Contacts of the helix formed by residues 128 - 142 (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 128 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G ARG 3.9 0.2 + - - -
127G LEU* 1.3 74.6 - - - +
129G GLY* 1.3 69.0 + - - +
130G GLY* 3.5 4.7 + - - -
131G GLU* 2.5 50.5 + - - +
132G ARG* 2.9 11.5 + - - +
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Residues in contact with GLY 129 (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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79G TYR* 4.6 1.2 - - - -
127G LEU 4.1 0.4 + - - -
128G SER* 1.3 75.1 - - - +
130G GLY* 1.3 53.1 + - - +
132G ARG* 3.1 20.4 + - - +
133G GLN* 2.7 32.5 + - - +
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Residues in contact with GLY 130 (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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128G SER* 3.1 5.9 + - - -
129G GLY* 1.3 75.7 - - - +
131G GLU* 1.3 60.4 + - - +
133G GLN* 2.8 26.1 + - - +
134G ARG* 3.1 30.9 + - - +
165G LEU* 5.4 0.2 - - - -
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Residues in contact with GLU 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ILE* 4.8 1.6 - - + +
118G HIS* 4.5 2.1 + - - -
119G LEU* 2.9 44.8 - - + +
122G ARG* 4.0 6.7 + - - -
126G ARG 3.8 5.4 - - - +
127G LEU* 3.4 15.3 - - + -
128G SER* 2.5 56.8 + - - +
130G GLY* 1.3 72.0 - - - +
132G ARG* 1.3 56.4 + - - +
134G ARG* 3.3 10.1 + - - +
135G VAL* 2.7 35.8 + - - +
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Residues in contact with ARG 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G TYR* 3.9 22.5 + - + -
81G LEU* 3.8 29.4 - - + +
124G PRO* 3.3 41.9 + - - +
125G ALA* 3.9 9.7 + - - +
127G LEU* 4.0 16.4 + - + -
128G SER 2.9 16.1 + - - +
129G GLY* 3.2 14.3 - - - +
131G GLU* 1.3 72.9 - - - +
133G GLN* 1.3 58.1 + - - +
135G VAL* 2.9 5.7 + - - +
136G ALA* 2.6 37.5 + - - +
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Residues in contact with GLN 133 (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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79G TYR* 3.1 37.6 + - + +
129G GLY* 2.7 19.6 - - - +
130G GLY* 2.8 26.5 + - - +
132G ARG* 1.3 72.5 - - - +
134G ARG* 1.3 58.5 + - + +
136G ALA* 3.3 4.6 - - - +
137G LEU* 2.9 33.9 + - - +
153G PRO 4.3 3.0 - - - +
154G LEU* 5.9 0.2 - - - -
157G VAL* 4.2 12.8 - - - +
161G THR* 5.7 1.8 - - - +
165G LEU* 3.3 46.7 - - + +
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Residues in contact with ARG 134 (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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114G LEU* 3.2 37.5 + - + +
115G GLY* 3.6 14.1 + - - -
116G ILE* 3.5 23.6 - - + -
130G GLY 3.1 18.0 + - - +
131G GLU* 3.5 6.3 - - - +
132G ARG 3.0 0.8 - - - -
133G GLN* 1.3 75.2 - - + +
135G VAL* 1.3 56.6 + - - +
137G LEU* 3.0 8.7 + - - +
138G ALA* 2.6 37.7 + - - +
165G LEU* 6.2 1.0 - - - +
168G GLU* 3.6 33.1 + - - +
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Residues in contact with VAL 135 (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* 4.2 19.3 - - + -
87G VAL* 3.7 44.6 - - + +
90G ASN* 4.3 8.5 - - + +
91G ILE* 4.3 3.4 - - + -
116G ILE* 4.1 9.6 - - + -
119G LEU* 5.5 1.6 - - + -
127G LEU* 3.6 23.8 - - + -
131G GLU* 2.7 25.5 + - + +
132G ARG 3.5 3.4 - - - +
134G ARG* 1.3 73.9 - - + +
136G ALA* 1.3 65.1 + - - +
138G ALA* 3.2 7.7 + - - +
139G ARG* 2.8 25.6 + - - +
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Residues in contact with ALA 136 (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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75G VAL* 4.6 11.0 - - + +
