Contacts of the helix formed by residues 79 - 93 (chain G) in PDB entry 5U07
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 79 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77G GLY 3.9 1.0 + - - -
78G TRP* 1.3 76.2 - - - +
80G ALA* 1.3 79.7 + - - +
81G ASP* 2.7 28.9 + - - +
82G LEU* 3.2 16.3 + - + +
83G ALA* 2.7 33.7 + - - +
135G ARG* 5.4 1.2 - - - +
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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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74G ARG* 4.7 23.4 + - - +
78G TRP 3.8 1.0 + - - -
79G ASP* 1.3 88.5 + - - +
81G ASP* 1.3 55.9 + - - +
83G ALA* 3.2 7.5 + - - +
84G ASP* 2.9 29.1 + - - +
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Residues in contact with ASP 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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79G ASP* 2.7 28.2 + - - +
80G ALA* 1.3 75.5 - - - +
82G LEU* 1.3 79.6 + - - +
84G ASP* 3.3 7.3 + - - +
85G ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 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 TRP* 3.5 27.1 - - + -
79G ASP* 3.2 19.6 + - + +
81G ASP* 1.3 95.2 + - - +
83G ALA* 1.3 56.9 + - - +
85G ALA* 4.0 1.6 - - - +
86G GLY 2.9 23.0 + - - -
135G ARG* 5.4 14.8 - - + +
138G VAL* 4.3 7.5 - - + +
139G ALA* 4.4 23.6 - - + +
142G ALA* 4.3 23.8 - - + -
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Residues in contact with ALA 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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70G ALA* 3.8 28.2 - - + +
73G LEU* 4.2 11.1 - - + +
74G ARG* 4.2 15.0 - - + +
78G TRP* 4.0 11.8 - - + -
79G ASP 2.7 18.8 + - - +
80G ALA* 3.5 8.3 - - - +
82G LEU* 1.3 77.0 - - - +
84G ASP* 1.3 57.1 + - - +
86G GLY* 3.3 1.0 + - - -
87G ALA* 2.9 30.7 + - - +
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Residues in contact with ASP 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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66G ILE* 4.2 2.1 - - - +
70G ALA* 4.6 11.0 - - + +
74G ARG* 5.8 1.6 - - - +
80G ALA 2.9 16.3 + - - +
81G ASP* 3.6 7.6 - - - +
83G ALA* 1.3 76.8 - - - +
85G ALA* 1.3 62.3 + - - +
87G ALA* 3.3 1.8 + - - +
88G ARG* 2.9 55.6 + - - +
109G GLU 5.9 0.3 - - - -
110G ALA* 3.9 23.2 + - - +
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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
----------------------------------------------------------
81G ASP 2.9 16.3 + - - +
82G LEU* 4.0 5.4 - - - +
84G ASP* 1.3 77.5 - - - +
86G GLY* 1.3 58.0 + - - +
88G ARG* 3.3 12.0 + - - +
89G GLN* 2.9 37.1 + - + +
138G VAL* 4.5 4.5 - - + -
142G ALA* 4.0 28.3 - - + -
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Residues in contact with GLY 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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73G LEU* 4.7 7.2 - - - -
78G TRP* 4.7 5.8 - - - -
82G LEU 2.9 17.8 + - - -
83G ALA 3.7 0.9 - - - -
85G ALA* 1.3 77.4 - - - +
87G ALA* 1.3 55.9 + - - +
89G GLN* 3.0 8.5 + - - +
90G VAL* 2.9 31.6 + - - +
131G ALA* 4.6 3.3 - - - +
138G VAL* 3.9 20.1 - - - +
151G LEU* 5.0 0.5 - - - +
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Residues in contact with ALA 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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66G ILE* 3.5 37.0 - - + +
