Contacts of the helix formed by residues 77 - 89 (chain G) in PDB entry 5UQ9
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 ALA 77 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76G LYS* 1.3 84.2 - - - +
78G GLY* 1.3 65.2 + - - +
79G GLN 3.7 1.3 - - - +
80G ALA* 4.0 6.9 + - + +
81G VAL* 3.5 15.6 + - - +
103G ASN 5.5 4.8 + - - -
104G SER* 4.8 7.5 + - - +
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Residues in contact with GLY 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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77G ALA* 1.3 72.0 - - - +
79G GLN* 1.3 65.7 + - - +
81G VAL* 3.2 12.0 + - - +
82G ASP* 3.4 11.1 + - - +
104G SER* 5.4 1.8 - - - -
108G ASP* 5.4 7.2 - - - -
112G ARG* 3.5 24.2 + - - -
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Residues in contact with GLN 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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77G ALA* 3.7 1.0 - - - +
78G GLY* 1.3 75.1 - - - +
80G ALA* 1.3 62.3 + - - +
82G ASP* 3.4 18.5 + - - +
83G ASP* 2.8 49.8 + - - +
86G GLU* 5.5 2.8 + - - -
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Residues in contact with ALA 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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34G ARG* 5.5 8.3 + - - +
75G VAL* 3.8 27.8 - - + -
76G LYS 4.0 10.3 - - - +
77G ALA* 4.0 5.2 + - + +
78G GLY 3.2 0.8 - - - -
79G GLN* 1.3 77.5 - - - +
81G VAL* 1.3 62.8 + - - +
83G ASP* 3.5 8.6 + - - +
84G PHE* 3.2 28.4 + - + +
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Residues in contact with VAL 81 (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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73G LEU* 3.9 26.2 - - + -
75G VAL* 5.1 5.2 - - + -
76G LYS 4.5 14.1 - - - +
77G ALA 3.5 16.6 - - - +
78G GLY 3.2 7.7 + - - +
80G ALA* 1.3 75.2 - - - +
82G ASP* 1.3 64.6 + - - +
84G PHE* 3.3 5.7 + - - +
85G ILE* 3.0 34.9 + - + +
100G ASP* 3.9 33.4 - - + +
104G SER* 4.6 5.6 - - - +
112G ARG* 3.9 19.3 - - - +
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Residues in contact with ASP 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 GLY 3.4 8.3 + - - +
79G GLN* 3.4 22.9 + - - +
81G VAL* 1.3 76.7 - - - +
83G ASP* 1.3 63.9 + - - +
85G ILE* 3.3 6.5 + - - +
86G GLU* 3.0 41.7 + - + +
108G ASP* 5.0 0.7 - - - +
111G ARG* 2.8 32.3 + - - -
112G ARG* 2.6 39.0 + - - +
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Residues in contact with ASP 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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34G ARG* 4.6 19.1 + - - +
79G GLN* 2.8 41.9 + - - +
80G ALA* 3.7 8.8 - - - +
82G ASP* 1.3 77.6 - - - +
84G PHE* 1.3 62.8 + - - +
86G GLU* 3.6 8.1 + - - +
87G LYS* 3.0 32.2 + - - +
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Residues in contact with PHE 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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9G ILE* 3.6 35.4 - - + -
32G PHE* 4.9 4.0 - + - -
33G ASN 4.9 0.4 - - - -
34G ARG* 4.1 34.5 - - + -
58G LEU* 4.8 12.8 - - + -
73G LEU* 4.3 26.9 - - + -
75G VAL* 4.0 28.3 - - + -
80G ALA* 3.2 13.9 + - + +
81G VAL* 3.3 7.1 + - - +
83G ASP* 1.3 78.5 - - - +
85G ILE* 1.3 52.7 + - - +
87G LYS* 3.3 32.9 + - - +
88G LEU* 2.7 40.3 + - + +
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Residues in contact with ILE 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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73G LEU* 4.1 13.9 - - + -
81G VAL* 3.0 24.2 + - + +
82G ASP* 3.7 7.0 - - - +
83G ASP 3.2 0.2 - - - -
84G PHE* 1.3 76.4 - - - +
86G GLU* 1.3 63.4 + - + +
88G LEU* 3.6 4.2 - - - -
89G VAL* 2.8 42.7 + - + +
98G ILE* 4.5 11.9 - - + -
112G ARG* 3.5 33.4 - - + -
116G LEU* 4.2 20.6 - - + -
123G PHE* 3.7 23.6 - - + -
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Residues in contact with GLU 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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79G GLN* 5.5 2.3 + - - -
82G ASP* 3.0 29.3 + - + +
83G ASP* 4.2 7.7 - - - +
85G ILE* 1.3 79.1 - - + +
87G LYS* 1.3 59.3 + - - +
89G VAL* 4.4 6.7 - - - +
90G PRO* 3.4 18.5 - - - +
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Residues in contact with LYS 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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34G ARG* 4.3 27.1 - - - +
58G LEU* 4.0 19.2 - - + +
83G ASP* 3.0 22.0 + - - +
84G PHE* 3.5 39.0 - - - +
86G GLU* 1.3 76.5 - - - +
88G LEU* 1.3 58.9 + - - +
89G VAL 3.6 0.2 - - - -
90G PRO* 3.8 7.8 - - - +
91G LEU* 5.0 7.3 - - - +
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Residues in contact with LEU 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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9G ILE* 4.0 11.7 - - + -
58G LEU* 3.7 33.4 - - + -
61G MET* 4.1 2.2 - - + -
62G VAL* 4.1 21.5 - - + -
71G ILE* 3.6 34.5 - - + -
73G LEU* 5.1 6.1 - - + -
84G PHE* 2.7 22.0 + - + +
85G ILE* 4.0 4.3 - - - +
87G LYS* 1.3 74.8 - - - +
89G VAL* 1.3 63.6 + - - +
90G PRO* 3.3 3.1 - - - -
91G LEU* 3.1 17.7 + - + +
92G LEU* 3.3 20.2 - - + +
98G ILE* 4.3 14.6 - - + -
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Residues in contact with VAL 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ILE* 2.8 33.6 + - + +
86G GLU* 4.4 5.2 - - - +
88G LEU* 1.3 73.9 - - - +
90G PRO* 1.3 74.4 - - + +
91G LEU 3.2 1.0 + - - -
92G LEU* 3.3 25.6 - - + +
98G ILE* 5.8 2.0 - - + -
116G LEU* 5.3 4.3 - - + -
119G LYS* 4.8 23.1 - - + -
121G ILE* 4.0 29.5 - - + +
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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