Contacts of the helix formed by residues 98 - 111 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C ILE* 3.9 8.5 - - + +
198C SER* 3.3 30.0 - - - +
213C ALA* 5.7 0.9 - - + -
214C PRO* 3.7 24.2 - - + -
236C LEU* 4.6 16.2 - - + +
237C ILE* 6.3 0.9 - - - -
240C SER* 4.9 4.7 - - - +
96D VAL 3.3 10.3 - - - +
97D ILE* 1.3 84.7 - - + +
99D HIS* 1.3 68.7 + - - +
100D THR 3.3 1.1 - - - +
101D VAL* 3.0 38.5 + - + +
102D ALA 3.1 9.4 + - - -
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Residues in contact with HIS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS* 3.7 19.1 + + - -
195C ARG* 3.8 11.4 + - - -
198C SER* 3.0 29.4 + - - +
199C GLU* 2.9 22.7 + - - -
200C PHE* 3.4 23.3 - - + -
214C PRO* 5.7 0.2 - - - +
97D ILE 3.5 2.0 + - - -
98D PRO* 1.3 68.9 - - - +
100D THR* 1.3 64.5 + - - +
102D ALA* 2.9 19.7 + - - +
103D GLY 3.0 11.1 + - - -
138D VAL* 4.7 3.9 - - - +
195D ARG* 3.3 30.0 + - - -
199D GLU* 3.5 18.9 + - - +
201D GLY* 4.0 6.5 - - - -
202D ALA* 3.4 12.2 - - - +
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PHE* 3.6 29.0 - - - +
214C PRO* 3.2 34.4 + - - +
217C ILE* 3.6 25.6 - - + -
218C TYR* 3.9 15.7 - - + +
221C TYR* 6.2 0.2 - - + -
98D PRO 3.2 0.8 + - - -
99D HIS* 1.3 76.7 - - - +
101D VAL* 1.3 64.8 + - - +
103D GLY* 2.9 4.9 + - - +
104D ILE* 2.9 25.8 + - + +
201D GLY 4.4 8.7 - - - -
202D ALA 4.3 0.2 - - - +
205D VAL* 4.4 5.9 - - + +
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C PRO* 5.8 0.7 - - + -
217C ILE* 3.5 28.3 - - + -
233C ALA* 3.9 18.2 - - + +
236C LEU* 4.2 7.6 - - + -
237C ILE* 3.7 27.8 - - + +
97D ILE* 3.6 16.2 - - + -
98D PRO* 3.0 32.2 + - + +
100D THR* 1.3 75.9 - - - +
102D ALA* 1.3 65.2 + - - +
104D ILE* 3.1 7.3 + - - +
105D ALA* 2.7 24.8 + - + +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ILE* 3.6 12.4 - - + +
98D PRO 3.1 6.8 + - - +
99D HIS* 2.9 14.6 + - - +
101D VAL* 1.3 78.3 - - - +
103D GLY* 1.3 52.9 + - - +
105D ALA* 3.2 5.5 + - - +
106D LEU* 2.7 41.7 + - + +
137D PHE* 3.7 34.3 - - + -
138D VAL* 5.3 2.7 - - + -
202D ALA* 4.1 10.1 - - + -
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Residues in contact with GLY 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS 3.0 7.5 + - - -
100D THR 2.9 7.1 + - - -
102D ALA* 1.3 75.4 - - - +
104D ILE* 1.3 50.9 + - - +
106D LEU* 3.0 6.4 + - - +
107D LEU* 2.7 35.7 + - - +
202D ALA* 3.4 29.0 - - - +
205D VAL* 3.3 12.1 - - - +
206D ILE* 4.0 6.3 - - - +
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C THR* 5.6 1.6 - - + -
217C ILE* 3.0 37.2 - - + -
221C TYR* 4.4 21.1 - - + -
226C LEU* 4.4 11.8 - - + +
229C ALA* 3.8 17.9 - - + -
230C MET* 4.9 5.6 - - + -
233C ALA* 4.1 20.6 - - + -
100D THR* 2.9 16.3 + - + +
101D VAL* 3.5 7.6 - - - +
103D GLY* 1.3 74.6 - - - +
105D ALA* 1.3 59.9 + - - +
107D LEU* 3.1 7.8 + - - +
108D VAL* 2.9 40.7 + - + +
