Contacts of the helix formed by residues 82 - 92 (chain G) in PDB entry 5B32
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 82 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78G VAL* 4.9 5.6 - - + -
80G ARG* 3.7 13.0 - - + +
81G ILE* 1.3 80.5 - - - +
83G PRO* 1.3 75.5 - - - +
84G ARG* 3.4 17.6 + - - +
85G HIS* 2.9 40.1 + - + +
86G LEU* 3.2 9.0 + - - +
55H SER* 3.8 8.7 - - - +
58H ALA* 3.8 3.8 - - - -
132I C 5.4 7.6 - - - +
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Residues in contact with PRO 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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82G THR* 1.3 88.0 - - - +
84G ARG* 1.3 60.6 + - - +
86G LEU* 3.3 8.2 + - + +
87G GLN* 3.0 23.0 + - - +
104G ILE* 3.9 2.3 - - - +
105G ALA 3.4 24.9 - - - +
106G GLY* 3.5 11.9 - - - +
107G GLY* 3.7 4.4 - - - +
55H SER* 3.5 15.0 - - - +
57H LYS* 3.9 21.5 - - + -
58H ALA* 3.8 3.4 - - + +
61H ILE* 3.5 23.3 - - + -
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Residues in contact with ARG 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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55A GLN 3.1 22.8 + - - -
56A LYS* 3.9 19.6 + - - +
57A SER 4.7 0.4 + - - -
58A THR* 3.7 21.6 - - + +
76G LEU* 5.8 4.3 - - + -
82G THR* 3.1 11.9 + - - +
83G PRO* 1.3 78.4 - - - +
85G HIS* 1.3 63.6 + - + +
87G GLN* 3.3 3.5 + - - +
88G LEU* 3.0 52.3 + - + +
106G GLY 3.7 2.2 + - - +
107G GLY* 2.9 27.7 + - - -
108G GLY* 3.6 3.0 - - - -
109G VAL 2.6 32.5 + - - +
111G PRO* 3.6 16.8 - - - +
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Residues in contact with HIS 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ALA* 3.8 20.5 - - - +
72G ALA* 4.2 12.3 - - + +
73G SER* 3.4 39.5 - - - -
76G LEU* 4.1 25.0 - - + +
78G VAL* 4.2 12.8 - - + +
80G ARG 3.6 10.8 - - - -
81G ILE* 3.7 4.9 - - + -
82G THR* 2.9 39.3 + - + +
84G ARG* 1.3 80.7 - - + +
86G LEU* 1.3 59.9 + - - +
88G LEU* 3.5 8.2 + - + +
89G ALA* 3.0 29.3 + - - +
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Residues in contact with LEU 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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65G VAL* 4.0 10.8 - - + -
66G LEU* 5.2 2.7 - - + -
69G ALA* 3.6 24.0 - - + -
81G ILE* 4.1 8.5 - - + -
82G THR 3.2 7.7 + - - +
83G PRO* 3.5 7.2 - - + +
85G HIS* 1.3 77.8 - - - +
87G GLN* 1.3 57.2 + - - +
89G ALA* 3.3 2.4 + - - +
90G ILE* 3.0 38.1 + - + +
104G ILE* 4.7 7.9 - - + -
54H ILE* 5.9 0.4 - - + -
58H ALA* 3.5 37.5 - - + +
61H ILE* 3.7 27.4 - - + -
62H MET* 3.9 24.0 - - + -
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Residues in contact with GLN 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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83G PRO 3.0 11.9 + - - +
84G ARG* 3.3 8.0 + - - +
86G LEU* 1.3 77.4 - - - +
88G LEU* 1.3 62.9 + - + +
90G ILE* 3.5 1.6 + - - -
91G ARG* 3.1 62.0 + - + +
104G ILE* 3.3 31.9 + - + +
107G GLY* 3.2 31.6 - - - +
108G GLY 3.1 20.2 + - - +
109G VAL* 4.2 10.3 - - - +
110G ILE* 4.8 2.5 - - + +
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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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72G ALA* 4.9 15.7 - - + -
76G LEU* 5.1 12.6 - - + -
84G ARG* 3.0 59.6 + - + +
85G HIS* 3.8 12.1 - - + +
87G GLN* 1.3 75.9 - - + +
89G ALA* 1.3 58.3 + - - +
92G GLY* 3.1 25.6 + - - -
110G ILE* 4.0 26.9 - - + +
111G PRO* 4.5 6.7 - - + -
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Residues in contact with ALA 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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65G VAL* 4.4 3.8 - - + +
68G LEU* 3.7 23.9 - - + +
69G ALA* 3.6 29.2 - - + +
72G ALA* 5.7 0.9 - - - +
85G HIS 3.0 17.4 + - - +
86G LEU* 3.7 4.7 - - - +
87G GLN 3.2 0.2 - - - -
88G LEU* 1.3 78.2 - - - +
90G ILE* 1.3 68.0 + - + +
92G GLY* 4.1 1.3 - - - -
93G ASP* 3.5 21.0 + - - +
96G LEU* 4.3 0.3 - - - +
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Residues in contact with ILE 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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65G VAL* 3.9 22.7 - - + -
86G LEU* 3.0 20.9 + - + +
87G GLN* 4.0 4.7 - - - +
88G LEU 3.4 0.2 - - - -
89G ALA* 1.3 74.9 - - + +
91G ARG* 1.3 79.1 + - - +
92G GLY 3.1 4.0 - - - -
93G ASP* 2.9 28.9 + - - +
96G LEU* 3.5 44.4 - - + +
97G ASP* 3.4 8.5 + - - -
100G ILE* 3.6 28.5 - - + -
104G ILE* 5.3 9.4 - - + -
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Residues in contact with ARG 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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87G GLN* 3.1 52.1 + - + +
90G ILE* 1.3 87.5 - - - +
92G GLY* 1.3 58.9 + - - +
93G ASP 3.2 2.2 + - - +
97G ASP* 2.8 46.1 + - - +
100G ILE* 2.6 27.1 + - - +
101G LYS* 4.5 6.9 - - - +
102G ALA 2.9 27.9 + - - +
104G ILE* 4.2 7.9 - - - +
110G ILE* 3.5 27.1 - - + +
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Residues in contact with GLY 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 LEU 3.1 18.7 + - - -
89G ALA* 4.1 2.5 - - - -
90G ILE 3.1 1.0 - - - -
91G ARG* 1.3 79.2 - - - +
93G ASP* 1.3 58.3 + - - +
94G GLU 4.2 1.4 + - - -
110G ILE* 4.4 6.3 - - - -
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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