Contacts of the helix formed by residues 83 - 97 (chain C) 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 GLY 83 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C PHE* 3.4 9.8 - - - -
82C PRO* 1.3 85.2 - - - +
84C LYS* 1.3 66.7 + - - +
85C SER* 2.6 2.3 + - - -
86C VAL* 2.6 26.9 + - - +
87C VAL* 4.3 8.1 - - - -
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Residues in contact with LYS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE 4.4 0.4 - - - -
76C LEU* 2.7 45.5 + - + +
77C ALA 5.1 0.6 + - - -
78C ARG 4.8 1.8 + - - -
79C LYS 3.1 20.9 + - - -
80C SER* 4.1 16.0 - - - -
81C PHE* 2.9 49.3 - - + +
82C PRO 4.9 0.2 - - - +
83C GLY* 1.3 70.7 - - - +
85C SER* 1.3 58.7 + - - +
87C VAL* 2.8 5.0 + - - -
88C GLU* 2.6 55.9 + - + +
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO 4.4 7.0 + - - -
83C GLY 2.6 5.8 + - - -
84C LYS* 1.3 75.2 - - - +
86C VAL* 1.3 63.1 + - - -
88C GLU* 3.7 10.3 + - - +
89C GLY* 3.2 14.2 + - - -
248D ARG* 3.7 15.0 + - - +
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Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLY* 2.6 18.9 + - - +
85C SER* 1.3 72.2 - - - +
87C VAL* 1.3 63.6 + - + +
88C GLU 3.0 1.3 - - - -
89C GLY* 2.7 24.2 + - - -
90C ILE* 2.9 33.8 + - + +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 3.9 18.6 - - + -
76C LEU* 4.1 11.4 - - + -
81C PHE* 3.9 25.1 - - + -
83C GLY* 4.3 4.5 - - - -
84C LYS* 2.8 16.4 + - - +
86C VAL* 1.3 79.9 - - + +
88C GLU* 1.3 60.4 + - - +
90C ILE* 3.6 6.0 + - + +
91C VAL* 3.3 21.7 + - + +
17D LEU* 3.8 34.5 - - + +
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LEU* 4.2 22.5 - - + +
84C LYS* 2.6 46.9 + - - +
85C SER* 3.9 13.3 + - - +
87C VAL* 1.3 73.0 - - - +
89C GLY* 1.3 61.3 + - - +
91C VAL* 3.4 9.6 - - - +
92C ASP* 3.0 28.6 + - - +
148C LYS* 4.0 19.0 + - - +
248D ARG* 4.5 12.5 + - - +
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Residues in contact with GLY 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C SER 3.2 6.0 + - - -
86C VAL* 2.7 14.3 + - - -
88C GLU* 1.3 71.5 - - - +
90C ILE* 1.3 64.2 + - - -
92C ASP* 2.8 16.5 + - - +
93C LEU* 3.0 12.0 + - - +
248D ARG* 3.9 18.1 - - - +
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Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C VAL* 2.9 34.0 + - + +
87C VAL* 3.8 8.5 - - + +
89C GLY* 1.3 74.3 - - - +
91C VAL* 1.3 61.6 + - - +
93C LEU* 3.1 21.6 + - + +
17D LEU* 3.6 40.2 - - + +
20D VAL* 3.2 23.8 - - + +
21D LEU* 3.8 35.0 - - + -
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 3.6 30.7 - - + -
76C LEU* 4.5 11.0 - - + -
87C VAL 3.3 14.7 + - - +
88C GLU* 3.4 11.2 - - - +
90C ILE* 1.3 78.5 - - - +
92C ASP* 1.3 63.0 + - - +
93C LEU 3.7 0.2 + - - -
94C PRO* 3.8 5.5 - - - +
140C VAL* 5.6 1.8 - - - +
141C PRO* 3.1 26.4 - - + +
144C ILE* 4.0 23.1 - - + -
145C ASN* 4.0 20.9 - - - +
17D LEU* 4.1 5.6 - - + -
20D VAL* 5.0 5.4 - - - +
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Residues in contact with ASP 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLU* 3.0 17.1 + - - +
89C GLY* 2.8 11.0 + - - +
91C VAL* 1.3 83.0 - - - +
93C LEU* 1.3 67.6 + - - +
94C PRO* 3.3 2.5 - - - -
95C VAL* 2.9 32.7 + - + +
96C VAL* 3.9 7.6 + - + +
141C PRO* 4.6 2.6 - - - +
145C ASN* 4.1 23.5 + - - +
248D ARG* 3.4 19.8 + - - +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C GLY 3.0 7.2 + - - +
90C ILE* 3.1 21.7 + - + +
92C ASP* 1.3 74.4 - - - +
94C PRO* 1.3 62.1 - - + +
95C VAL 2.7 0.2 + - - -
96C VAL* 2.7 35.5 + - + +
97C ILE* 3.4 20.7 + - + +
20D VAL* 3.4 25.4 - - + +
21D LEU* 3.9 21.5 - - + -
24D VAL* 3.8 24.0 - - + -
241D LEU* 3.6 31.4 - - + -
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Residues in contact with PRO 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL 3.8 6.3 - - - +
92C ASP 3.5 0.2 - - - -
93C LEU* 1.3 94.9 - - + +
95C VAL* 1.3 59.4 + - - +
96C VAL 3.2 1.0 + - - -
97C ILE* 3.5 18.0 - - + +
137C PHE* 3.1 50.8 - - + +
138C VAL* 4.6 12.6 - - - +
141C PRO* 3.6 27.6 - - + -
20D VAL* 3.4 20.9 - - + -
198D SER* 5.0 1.2 + - - -
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Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASP* 2.9 31.1 + - + +
93C LEU 2.7 3.2 + - - -
94C PRO* 1.3 74.0 - - - +
96C VAL* 1.3 60.2 + - + +
141C PRO* 4.3 20.0 - - + -
142C ILE* 6.3 1.6 - - + -
142D ILE* 6.0 5.8 - - + -
191D MET* 5.2 13.0 - - + +
194D ALA* 3.6 25.6 - - + +
195D ARG* 5.1 4.1 - - - +
198D SER* 3.6 12.8 + - - -
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASP* 4.1 9.9 - - + +
93C LEU* 2.7 14.9 + - + +
95C VAL* 1.3 85.4 - - + +
97C ILE* 1.3 58.9 + - + +
98C PRO* 3.3 12.1 - - - +
194D ALA* 4.8 4.3 - - + -
197D ILE* 4.3 5.5 - - - +
198D SER* 3.5 7.2 + - - -
240D SER* 3.0 38.7 + - - -
241D LEU* 4.9 2.5 - - + +
244D PHE* 3.1 46.4 - - + -
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C LEU* 3.4 24.6 + - + +
94C PRO* 3.5 15.2 + - + +
96C VAL* 1.3 80.2 - - + +
98C PRO* 1.4 73.3 - - + +
99C HIS* 3.5 3.6 + - - -
101C VAL* 3.5 31.9 - - + -
102C ALA* 3.6 17.3 - - + +
105C ALA* 6.0 0.4 - - + -
137C PHE* 4.0 12.1 - - + -
24D VAL* 3.4 44.0 - - + -
198D SER* 3.6 4.5 + - - -
237D ILE* 4.8 14.6 - - + +
240D SER* 5.3 2.0 - - - -
241D LEU* 6.3 0.4 - - + -
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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