Contacts of the helix formed by residues 76 - 89 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71G TYR* 3.6 15.1 - - - +
74G LYS 2.8 11.8 + - - +
75G GLY* 1.3 69.6 - - - -
77G THR* 1.3 66.2 + - - +
78G THR* 2.6 31.5 + - - +
79G LYS* 3.2 19.6 + - + +
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Residues in contact with THR 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G TYR* 4.1 9.9 - - - -
75G GLY 3.6 6.4 + - - -
76G ASP* 1.3 73.5 + - - +
78G THR* 1.3 65.8 + - - +
80G LEU* 3.2 24.5 + - + +
81G GLY 3.6 3.5 + - - -
839G GLY* 4.3 25.2 - - - +
842G GLY 6.0 0.7 - - - -
843G LEU* 5.0 16.5 - - + +
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Residues in contact with THR 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ASP* 2.6 33.1 + - - +
77G THR* 1.3 79.6 - - - +
79G LYS* 1.3 62.0 + - - +
81G GLY* 3.2 11.8 + - - +
82G GLU* 3.2 22.1 + - - +
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Residues in contact with LYS 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G VAL* 3.9 48.5 - - + +
70G ASP* 4.8 15.7 - - + -
71G TYR* 4.9 8.1 - - + +
76G ASP* 3.2 17.1 + - + +
78G THR* 1.3 80.7 + - - +
80G LEU* 1.3 62.8 + - - +
82G GLU* 3.3 22.7 + - + +
83G LEU* 3.2 21.1 + - - +
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Residues in contact with LEU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G VAL* 5.6 2.0 - - + +
68G SER* 4.9 6.1 - - - +
71G TYR* 3.4 52.9 - - + +
77G THR* 3.2 17.8 + - + +
79G LYS* 1.3 76.2 - - - +
81G GLY* 1.3 59.5 + - - +
83G LEU* 3.3 7.1 + - + +
84G GLY 2.8 24.1 + - - -
839G GLY 5.3 0.2 - - - -
840G ILE* 4.2 13.9 - - + -
843G LEU* 4.1 14.8 - - + -
899G THR* 3.5 31.0 - - + -
903G VAL* 3.5 29.9 - - + +
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Residues in contact with GLY 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G THR 3.6 5.2 + - - -
78G THR* 3.2 8.8 + - - -
80G LEU* 1.3 78.7 - - - +
82G GLU* 1.3 56.9 + - - +
84G GLY 3.3 0.5 + - - -
85G ALA* 2.9 27.2 + - - +
843G LEU* 5.0 7.4 - - - +
907G TYR* 3.5 24.8 + - - -
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Residues in contact with GLU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G THR* 3.2 17.2 + - - +
79G LYS* 3.6 29.2 + - + +
80G LEU 3.2 0.8 - - - -
81G GLY* 1.3 73.4 - - - +
83G LEU* 1.3 65.5 + - - +
85G ALA* 3.2 16.5 + - - +
86G LYS* 3.2 22.2 + - - +
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Residues in contact with LEU 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G CYS* 3.6 41.1 - - + -
67G VAL* 3.5 31.0 - - + -
68G SER* 3.8 17.0 - - - +
79G LYS 3.2 9.3 + - - +
80G LEU* 3.7 8.7 - - + +
82G GLU* 1.3 74.3 - - - +
84G GLY* 1.3 59.6 + - - +
86G LYS* 2.9 14.1 + - + +
87G LEU* 2.9 46.4 + - + +
900G THR* 4.4 9.2 - - + +
903G VAL* 4.4 10.8 - - + -
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Residues in contact with GLY 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G LEU 2.8 11.5 + - - -
81G GLY 3.3 1.1 + - - -
83G LEU* 1.3 75.6 - - - +
85G ALA* 1.3 58.6 + - - +
87G LEU* 3.4 5.5 + - - +
88G THR* 2.8 35.5 + - - +
903G VAL* 3.5 21.6 - - - +
907G TYR* 3.6 20.8 - - - -
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G GLY 2.9 13.1 + - - +
82G GLU* 3.3 13.9 - - - +
83G LEU 3.2 0.4 - - - -
84G GLY* 1.3 76.5 - - - +
86G LYS* 1.3 75.5 + - - +
88G THR* 2.3 23.9 + - - -
89G GLY* 3.7 4.2 + - - -
907G TYR* 4.6 3.3 - - - -
919G VAL* 4.2 12.6 - - + +
922G GLN* 4.3 2.3 + - - -
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Residues in contact with LYS 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G PHE* 4.2 23.5 - - + -
82G GLU* 3.2 22.9 + - - +
83G LEU* 2.9 15.9 + - + +
85G ALA* 1.3 89.2 + - - +
87G LEU* 1.3 67.3 + - - +
88G THR 3.2 0.7 + - - -
89G GLY 3.2 2.9 + - - -
90G LEU* 4.0 5.5 + - - +
922G GLN* 2.8 31.6 + - - +
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Residues in contact with LEU 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G PHE* 4.1 22.0 - - + -
64G CYS* 4.5 5.8 - - - -
83G LEU* 2.9 41.4 + - + +
84G GLY* 3.9 4.3 - - - +
86G LYS* 1.3 72.9 - - - +
88G THR* 1.3 63.4 + - + +
89G GLY 3.2 0.7 + - - -
90G LEU* 3.4 23.0 + - + +
95G ALA* 5.4 0.5 - - - +
98G VAL* 4.1 7.9 - - + -
900G THR* 4.1 11.0 - - + +
903G VAL* 4.2 7.0 - - + -
904G PHE* 3.5 74.0 - - + +
907G TYR* 6.1 1.3 - - + -
911G ARG* 4.2 3.3 + - - -
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Residues in contact with THR 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G GLY 2.8 20.2 + - - +
85G ALA* 2.3 35.0 + - - -
87G LEU* 1.3 76.3 - - - +
89G GLY* 1.3 57.9 + - - +
90G LEU 3.4 0.3 + - - -
904G PHE* 5.8 0.2 - - - -
907G TYR* 3.5 37.9 - - + -
911G ARG* 2.7 46.6 + - - +
917G PHE* 4.7 6.7 - - + -
919G VAL* 3.4 26.4 - - + +
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Residues in contact with GLY 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G ALA 3.7 1.9 + - - -
86G LYS 3.2 4.8 + - - -
87G LEU 3.2 1.2 - - - -
88G THR* 1.3 78.2 + - - +
90G LEU* 1.3 66.5 + - - +
91G ALA 3.5 0.9 + - - -
919G VAL* 4.0 4.3 - - - -
920G THR 3.6 21.8 - - - -
921G PRO* 3.8 4.3 - - - +
922G GLN* 2.9 39.7 + - - +
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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