Contacts of the helix formed by residues 98 - 111 (chain I) 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 PRO 98 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H ILE* 3.8 15.0 - - + +
198H SER* 3.4 28.4 - - - +
213H ALA* 5.7 0.7 - - + -
214H PRO* 3.9 15.5 - - + -
236H LEU* 4.5 19.7 - - + +
240H SER* 4.6 6.1 - - - +
96I VAL 3.3 10.3 - - - +
97I ILE* 1.3 85.7 - - + +
99I HIS* 1.3 68.7 + - - +
100I THR 3.3 1.1 - - - +
101I VAL* 3.0 39.2 + - + +
102I ALA 3.1 8.8 + - - -
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Residues in contact with HIS 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H HIS* 3.8 17.3 + + - -
195H ARG* 4.2 9.6 - - - -
198H SER* 2.9 31.1 + - - +
199H GLU* 3.0 22.4 + - - -
200H PHE* 3.4 25.1 - - + +
97I ILE 3.4 2.0 + - - -
98I PRO* 1.3 68.9 - - - +
100I THR* 1.3 66.1 + - - +
102I ALA* 2.9 20.4 + - - +
103I GLY 3.0 10.0 + - - -
138I VAL* 4.8 3.8 - - - +
195I ARG* 3.4 28.7 + - - -
199I GLU* 3.5 18.2 + - - +
201I GLY* 3.8 6.1 - - - -
202I ALA* 3.3 12.6 - - - +
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Residues in contact with THR 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H PHE* 3.7 26.4 - - - +
214H PRO* 3.1 26.6 + - - +
217H ILE* 3.3 39.0 - - + -
218H TYR* 3.9 10.7 - - + +
221H TYR* 6.1 0.2 - - + -
98I PRO* 3.3 1.0 - - - +
99I HIS* 1.3 76.5 - - - +
101I VAL* 1.3 64.9 + - - +
103I GLY* 2.9 4.7 + - - -
104I ILE* 2.9 25.1 + - + +
201I GLY* 4.3 2.1 - - - -
202I ALA 4.2 0.2 - - - +
205I VAL* 4.2 16.3 - - + +
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Residues in contact with VAL 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H PRO* 6.1 0.4 - - + -
217H ILE* 3.5 26.9 - - + -
233H ALA* 3.8 17.3 - - + +
236H LEU* 4.1 8.3 - - + -
237H ILE* 3.4 37.9 - - + -
97I ILE* 3.5 9.4 - - + -
98I PRO* 3.0 32.6 + - + +
100I THR* 1.3 76.3 - - - +
102I ALA* 1.3 55.2 + - - +
104I ILE* 3.1 7.1 + - - +
105I ALA* 2.7 34.8 + - + +
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Residues in contact with ALA 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H VAL* 6.5 0.2 - - - -
97I ILE* 3.6 12.4 - - + +
98I PRO 3.1 5.7 + - - +
99I HIS* 2.9 15.6 + - - +
101I VAL* 1.3 79.0 - - - +
103I GLY* 1.3 52.1 + - - +
105I ALA* 3.5 4.8 - - - +
106I LEU* 2.7 41.9 + - + +
137I PHE* 3.9 33.7 - - + -
138I VAL* 5.4 2.0 - - + -
202I ALA* 4.1 10.8 - - + -
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Residues in contact with GLY 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I HIS 3.0 6.5 + - - -
100I THR 2.9 5.7 + - - -
102I ALA* 1.3 76.7 - - - +
104I ILE* 1.3 51.0 + - - +
106I LEU* 3.0 4.2 + - - +
107I LEU* 2.7 35.0 + - - +
202I ALA* 3.3 28.4 - - - +
205I VAL* 3.1 14.4 - - - +
206I ILE* 4.0 7.0 - - - +
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Residues in contact with ILE 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H THR* 5.4 2.0 - - + -
217H ILE* 3.1 35.4 - - + -
221H TYR* 4.6 17.3 - - + -
226H LEU* 4.4 11.8 - - + +
229H ALA* 3.6 21.1 - - + -
230H MET* 4.6 6.5 - - - -
233H ALA* 3.9 23.6 - - + -
100I THR* 2.9 15.0 + - + +
101I VAL* 3.5 6.7 - - - +
103I GLY* 1.3 74.7 - - - +
105I ALA* 1.3 60.9 + - - +
107I LEU* 3.1 7.7 + - - +
108I VAL* 2.9 40.5 + - + +
205I VAL* 3.2 13.7 - - + +
