Contacts of the helix formed by residues 83 - 93 (chain G) in PDB entry 6M4G
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 83 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79G GLU* 5.9 5.4 - - + +
81G ASN* 4.0 1.8 - - - +
82G ILE* 1.3 72.5 - - - +
84G PRO* 1.3 73.0 - - - +
85G LEU* 3.5 17.5 + - + +
86G LEU* 3.0 47.6 + - + +
87G LEU* 3.2 16.2 - - - +
55H SER* 4.4 3.8 - - - -
58H ALA* 4.3 0.2 - - - -
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Residues in contact with PRO 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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82G ILE 4.6 0.2 - - - +
83G THR* 1.3 89.6 - - - +
85G LEU* 1.3 59.2 + - - +
86G LEU 3.2 0.2 - - - -
87G LEU* 3.2 11.8 + - + +
88G ASP* 2.9 29.1 + - - +
106G ILE* 4.1 9.2 - - + +
108G GLN* 4.6 15.9 - - - +
55H SER* 4.7 4.7 - - - +
57H LYS* 3.7 29.8 - - + -
58H ALA* 4.0 9.9 - - + +
61H ILE* 3.5 30.1 - - + -
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Residues in contact with LEU 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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83G THR* 3.1 16.2 + - + +
84G PRO* 1.3 77.7 - - - +
86G LEU* 1.3 58.0 + - + +
88G ASP* 4.5 1.1 - - + +
89G MET* 2.9 34.8 + - + +
108G GLN* 3.8 28.8 - - + +
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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
----------------------------------------------------------
70G ALA* 4.6 8.3 - - + +
73G GLU* 4.4 12.8 - - + +
74G ALA* 3.9 17.5 - - + +
77G SER* 4.6 2.2 - - - +
79G GLU* 4.4 16.2 - - + -
81G ASN 3.5 24.7 - - - +
82G ILE* 3.6 21.1 - - + -
83G THR* 3.0 22.4 + - + +
85G LEU* 1.3 79.3 - - + +
87G LEU* 1.3 56.8 + - - +
89G MET* 3.1 34.7 - - + +
90G VAL* 2.9 34.5 + - + +
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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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66G VAL* 5.6 3.1 - - + -
67G LEU* 5.7 0.7 - - + -
70G ALA* 5.0 6.3 - - + -
82G ILE* 3.5 22.7 - - + -
83G THR 3.2 24.9 - - - +
84G PRO* 3.2 8.6 + - + +
86G LEU* 1.3 79.5 - - - +
88G ASP* 1.3 57.5 + - - +
90G VAL* 3.1 9.3 - - + +
91G VAL* 2.9 41.6 + - + +
106G ILE* 4.7 8.1 - - + -
54H ILE* 5.7 0.7 - - + -
58H ALA* 3.7 13.2 - - + +
61H ILE* 3.5 35.9 - - + -
62H MET* 3.8 28.9 - - + -
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Residues in contact with ASP 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 PRO 2.9 13.1 + - - +
85G LEU* 4.0 2.9 - - + +
87G LEU* 1.3 77.5 - - - +
89G MET* 1.3 62.4 + - - +
92G HIS* 2.8 50.8 + - - +
106G ILE* 4.1 26.5 + - + +
108G GLN* 2.4 40.2 + - - +
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Residues in contact with MET 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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73G GLU* 3.6 38.6 - - + +
77G SER* 5.1 6.7 - - - -
85G LEU* 2.9 22.7 + - + +
86G LEU* 3.1 45.1 - - + +
88G ASP* 1.3 78.8 - - - +
90G VAL* 1.3 57.8 + - + +
92G HIS* 4.9 0.4 - - - +
93G ASN* 2.5 42.5 + - - +
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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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66G VAL* 5.1 6.5 - - + +
69G LEU* 4.1 17.3 - - + +
70G ALA* 4.5 13.5 - - + +
73G GLU* 3.5 37.2 - - + -
86G LEU 2.9 25.0 + - - +
87G LEU* 3.1 15.0 - - - +
89G MET* 1.3 81.7 - - + +
91G VAL* 1.3 79.4 + - + +
93G ASN* 2.8 31.8 + - - +
94G ASP* 3.6 10.1 - - + +
97G LEU* 5.0 1.8 - - + -
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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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66G VAL* 4.3 13.9 - - + -
87G LEU* 2.9 26.1 + - + +
90G VAL* 1.3 86.2 - - + +
92G HIS* 1.3 77.9 + - + +
93G ASN 3.6 0.9 - - - -
97G LEU* 3.7 17.3 - - + +
98G SER* 3.3 24.6 + - - +
101G PHE* 3.6 40.1 - - + +
106G ILE* 3.6 19.1 - - + -
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Residues in contact with HIS 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 ASP* 2.8 40.3 + - - +
89G MET* 4.9 0.4 - - - +
90G VAL 3.1 0.4 - - - -
91G VAL* 1.3 90.8 - - + +
93G ASN* 1.3 66.9 + - - +
98G SER* 3.9 10.7 - - - -
101G PHE* 3.6 22.2 + - + -
102G ASN* 5.4 2.2 + - - -
104G THR 3.4 25.5 + - - -
105G THR* 5.0 0.9 - - - -
106G ILE* 3.9 12.6 - - + -
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Residues in contact with ASN 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 MET* 2.5 33.4 + - - +
90G VAL* 2.8 13.4 + - - +
91G VAL* 3.5 2.4 - - - +
92G HIS* 1.3 82.7 - - - +
94G ASP* 1.3 73.2 + - + +
95G ARG 3.7 0.9 - - - -
98G SER* 3.3 8.6 + - - -
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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