Contacts of the helix formed by residues 86 - 93 (chain G) in PDB entry 2ONK
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 SER 86 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85G LEU* 1.3 75.8 - - - +
87G VAL* 1.3 66.7 + - - +
88G TYR* 3.7 2.1 - - - +
89G ARG* 2.9 30.0 + - - +
90G ASN* 2.7 21.1 + - - +
120G LEU 3.5 10.4 + - - -
121G ASP* 3.6 17.9 + - - -
122G ARG 3.1 14.1 - - - -
123G LYS* 3.9 13.4 - - - +
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Residues in contact with VAL 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LEU 3.8 0.8 + - - -
86G SER* 1.3 69.8 - - - +
88G TYR* 1.3 64.4 + - - +
90G ASN* 3.1 9.8 + - - +
91G ILE* 2.9 41.1 + - + +
116G ILE* 4.5 7.6 - - + +
119G LEU* 3.2 34.1 - - + +
120G LEU* 4.2 8.3 - - + -
122G ARG 2.8 16.7 + - - +
123G LYS* 4.7 0.9 - - - +
124G PRO* 5.2 0.6 - - + +
127G LEU* 3.9 36.6 - - + -
135G VAL* 3.7 23.8 - - + -
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Residues in contact with TYR 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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86G SER* 3.7 3.6 - - - +
87G VAL* 1.3 76.3 - - - +
89G ARG* 1.3 66.3 + - + +
91G ILE* 3.0 8.8 + - - +
92G ALA* 2.8 48.8 + - + +
104G ASP* 2.8 42.4 + - - +
107G VAL* 3.8 25.2 - - + +
108G ARG* 4.0 19.5 - - - -
120G LEU* 3.0 49.7 + - + +
121G ASP* 5.6 1.1 - - - +
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Residues in contact with ARG 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 LEU* 3.7 39.0 - - + +
86G SER* 2.9 21.7 + - - +
88G TYR* 1.3 86.6 - - + +
90G ASN* 1.3 61.4 + - - +
92G ALA* 3.7 5.9 - - - +
93G TYR* 3.0 23.2 + - - +
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Residues in contact with ASN 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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81G LEU* 4.6 9.1 - - + +
82G PHE* 3.0 43.5 + - - +
85G LEU* 2.8 33.0 + - - +
86G SER 2.7 12.5 + - - -
87G VAL* 3.2 13.9 - - - +
89G ARG* 1.3 73.4 - - - +
91G ILE* 1.3 65.4 + - - +
93G TYR* 3.1 21.9 + - - +
124G PRO* 4.0 7.5 - - - +
135G VAL* 4.3 10.4 - - + +
139G ARG* 3.4 27.9 + - - -
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Residues in contact with ILE 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 VAL* 2.9 38.9 + - + +
88G TYR* 3.5 4.5 - - - +
90G ASN* 1.3 74.7 - - - +
92G ALA* 1.3 63.2 + - - +
93G TYR 3.2 9.4 - - - +
95G LEU* 4.5 7.4 - - - +
107G VAL* 4.0 22.0 - - + +
110G MET* 5.1 0.4 - - + -
111G ALA* 4.5 7.6 - - + -
116G ILE* 4.0 8.7 - - + -
120G LEU* 4.4 13.0 - - + -
135G VAL* 4.3 7.4 - - + +
138G ALA* 3.8 26.5 - - + -
139G ARG* 3.8 19.7 - - - +
142G VAL* 3.5 31.3 - - + +
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Residues in contact with ALA 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 TYR* 2.8 31.6 + - + +
89G ARG* 3.8 10.1 - - + +
91G ILE* 1.3 71.1 - - - +
93G TYR* 1.3 65.1 + - - +
95G LEU* 3.0 27.0 + - - +
96G ARG 4.3 1.0 + - - -
103G ARG* 4.5 13.4 + - + +
107G VAL* 3.9 21.5 - - + +
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Residues in contact with TYR 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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82G PHE* 3.4 31.4 - + + -
84G HIS* 6.2 0.2 - - - -
85G LEU* 4.3 11.0 - - + -
89G ARG 3.0 13.8 + - - +
90G ASN 3.1 14.1 + - - +
91G ILE 3.2 10.4 - - - +
92G ALA* 1.3 76.1 - - - +
94G GLY* 1.3 63.7 + - - +
95G LEU* 5.0 0.2 - - - +
96G ARG* 5.6 0.4 - - - +
139G ARG* 4.9 6.2 - - - +
143G ILE* 5.0 1.2 - - - +
162I ALA* 3.6 29.6 - - + +
165I LEU* 3.6 30.0 - - + +
167I SER* 2.8 29.8 + - - -
172I VAL* 4.6 0.9 - - - -
175I THR* 4.1 32.9 + - + -
176I VAL* 4.2 4.7 - - + +
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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