 64.2 - - - +
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Residues in contact with LYS1073 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989D GLU* 3.3 28.2 - - + +
993D THR* 4.9 1.3 - - - -
1069D HIS* 3.1 43.9 + - + +
1070D LYS* 3.7 14.6 + - - +
1071D ILE 5.0 0.7 - - - +
1072D TRP* 1.3 82.2 - - - +
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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