Contacts of the helix formed by residues 76 - 89 (chain H) in PDB entry 6V3O
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 ASP 76 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71H TYR* 3.4 8.7 - - - -
74H LYS* 2.3 33.7 + - + +
75H GLY* 1.3 65.4 - - - -
77H THR* 1.3 66.0 + - - +
78H THR* 3.1 28.4 + - - +
79H LYS* 3.1 38.6 + - + +
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Residues in contact with THR 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H TYR* 4.0 12.8 - - + +
75H GLY 4.1 9.6 - - - +
76H ASP* 1.3 74.0 + - - +
78H THR* 1.3 68.3 + - - +
80H LEU* 3.0 32.1 + - - +
81H GLY 3.7 1.9 + - - -
839H GLY* 4.8 19.1 - - - +
843H LEU* 5.5 2.1 - - - +
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Residues in contact with THR 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H ASP* 3.1 22.2 + - - +
77H THR* 1.3 81.7 - - - +
79H LYS* 1.3 66.8 + - - +
81H GLY* 3.3 4.8 + - - +
82H GLU* 3.2 32.9 + - - +
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Residues in contact with LYS 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H VAL* 3.9 33.9 - - + +
70H ASP* 4.1 31.9 + - + +
71H TYR* 4.7 14.1 - - + +
74H LYS* 5.3 3.8 - - - -
76H ASP* 3.1 34.9 + - + +
78H THR* 1.3 78.4 + - - +
80H LEU* 1.3 62.6 + - + +
82H GLU* 3.3 15.6 + - - +
83H LEU* 3.2 21.7 + - - +
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Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H VAL* 5.8 1.1 - - + -
68H SER* 5.2 5.2 - - - +
71H TYR* 3.7 48.2 - - + +
77H THR* 3.0 14.0 + - - +
79H LYS* 1.3 77.9 - - + +
81H GLY* 1.3 57.9 + - - +
83H LEU* 3.3 7.8 + - + +
84H GLY* 2.8 26.5 + - - -
839H GLY 4.8 3.6 - - - +
840H ILE* 4.0 23.3 - - + +
843H LEU* 4.6 14.6 - - + -
899H THR* 3.8 27.1 - - + -
903H VAL* 3.8 25.7 - - + +
907H TYR* 4.7 0.5 - - - -
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Residues in contact with GLY 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H THR 3.7 4.4 + - - -
78H THR* 3.3 8.2 + - - -
80H LEU* 1.3 78.7 - - - +
82H GLU* 1.3 56.6 + - - +
84H GLY 3.3 0.7 + - - -
85H ALA* 2.9 28.1 + - - +
843H LEU* 4.7 6.3 - - - +
907H TYR* 3.5 22.2 + - - -
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Residues in contact with GLU 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H VAL* 6.0 1.5 - - + +
78H THR* 3.2 22.6 + - - +
79H LYS* 3.8 13.6 - - - +
80H LEU 3.2 0.4 - - - -
81H GLY* 1.3 76.3 - - - +
83H LEU* 1.3 63.4 + - - +
85H ALA* 3.1 17.2 + - - +
86H LYS* 3.2 19.2 + - - +
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Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H CYS* 3.4 39.3 - - - -
67H VAL* 4.4 15.0 - - + +
68H SER* 3.9 20.9 - - - +
79H LYS 3.2 13.8 + - - +
80H LEU* 3.7 9.2 - - + +
82H GLU* 1.3 77.9 - - - +
84H GLY* 1.3 61.3 + - - +
86H LYS* 3.0 29.9 + - - +
87H LEU* 3.0 29.1 + - + +
899H THR* 6.3 0.2 - - + -
900H THR* 4.4 9.4 - - + -
903H VAL* 3.5 28.3 - - + -
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Residues in contact with GLY 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H LEU 2.8 15.3 + - - -
81H GLY 3.3 4.0 + - - -
83H LEU* 1.3 73.5 - - - +
85H ALA* 1.3 55.3 + - - +
87H LEU* 3.4 11.1 + - - +
88H THR* 2.3 36.5 + - - -
903H VAL* 4.8 2.0 - - - -
907H TYR* 3.7 33.0 - - - -
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Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H GLY 2.9 13.1 + - - +
82H GLU* 3.1 14.3 + - - +
84H GLY* 1.3 78.4 - - - +
86H LYS* 1.3 63.4 + - + +
88H THR* 3.5 12.0 + - - -
89H GLY* 3.8 6.2 + - - -
907H TYR* 4.7 3.3 - - - -
919H VAL* 4.5 15.0 - - + +
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Residues in contact with LYS 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H PHE* 4.0 25.6 + - + -
63H GLU* 3.9 31.3 + - - +
64H CYS* 4.4 2.2 - - - +
67H VAL* 4.2 11.4 - - - +
82H GLU 3.2 10.9 + - - +
83H LEU* 3.0 37.3 + - + +
85H ALA* 1.3 77.7 - - + +
87H LEU* 1.3 62.3 + - - +
88H THR 3.2 0.7 + - - -
89H GLY* 3.3 10.7 + - - -
90H LEU* 3.7 15.2 - - - +
922H GLN* 5.9 0.3 - - - +
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Residues in contact with LEU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H PHE* 3.9 22.7 - - + -
64H CYS* 4.1 9.4 - - - -
83H LEU* 3.0 27.6 + - + +
84H GLY* 3.4 6.0 + - - +
86H LYS* 1.3 77.1 - - - +
88H THR* 1.3 63.8 + - - +
89H GLY 3.2 0.7 + - - -
90H LEU* 3.3 22.7 + - + +
95H ALA* 5.3 1.0 - - - +
98H VAL* 4.4 5.2 - - + -
900H THR* 4.4 4.7 - - + +
903H VAL* 3.8 28.9 - - + -
904H PHE* 3.6 63.4 - - + -
907H TYR* 6.0 2.2 - - + -
911H ARG* 4.4 3.1 + - - -
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Residues in contact with THR 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H GLY 2.3 30.8 + - - -
85H ALA* 3.8 7.7 + - - -
86H LYS 3.2 0.4 - - - -
87H LEU* 1.3 77.3 - - - +
89H GLY* 1.3 60.0 + - - +
90H LEU 3.4 0.3 + - - +
907H TYR* 3.8 20.8 - - + +
911H ARG* 2.9 57.2 + - - +
917H PHE* 4.5 13.9 - - + -
919H VAL* 4.0 31.4 - - + +
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Residues in contact with GLY 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H ALA 3.8 4.5 + - - -
86H LYS 3.3 7.9 + - - -
87H LEU 3.2 1.2 - - - -
88H THR* 1.3 78.6 - - - +
90H LEU* 1.3 64.4 + - - +
91H ALA* 3.6 0.5 + - - -
919H VAL* 5.1 3.1 - - - +
920H THR 3.6 21.1 - - - -
921H PRO* 3.8 4.2 - - - +
922H GLN* 3.0 34.6 + - - +
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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