Contacts of the helix formed by residues 98 - 111 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H VAL 3.3 10.7 - - - +
97H ILE* 1.3 85.8 - - + +
99H HIS* 1.3 68.3 + - - +
100H THR 3.3 0.9 - - - -
101H VAL* 3.0 39.4 + - + +
102H ALA 3.1 9.0 + - - -
197I ILE* 4.1 7.6 - - + +
198I SER* 3.5 26.5 - - - +
213I ALA* 5.8 0.2 - - + -
214I PRO* 3.7 23.3 - - + -
236I LEU* 4.3 20.4 - - + +
240I SER* 4.8 5.6 - - - +
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Residues in contact with HIS 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ILE 3.5 2.5 + - - -
98H PRO* 1.3 68.3 - - - +
100H THR* 1.3 65.5 + - - +
102H ALA* 2.9 20.1 + - - +
103H GLY 3.0 10.0 + - - -
138H VAL* 4.7 4.3 - - - +
195H ARG* 3.3 29.6 + - - -
199H GLU* 3.5 18.7 + - - +
201H GLY* 3.9 6.5 - - - -
202H ALA* 3.5 12.4 - - - +
99I HIS* 3.8 18.5 + + - -
195I ARG* 4.0 9.4 + - - -
198I SER* 3.1 31.0 + - - +
199I GLU* 3.1 22.4 + - - -
200I PHE* 3.5 23.1 - - + -
214I PRO* 5.4 0.2 - - - +
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Residues in contact with THR 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H PRO* 3.1 0.8 + - - +
99H HIS* 1.3 76.3 - - - +
101H VAL* 1.3 63.5 + - - +
103H GLY* 2.9 4.3 + - - -
104H ILE* 2.9 24.9 + - + +
201H GLY* 4.4 8.3 - - - -
202H ALA 4.3 0.4 - - - +
205H VAL* 4.5 9.9 - - + +
200I PHE* 4.0 20.3 - - - +
214I PRO* 2.9 28.5 + - - +
217I ILE* 3.2 39.0 - - + -
218I TYR* 3.6 15.7 - - + +
221I TYR* 5.9 0.4 - - + -
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Residues in contact with VAL 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ILE* 3.6 10.8 - - + -
98H PRO* 3.0 32.6 + - + +
100H THR* 1.3 76.7 - - - +
102H ALA* 1.3 54.5 + - - +
104H ILE* 3.1 6.6 + - - +
105H ALA* 2.7 34.5 + - + +
214I PRO* 5.9 0.2 - - + -
217I ILE* 3.3 28.5 - - + -
233I ALA* 3.7 17.9 - - + +
236I LEU* 4.1 7.4 - - + -
237I ILE* 3.6 34.5 - - + -
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Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ILE* 3.6 12.2 - - + +
98H PRO 3.1 5.3 + - - +
99H HIS* 2.9 16.5 + - - +
101H VAL* 1.3 80.0 - - - +
103H GLY* 1.3 51.1 + - - +
105H ALA* 3.2 5.1 + - - +
106H LEU* 2.7 41.8 + - + +
137H PHE* 3.6 34.7 - - + -
138H VAL* 5.4 2.7 - - + -
202H ALA* 4.3 9.4 - - + -
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Residues in contact with GLY 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H HIS 3.0 6.5 + - - -
100H THR 2.9 7.8 + - - -
102H ALA* 1.3 75.3 - - - +
104H ILE* 1.3 50.5 + - - +
106H LEU* 3.0 9.0 + - - +
107H LEU* 2.7 35.9 + - - +
202H ALA* 3.5 27.9 - - - +
205H VAL* 3.5 12.8 - - - +
206H ILE* 4.3 3.5 - - - +
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Residues in contact with ILE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H THR* 2.9 14.1 + - + +
101H VAL* 3.5 7.2 - - - +
103H GLY* 1.3 73.7 - - - +
105H ALA* 1.3 61.7 + - - +
107H LEU* 3.1 10.3 + - - +
108H VAL* 2.9 37.3 + - + +
205H VAL* 3.7 10.9 - - + +
27I THR* 5.5 1.6 - - + -
217I ILE* 3.1 35.7 - - + -
221I TYR* 4.5 18.4 - - + -
226I LEU* 4.3 15.7 - - + +
229I ALA* 3.5 22.7 - - + -
230I MET* 4.6 6.1 - - - -
233I ALA* 4.0 20.6 - - + -
