Contacts of the helix formed by residues 77 - 90 (chain A) in PDB entry 1JQO
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 THR 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR* 4.3 19.7 - - + -
75A GLY 3.6 5.1 + - - +
76A ASP* 1.3 69.6 - - - +
78A THR* 1.3 64.2 + - - +
79A LYS 3.1 1.5 + - - -
80A LEU* 3.2 24.6 + - + +
81A GLY 3.7 3.3 + - - -
839A GLY* 6.0 5.4 - - - -
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Residues in contact with THR 78 (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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76A ASP* 2.4 29.6 + - - +
77A THR* 1.3 76.8 + - - +
79A LYS* 1.3 63.1 + - - +
81A GLY* 3.3 3.9 + - - +
82A GLU* 3.0 22.2 + - - +
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Residues in contact with LYS 79 (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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67A VAL* 3.5 35.8 - - + +
68A SER* 5.4 0.4 - - - -
70A ASP* 3.3 32.6 + - + -
71A TYR* 3.8 11.4 - - + +
76A ASP* 3.0 36.3 + - - +
77A THR 3.1 0.6 - - - -
78A THR* 1.3 76.9 - - - +
80A LEU* 1.3 60.5 + - - +
82A GLU* 3.1 28.2 + - - +
83A LEU* 2.7 33.5 + - - +
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Residues in contact with LEU 80 (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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71A TYR* 3.5 45.1 - - + +
77A THR* 3.2 17.3 + - + +
79A LYS* 1.3 76.9 - - - +
81A GLY* 1.3 59.1 + - - +
83A LEU* 3.4 8.0 + - + +
84A GLY* 2.9 23.0 + - - -
839A GLY 4.9 6.5 - - - +
840A ILE* 4.3 10.8 - - + -
843A LEU* 4.3 27.4 - - + -
899A THR* 3.4 33.4 - - + -
903A VAL* 3.7 19.8 - - + +
907A TYR* 4.6 1.1 + - - -
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Residues in contact with GLY 81 (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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77A THR 3.7 4.4 + - - -
78A THR* 3.3 7.1 + - - -
79A LYS 3.2 0.4 - - - -
80A LEU* 1.3 78.7 - - - +
82A GLU* 1.3 60.8 + - - +
84A GLY* 3.3 2.6 + - - -
85A ALA* 3.2 18.9 + - - +
843A LEU* 6.3 1.3 - - - -
907A TYR* 4.2 14.3 + - - -
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Residues in contact with GLU 82 (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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67A VAL* 3.8 23.3 - - + +
78A THR* 3.0 12.8 + - - +
79A LYS* 3.1 39.4 + - - +
81A GLY* 1.3 73.8 - - - +
83A LEU* 1.3 67.7 + - - +
85A ALA* 3.0 18.3 + - + +
86A LYS* 3.0 16.4 + - + +
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Residues in contact with LEU 83 (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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64A CYS* 4.4 8.7 - - - +
67A VAL* 4.3 12.1 - - + -
68A SER* 3.0 39.3 - - - +
79A LYS 2.7 16.9 + - - +
80A LEU* 3.5 7.6 - - + +
82A GLU* 1.3 78.3 - - - +
84A GLY* 1.3 64.4 + - - +
86A LYS* 3.1 18.3 + - + +
87A LEU* 3.1 42.2 + - + +
899A THR* 4.7 3.4 - - + +
900A THR* 3.8 23.8 - - + +
903A VAL* 4.2 16.6 - - + -
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Residues in contact with GLY 84 (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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80A LEU 2.9 10.9 + - - -
81A GLY 3.3 5.8 + - - -
82A GLU 3.1 0.6 - - - -
83A LEU* 1.3 77.6 - - - +
85A ALA* 1.3 57.8 + - - +
87A LEU* 3.5 3.1 + - - +
88A THR* 2.9 35.1 + - - +
903A VAL* 3.7 19.7 - - - +
907A TYR* 3.7 18.8 - - - -
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Residues in contact with ALA 85 (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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81A GLY 3.2 10.4 + - - +
82A GLU* 3.0 13.3 + - - +
84A GLY* 1.3 72.8 - - - +
86A LYS* 1.3 67.7 + - - +
87A LEU 3.4 0.3 + - - -
88A THR* 3.4 15.6 + - - -
89A GLY* 3.7 2.8 + - - -
922A GLN* 3.6 9.0 - - - +
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Residues in contact with LYS 86 (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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60A PHE* 3.3 46.3 - - + -
63A GLU* 2.9 35.1 + - + +
64A CYS* 5.4 5.6 - - - +
67A VAL* 5.7 7.6 - - + -
82A GLU* 3.0 18.8 + - + +
83A LEU* 3.2 15.3 - - + +
85A ALA* 1.3 76.3 - - - +
87A LEU* 1.3 62.1 + - + +
89A GLY 3.9 0.2 + - - -
90A LEU* 4.1 0.7 - - - +
922A GLN* 3.0 29.1 + - - +
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Residues in contact with LEU 87 (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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60A PHE* 3.7 28.3 - - + -
64A CYS* 4.1 13.5 - - - -
83A LEU* 3.1 35.2 + - + +
84A GLY* 4.2 2.7 - - - +
86A LYS* 1.3 73.9 - - + +
88A THR* 1.3 63.2 + - + +
89A GLY 3.0 6.7 + - - -
90A LEU* 3.3 28.0 + - + +
95A ALA* 5.7 0.2 - - - +
98A VAL* 4.5 7.9 - - + -
900A THR* 4.1 7.6 - - + +
903A VAL* 4.7 3.1 - - + -
904A PHE* 3.7 57.9 - - + +
907A TYR* 6.4 1.6 - - + -
911A ARG* 5.5 0.7 + - - -
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Residues in contact with THR 88 (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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84A GLY 2.9 19.3 + - - +
85A ALA* 3.4 11.3 + - - -
87A LEU* 1.3 75.1 - - + +
89A GLY* 1.3 59.5 + - - +
90A LEU 4.4 0.9 - - - +
904A PHE* 5.9 0.7 - - - -
907A TYR* 3.6 38.8 - - + -
911A ARG* 3.9 22.9 + - - +
917A PHE* 4.7 2.7 - - + -
919A VAL* 2.8 45.4 - - + +
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Residues in contact with GLY 89 (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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85A ALA 3.7 6.0 + - - -
86A LYS 3.9 0.2 + - - -
87A LEU 3.0 1.4 - - - -
88A THR* 1.3 81.3 + - - +
90A LEU* 1.3 67.0 + - - +
91A ALA* 3.6 0.9 + - - -
920A THR 3.2 21.3 - - - -
921A PRO* 3.5 7.1 - - - +
922A GLN* 2.8 42.5 + - - +
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Residues in contact with LEU 90 (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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60A PHE* 3.5 33.9 - - + -
86A LYS 4.1 1.1 - - - +
87A LEU* 3.3 23.4 + - + +
88A THR 4.4 3.8 - - - +
89A GLY* 1.3 79.3 - - - +
91A ALA* 1.3 62.2 + - - +
92A PRO* 4.0 0.5 - - - +
94A ASP* 4.0 4.7 - - + -
95A ALA* 4.0 23.9 - - + +
98A VAL* 3.4 32.3 - - + -
904A PHE* 4.3 3.8 - - + -
911A ARG* 4.9 6.6 + - - -
922A GLN* 3.8 12.2 - - - +
925A LEU* 3.6 32.8 - - + -
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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