79G TYR* 3.9 35.2 - - + -
81G LEU* 3.9 12.0 - - + +
132G ARG 2.6 20.4 + - - +
133G GLN* 3.3 8.3 - - - +
135G VAL* 1.3 74.5 - - - +
137G LEU* 1.3 63.0 + - - +
139G ARG* 3.3 10.3 + - - +
140G ALA* 3.0 22.0 + - - +
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Residues in contact with LEU 137 (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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75G VAL* 5.6 1.3 - - - -
114G LEU* 4.2 12.6 - - + -
133G GLN* 2.9 14.4 + - + +
134G ARG* 3.4 8.3 - - + +
136G ALA* 1.3 75.7 - - - +
138G ALA* 1.3 67.8 + - - +
140G ALA* 2.9 7.4 + - + -
141G LEU* 2.9 45.2 + - + +
148G LEU* 4.0 24.5 - - + -
150G LEU* 5.2 8.7 - - + -
168G GLU* 6.5 0.7 - - + -
169G LEU* 4.5 19.7 - - + -
172G VAL* 4.1 28.7 - - + -
180G ILE* 6.2 0.2 - - + -
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Residues in contact with ALA 138 (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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91G ILE* 3.8 15.3 - - + -
110G MET* 4.4 9.4 - - + +
114G LEU* 3.5 16.9 - - + +
116G ILE* 3.7 24.2 - - + -
134G ARG 2.6 17.2 + - - +
135G VAL 3.3 8.1 - - - +
137G LEU* 1.3 75.0 - - - +
139G ARG* 1.3 61.4 + - - +
141G LEU* 3.1 6.6 + - - +
142G VAL* 2.9 26.1 + - - +
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Residues in contact with ARG 139 (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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74G PHE 5.7 2.8 + - - -
75G VAL* 5.7 5.5 - - - +
76G PRO* 5.5 2.6 - - - +
79G TYR* 4.6 2.8 - - - +
80G ALA* 2.5 50.5 + - - +
81G LEU* 3.4 18.8 - - - +
82G PHE* 3.5 17.1 - - - +
90G ASN* 3.4 36.4 + - + +
91G ILE* 3.8 33.3 - - + +
93G TYR 4.9 2.6 - - - +
135G VAL 2.8 17.1 + - - +
136G ALA* 3.7 8.6 + - - +
138G ALA* 1.3 74.2 - - - +
140G ALA* 1.3 63.5 + - + +
142G VAL* 4.2 3.3 + - - +
143G ILE* 4.2 18.7 + - - +
161I VAL* 4.4 11.2 - - - +
165I LEU* 4.0 24.9 - - + +
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Residues in contact with ALA 140 (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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73G GLY* 4.4 9.4 - - - -
74G PHE 4.8 5.2 - - - +
75G VAL* 4.3 17.0 - - + -
136G ALA 3.0 12.5 + - - +
137G LEU* 2.9 13.9 + - + +
139G ARG* 1.3 81.8 - - + +
141G LEU* 1.3 63.2 + - + +
143G ILE* 4.1 8.1 - - - +
145G PRO* 3.6 20.6 - - - +
148G LEU* 4.1 20.2 - - + -
165I LEU* 5.5 4.5 - - - -
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Residues in contact with LEU 141 (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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110G MET* 3.6 24.9 - - - -
114G LEU* 4.4 7.0 - - + -
137G LEU* 2.9 30.2 + - + +
140G ALA* 1.3 76.3 - - - +
142G VAL* 1.3 53.0 + - - +
143G ILE 2.7 6.0 + - - -
144G GLN* 2.6 30.7 + - - +
145G PRO* 3.1 18.4 - - + +
148G LEU* 4.1 24.5 - - + -
172G VAL* 3.9 28.0 - - + -
176G PHE* 4.1 18.4 - - + -
178G VAL* 4.4 14.8 - - + -
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Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G ILE* 3.5 26.5 - - + +
95G LEU* 3.4 41.0 - - + +
106G ARG* 3.7 29.9 + - + +
107G VAL* 4.4 0.7 - - - +
110G MET* 3.6 23.5 - - + -
138G ALA 2.9 17.9 + - - +
139G ARG* 4.2 4.7 + - - +
140G ALA 3.8 0.4 - - - -
141G LEU* 1.3 71.7 - - - +
143G ILE* 1.3 59.3 + - + +
144G GLN* 3.2 16.4 + - - +
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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