69G ILE* 4.1 11.8 - - + +
70G ALA* 4.1 12.3 - - + +
73G LEU* 4.5 1.2 - - - +
83G ALA 2.9 17.3 + - - +
84G ASP 3.9 1.6 - - - +
86G GLY* 1.3 73.4 - - - +
88G ARG* 1.3 66.7 + - - +
90G VAL* 2.9 22.4 + - - +
91G VAL* 3.1 16.1 + - - +
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Residues in contact with ARG 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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66G ILE* 4.5 11.7 - - + -
84G ASP* 2.9 52.6 + - - +
85G ALA* 3.5 9.2 - - - +
87G ALA* 1.3 76.1 - - - +
89G GLN* 1.3 60.2 + - + +
91G VAL* 3.3 10.7 - - - +
92G LEU* 2.8 37.7 + - + +
102G LEU* 4.9 8.6 - - + +
105G GLU* 3.7 20.0 + - - +
110G ALA* 4.7 1.2 - - - +
111G PRO* 3.2 39.0 - - - +
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Residues in contact with GLN 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* 2.9 24.0 + - + +
86G GLY* 3.2 11.0 - - - +
88G ARG* 1.3 77.1 - - - +
90G VAL* 1.3 65.2 + - - +
92G LEU* 3.9 7.6 - - - +
93G SER* 3.0 28.8 + - - -
138G VAL* 4.5 9.2 - - + -
141G GLU* 2.4 31.4 + - + +
142G ALA* 5.9 0.6 - - - +
147G PRO* 3.5 17.6 + - - +
148G LYS 2.6 25.7 + - - +
149G GLY* 3.2 5.5 - - - -
150G ILE* 3.1 14.2 - - + +
151G LEU* 3.7 17.8 - - + +
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Residues in contact with VAL 90 (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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69G ILE* 4.0 28.5 - - + -
86G GLY 2.9 20.2 + - - +
87G ALA* 2.9 14.7 + - - +
89G GLN* 1.3 76.5 - - - +
91G VAL* 1.3 62.1 + - + +
93G SER* 3.2 17.2 + - - -
94G VAL* 3.9 8.5 - - - +
127G LEU* 4.6 20.9 - - + +
131G ALA* 3.5 27.6 - - + -
151G LEU* 4.7 5.4 - - + -
156G ILE* 3.9 20.8 - - + +
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Residues in contact with VAL 91 (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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65G ILE* 4.0 19.5 - - + -
66G ILE* 3.5 42.6 - - + -
69G ILE* 5.7 2.0 - - + -
87G ALA 3.1 5.3 + - - +
88G ARG* 3.3 11.7 - - - +
90G VAL* 1.3 81.6 - - + +
92G LEU* 1.3 66.9 + - + +
93G SER 3.4 0.7 - - - -
94G VAL* 3.3 18.0 - - - +
100G ILE* 3.4 26.7 + - + +
102G LEU* 4.3 17.0 - - + -
113G THR* 4.6 4.0 - - + -
117G PHE* 5.2 5.4 - - + -
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Residues in contact with LEU 92 (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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88G ARG* 2.8 23.7 + - + +
89G GLN* 3.3 13.2 + - - +
91G VAL* 1.3 77.0 - - + +
93G SER* 1.3 55.8 + - - +
94G VAL 3.1 10.6 + - - -
98G SER* 2.6 41.2 - - - +
99G GLY* 3.5 7.0 - - - -
100G ILE 4.9 0.2 - - - +
102G LEU* 6.3 2.9 - - + -
147G PRO* 3.7 24.2 - - + +
148G LYS* 3.9 11.9 - - + +
149G GLY 3.4 27.6 - - - +
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Residues in contact with SER 93 (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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89G GLN 3.0 18.0 + - - -
90G VAL 3.2 10.4 + - - -
91G VAL 3.4 0.4 - - - -
92G LEU* 1.3 75.2 - - - +
94G VAL* 1.3 59.5 + - - +
149G GLY* 4.0 20.0 - - - -
151G LEU* 3.8 25.1 - - - +
153G ALA* 3.8 19.2 - - - +
156G ILE* 3.2 19.5 - - - +
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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