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Residues in contact with ALA 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ILE* 6.0 0.7 - - + -
101H VAL* 2.7 21.9 + - + +
102H ALA* 3.5 5.8 - - - +
104H ILE* 1.3 74.5 - - + +
106H LEU* 1.3 65.1 + - - +
108H VAL* 3.1 17.0 + - - +
109H VAL* 3.6 3.8 + - - +
137H PHE* 6.1 0.4 - - + -
23I PRO* 3.5 22.2 - - + +
24I VAL* 4.0 11.9 - - + +
27I THR* 3.2 30.3 - - + +
237I ILE* 4.9 5.8 - - + -
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H ALA* 2.7 25.2 + - + +
103H GLY* 3.3 7.9 - - - +
105H ALA* 1.3 71.9 - - - +
107H LEU* 1.3 56.7 + - - +
109H VAL* 2.9 17.2 + - - +
110H PHE* 2.9 29.2 + - + +
133H VAL* 3.4 42.0 - - + +
134H ALA* 3.6 17.3 - - - +
137H PHE* 3.9 35.2 - - + -
202H ALA* 5.2 1.3 - - + -
206H ILE* 3.8 15.7 - - + -
19I PHE* 4.6 3.8 - - + -
23I PRO* 4.0 15.7 - - + -
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Residues in contact with LEU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLY 2.7 15.9 + - - +
104H ILE* 3.2 11.4 - - - +
106H LEU* 1.3 69.1 - - - +
108H VAL* 1.3 54.2 + - - +
109H VAL 2.7 16.0 + - - -
110H PHE* 4.5 0.9 - - - +
111H GLY* 3.1 23.1 + - - +
114H GLY* 4.8 0.9 + - - -
125H VAL* 4.9 6.1 - - + -
205H VAL* 3.8 15.3 - - + +
206H ILE* 4.9 14.3 - - + +
221I TYR* 3.3 39.9 - - + +
226I LEU* 4.3 16.8 - - + +
223J HIS* 5.1 1.1 - - + -
227J SER* 3.2 36.0 - - - +
229J GLU* 4.8 1.1 - - - +
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Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ILE* 2.9 29.0 + - + +
105H ALA 3.1 10.0 + - - +
107H LEU* 1.3 74.7 - - - +
109H VAL* 1.3 62.9 + - + +
114H GLY* 3.5 14.0 - - - -
115H LEU* 4.2 4.5 + - - +
26I ALA* 4.7 2.2 - - + -
27I THR* 4.0 19.5 - - + +
30I LEU* 3.7 30.5 - - + +
226I LEU* 4.4 11.4 - - + -
230I MET* 3.4 31.0 - - + -
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Residues in contact with VAL 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H ALA 3.7 4.3 - - - +
106H LEU 2.9 6.7 + - - +
107H LEU 2.7 4.2 + - - -
108H VAL* 1.3 85.7 - - - +
110H PHE* 1.3 66.7 + - + +
111H GLY 3.5 1.8 - - - -
114H GLY* 3.3 6.8 - - - -
115H LEU* 4.1 7.2 - - + +
116H ILE* 3.2 41.5 + - + +
117H GLY 2.9 21.3 + - - -
22I LEU* 4.1 11.9 - - + -
23I PRO* 3.7 31.2 - - + -
26I ALA* 4.2 16.2 - - + -
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Residues in contact with PHE 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H LEU* 2.9 27.1 + - + +
107H LEU* 5.4 0.7 - - - -
109H VAL* 1.3 85.5 - - + +
111H GLY* 1.3 67.9 + - - +
116H ILE* 3.8 35.2 - - + -
117H GLY* 3.7 6.8 - - - +
124H PHE* 3.3 72.5 + + + +
125H VAL* 4.5 2.2 - - - +
130H GLY* 6.2 0.2 - - - -
133H VAL* 3.7 33.2 - - + -
206H ILE* 5.5 5.8 - - + -
19I PHE* 4.1 20.2 - + - -
23I PRO* 5.6 4.5 - - + -
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Residues in contact with GLY 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H LEU* 3.1 22.8 + - - +
109H VAL 3.5 0.2 - - - -
110H PHE* 1.3 83.6 - - - +
112H SER* 1.3 55.2 + - - -
113H SER 2.9 6.1 - - - -
114H GLY 2.7 20.8 + - - +
117H GLY* 3.3 7.8 - - - -
125H VAL* 3.9 12.3 - - - -
227J SER* 3.8 5.4 - - - -
229J GLU* 3.4 9.9 - - - -
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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