205D VAL* 3.4 13.3 - - + +
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PRO* 3.5 14.7 - - + +
24C VAL* 4.1 11.2 - - + +
27C THR* 3.5 28.0 - - + +
237C ILE* 5.0 1.6 - - + -
97D ILE* 6.0 0.9 - - + -
101D VAL* 2.7 26.5 + - + +
102D ALA* 3.5 6.1 - - - +
104D ILE* 1.3 74.9 - - + +
106D LEU* 1.3 62.8 + - - +
108D VAL* 3.1 15.6 + - - +
109D VAL* 3.4 12.1 - - - +
137D PHE* 6.2 1.3 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 4.4 4.9 - - + -
23C PRO* 4.2 22.9 - - + -
102D ALA 2.7 24.2 + - - +
103D GLY* 3.3 7.9 - - - +
105D ALA* 1.3 72.7 - - - +
107D LEU* 1.3 57.1 + - - +
109D VAL* 2.9 16.6 + - - -
110D PHE* 3.0 27.2 + - + +
133D VAL* 3.3 44.2 - - + +
134D ALA* 3.4 19.3 - - + +
137D PHE* 4.0 22.9 - - + -
202D ALA* 5.0 2.0 - - + -
206D ILE* 3.6 17.9 - - + -
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C TYR* 3.2 39.9 - - + +
226C LEU* 4.5 21.9 - - + +
103D GLY 2.7 15.9 + - - +
104D ILE* 3.2 10.5 - - - +
106D LEU* 1.3 68.4 - - - +
108D VAL* 1.3 54.8 + - + +
109D VAL 2.8 10.3 + - - -
110D PHE* 5.0 0.7 - - - -
111D GLY* 2.5 55.5 + - - +
113D SER* 6.0 0.4 - - - -
114D GLY 4.7 0.5 + - - -
125D VAL* 4.6 9.4 - - + -
205D VAL* 3.5 20.2 - - + +
206D ILE* 4.8 13.4 - - + +
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA* 4.8 3.0 - - + +
27C THR* 4.1 16.2 - - + +
30C LEU* 4.0 17.3 - - + -
226C LEU* 4.2 19.7 - - + -
230C MET* 3.6 35.4 - - + -
104D ILE* 2.9 27.3 + - + +
105D ALA* 3.3 13.2 - - - +
107D LEU* 1.3 74.3 - - - +
109D VAL* 1.3 61.6 + - + +
114D GLY* 3.1 24.3 - - - +
115D LEU* 3.9 2.8 + - - +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 4.1 19.3 - - + -
23C PRO* 3.5 25.8 - - + -
26C ALA* 4.6 9.4 - - + -
105D ALA 3.4 14.4 - - - +
106D LEU 2.9 6.2 + - - +
107D LEU 2.8 2.4 + - - -
108D VAL* 1.3 88.7 - - + +
110D PHE* 1.3 67.5 + - + +
111D GLY 3.6 0.7 - - - -
114D GLY* 4.6 2.2 - - - -
115D LEU* 4.6 5.8 - - + +
116D ILE* 3.0 46.1 + - + +
117D GLY 2.7 25.8 + - - -
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Residues in contact with PHE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 4.3 14.6 - + - -
23C PRO* 5.7 3.4 - - + -
106D LEU* 3.0 25.2 + - + +
107D LEU* 5.0 0.9 - - - -
109D VAL* 1.3 90.9 - - + +
111D GLY* 1.3 63.7 - - - +
112D SER 3.6 1.6 + - - -
116D ILE* 4.3 25.8 - - + -
117D GLY* 3.3 16.4 - - - +
124D PHE* 3.4 67.6 + + + +
125D VAL* 4.3 3.2 - - - +
130D GLY* 6.1 0.2 - - - -
133D VAL* 3.9 37.7 - - + -
206D ILE* 5.7 4.7 - - + -
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Residues in contact with GLY 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 2.5 45.8 + - - +
110D PHE* 1.3 75.2 - - - +
112D SER* 1.3 57.3 + - - +
113D SER* 2.6 18.8 + - - -
114D GLY* 2.9 13.7 + - - +
117D GLY* 3.4 5.8 - - - -
125D VAL* 3.8 9.0 - - - -
206D 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