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Residues in contact with ALA 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H PRO* 3.4 14.3 - - + +
24H VAL* 3.9 12.1 - - + +
27H THR* 3.3 29.2 - - + +
233H ALA* 6.3 0.2 - - + -
237H ILE* 4.8 5.8 - - + -
97I ILE* 6.0 0.7 - - + -
101I VAL* 2.7 21.7 + - + +
102I ALA* 3.5 6.5 - - - +
104I ILE* 1.3 73.6 - - + +
106I LEU* 1.3 63.2 + - - +
108I VAL* 3.1 15.8 + - - +
109I VAL* 3.3 13.0 - - - +
137I PHE* 6.4 0.7 - - + -
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Residues in contact with LEU 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE* 4.5 3.6 - - + -
23H PRO* 4.0 24.0 - - + -
102I ALA 2.7 25.4 + - - +
103I GLY* 3.3 7.6 - - - +
105I ALA* 1.3 72.5 - - - +
107I LEU* 1.3 57.3 + - - +
109I VAL* 2.9 16.6 + - - -
110I PHE* 2.9 28.3 + - + +
133I VAL* 3.2 28.9 - - + +
134I ALA* 3.4 33.4 - - - +
137I PHE* 4.2 20.4 - - + -
202I ALA* 5.1 3.4 - - + -
206I ILE* 3.5 18.6 - - + -
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Residues in contact with LEU 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H TYR* 3.5 29.2 - - + +
226H LEU* 4.2 25.7 - - + +
103I GLY 2.7 15.5 + - - +
104I ILE* 3.2 10.1 - - - +
106I LEU* 1.3 69.2 - - - +
108I VAL* 1.3 57.1 + - - +
109I VAL 2.8 6.9 + - - -
110I PHE* 4.9 0.7 - - - -
111I GLY* 2.5 54.8 + - - +
113I SER* 6.0 0.6 - - - -
114I GLY 4.7 0.7 + - - -
125I VAL* 4.6 10.3 - - + -
205I VAL* 3.4 26.5 - - + +
206I ILE* 4.8 12.7 - - + +
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Residues in contact with VAL 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 4.6 5.9 - - + +
27H THR* 4.0 20.9 - - + +
30H LEU* 3.7 20.1 - - + +
226H LEU* 4.4 10.3 - - + -
230H MET* 3.3 40.6 - - + -
104I ILE* 2.9 30.2 + - + +
105I ALA 3.1 9.6 + - - +
107I LEU* 1.3 74.6 - - - +
109I VAL* 1.3 58.9 + - - +
113I SER* 6.3 0.2 - - - -
114I GLY* 3.0 25.5 - - - +
115I LEU* 3.8 2.4 + - - +
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Residues in contact with VAL 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU* 3.9 16.8 - - + -
23H PRO* 3.3 25.8 - - + -
26H ALA* 4.3 13.7 - - + -
105I ALA 3.3 16.6 - - - +
106I LEU 2.9 6.8 + - - +
107I LEU 2.8 0.4 - - - -
108I VAL* 1.3 84.9 - - + +
110I PHE* 1.3 68.2 + - + +
111I GLY 3.6 0.7 - - - -
114I GLY* 4.6 2.0 - - - -
115I LEU* 4.6 6.1 - - + +
116I ILE* 3.0 46.4 + - + +
117I GLY 2.7 25.7 + - - -
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Residues in contact with PHE 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE* 4.3 14.4 - + - -
23H PRO* 5.5 3.6 - - + -
106I LEU* 2.9 28.1 + - + +
107I LEU* 4.9 0.7 - - - -
109I VAL* 1.3 90.9 - - + +
111I GLY* 1.3 64.8 + - - +
112I SER 3.7 1.6 + - - -
116I ILE* 4.3 26.5 - - + -
117I GLY* 3.3 16.4 - - - +
124I PHE* 3.5 66.5 + + + +
125I VAL* 4.3 2.3 - - - +
130I GLY* 6.1 0.4 - - - -
133I VAL* 3.9 37.7 - - + -
206I ILE* 5.7 5.2 - - + -
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Residues in contact with GLY 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I LEU* 2.5 45.6 + - - +
110I PHE* 1.3 75.9 - - - +
112I SER* 1.3 68.7 + - - +
113I SER* 2.6 6.3 + - - -
114I GLY 2.9 14.3 + - - +
117I GLY* 3.4 5.6 - - - -
125I VAL* 3.8 8.7 - - - -
206I ILE* 6.6 0.2 - - - -
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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