Contacts of the helix formed by residues 79 - 90 (chain M) in PDB entry 5OXV
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 ILE 79 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-176J A 5.4 9.6 - - - +
75M LYS* 5.3 10.1 - - - -
77M ARG* 3.5 5.4 + - + +
78M ILE* 1.3 78.8 - - - +
80M PRO* 1.3 77.1 - - + +
81M ARG* 3.1 18.2 - - + +
82M HIS* 2.9 45.3 + - + +
83M LEU 3.5 2.8 + - - -
52N SER* 3.6 20.2 - - - +
55N ALA* 3.8 4.0 - - - -
58O THR* 6.0 1.8 - - - +
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Residues in contact with PRO 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M ILE* 1.3 89.8 - - + +
81M ARG* 1.3 62.9 + - - +
83M LEU* 3.0 9.2 + - + +
84M GLN* 2.9 19.8 + - - +
102M ILE* 4.3 3.3 - - + +
103M ALA 3.2 24.9 - - - +
104M GLN* 3.4 18.8 - - + +
105M GLY* 4.8 0.2 - - - -
52N SER* 3.8 11.0 - - - +
54N LYS* 3.9 22.7 - - + -
55N ALA* 3.7 6.3 - - + +
58N ILE* 3.3 26.2 - - + -
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Residues in contact with ARG 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M ASN* 5.2 4.5 - - - +
79M ILE* 3.0 18.4 + - + +
80M PRO* 1.3 78.0 - - - +
82M HIS* 1.3 61.2 + - + +
84M GLN* 2.9 5.4 + - - +
85M LEU* 2.7 71.0 + - + +
104M GLN 3.5 6.9 + - - +
105M GLY 2.8 31.2 + - - -
106M GLY* 3.3 2.6 - - - -
107M VAL 2.6 38.6 + - - +
109M PRO* 5.2 4.6 - - - +
55O GLN 3.5 16.7 + - - -
56O LYS* 4.3 15.9 + - - +
57O SER 5.0 0.2 - - - -
58O THR* 3.1 24.2 - - + +
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Residues in contact with HIS 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M ALA* 3.6 19.1 - - - +
69M ALA* 4.0 12.8 - - - +
70M ALA* 3.6 23.1 - - + +
73M ASN* 3.9 25.1 + - + +
75M LYS* 4.2 14.6 - - + +
77M ARG 3.5 15.0 - - - -
78M ILE* 3.4 16.9 - - + -
79M ILE* 2.9 47.2 + - + +
81M ARG* 1.3 83.6 - - + +
83M LEU* 1.3 62.3 + - - +
85M LEU* 4.5 2.7 - - + -
86M ALA* 3.1 24.4 + - - +
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Residues in contact with LEU 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M ILE* 3.6 29.2 - - + -
63M LEU* 5.6 2.9 - - + -
66M ALA* 3.7 16.4 - - + -
78M ILE* 4.2 13.7 - - + -
79M ILE 3.5 0.9 + - - +
80M PRO* 3.0 7.9 + - + +
82M HIS* 1.3 74.2 - - - +
84M GLN* 1.3 67.8 + - - +
86M ALA* 2.9 4.8 + - - +
87M VAL* 2.8 31.2 + - + +
102M ILE* 4.7 9.4 - - + -
51N ILE* 5.8 0.2 - - + -
55N ALA* 3.7 35.2 - - + +
58N ILE* 3.7 28.0 - - + -
59N MET* 3.9 15.5 - - + -
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Residues in contact with GLN 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M PRO 2.9 6.3 + - - +
81M ARG* 2.9 12.4 + - - +
83M LEU* 1.3 75.3 - - - +
85M LEU* 1.3 59.7 + - + +
87M VAL* 3.0 1.8 + - - -
88M ARG* 2.8 80.5 + - + +
102M ILE* 3.8 20.6 + - + +
105M GLY* 3.3 36.7 - - - +
106M GLY 2.7 23.2 + - - +
107M VAL* 4.4 7.3 - - - +
108M LEU* 5.7 0.9 - - + +
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Residues in contact with LEU 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M ALA* 4.5 8.7 - - + -
73M ASN* 3.7 30.5 - - - +
81M ARG* 2.7 65.6 + - + +
82M HIS* 4.0 9.0 - - + +
84M GLN* 1.3 71.7 - - + +
86M ALA* 1.3 63.3 + - - +
89M ASN* 2.8 38.5 + - - +
108M LEU* 3.5 27.1 - - + -
109M PRO* 5.1 3.8 - - + -
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Residues in contact with ALA 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M ILE* 4.5 4.9 - - + +
65M LEU* 3.6 20.4 - - + +
66M ALA* 3.4 28.9 - - + +
69M ALA* 4.8 1.3 - - - +
82M HIS 3.1 18.9 + - - +
83M LEU* 2.9 5.8 + - - +
85M LEU* 1.3 77.1 - - - +
87M VAL* 1.3 59.9 - - + +
89M ASN* 4.2 1.8 - - - +
90M ASP* 3.2 28.8 + - - +
93M LEU* 4.4 5.4 - - + +
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Residues in contact with VAL 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M ILE* 4.1 22.0 - - + -
83M LEU* 2.8 25.3 + - + +
84M GLN* 3.5 5.8 - - - +
86M ALA* 1.3 78.8 - - + +
88M ARG* 1.3 84.7 + - - +
90M ASP* 2.9 26.0 + - - +
93M LEU* 4.4 7.4 - - + +
94M ASN* 3.3 16.6 + - - +
97M LEU* 3.6 33.7 - - + -
102M ILE* 4.2 8.1 - - + -
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Residues in contact with ARG 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M GLN* 2.8 59.7 + - + +
87M VAL* 1.3 87.5 - - - +
89M ASN* 1.3 61.3 + - - +
90M ASP 4.0 4.0 - - - +
91M GLU* 5.4 0.7 - - - -
94M ASN* 2.9 33.3 + - - +
97M LEU* 2.8 28.3 + - - +
98M GLY* 4.8 1.6 + - - -
100M VAL 2.7 29.5 + - - -
101M THR* 4.9 0.2 - - - +
102M ILE* 4.2 13.1 - - - +
108M LEU* 3.7 31.2 - - + +
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Residues in contact with ASN 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M LEU* 2.8 34.7 + - - +
86M ALA* 4.5 1.6 - - - +
88M ARG* 1.3 76.4 - - - +
90M ASP* 1.3 61.7 + - - +
91M GLU* 3.4 3.8 + - - +
108M LEU* 3.3 34.6 - - - +
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Residues in contact with ASP 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M GLU* 4.9 5.5 - - - +
65M LEU* 3.7 17.3 - - + +
86M ALA 3.2 20.3 + - - +
87M VAL 2.9 17.4 + - - +
88M ARG 4.3 0.7 - - - -
89M ASN* 1.3 75.4 - - - +
91M GLU* 1.3 75.3 + - - +
92M GLU* 3.1 14.0 + - - +
93M LEU* 3.3 39.4 + - + +
94M ASN* 3.0 14.3 + - - +
103N LEU* 5.5 2.6 - - - +
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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