Contacts of the helix formed by residues 128 - 142 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B LEU* 1.3 75.8 - - - +
129B GLY* 1.3 69.6 + - - +
130B GLY* 3.5 4.7 + - - -
131B GLU* 2.5 49.4 + - - +
132B ARG* 2.9 10.6 + - - +
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TYR* 4.7 1.1 - - - -
127B LEU 4.1 0.2 + - - -
128B SER* 1.3 75.0 - - - +
130B GLY* 1.3 54.1 + - - +
132B ARG* 3.1 20.0 + - - +
133B GLN* 2.7 32.6 + - - +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B SER* 3.1 5.6 + - - -
129B GLY* 1.3 75.1 - - - +
131B GLU* 1.3 61.0 + - - +
133B GLN* 2.8 25.8 + - - +
134B ARG* 3.1 31.9 + - - +
165B LEU* 5.4 0.2 - - - -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 4.8 1.5 - - + +
118B HIS* 4.5 2.6 + - - -
119B LEU* 2.9 45.1 - - + +
122B ARG* 4.0 6.7 + - - -
126B ARG 3.8 5.0 - - - +
127B LEU* 3.4 14.8 - - + -
128B SER* 2.5 57.1 + - - +
130B GLY* 1.3 71.9 - - - +
132B ARG* 1.3 56.8 + - - +
134B ARG* 3.3 10.3 + - - +
135B VAL* 2.7 35.7 + - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TYR* 4.0 23.9 + - + -
81B LEU* 3.9 25.2 - - + +
124B PRO* 3.3 42.1 + - - +
125B ALA* 3.9 9.3 + - - +
127B LEU* 4.0 17.2 + - + +
128B SER 2.9 15.4 + - - +
129B GLY* 3.2 14.8 - - - +
131B GLU* 1.3 76.7 - - - +
133B GLN* 1.3 54.7 + - - +
135B VAL* 2.9 6.0 + - - +
136B ALA* 2.6 37.1 + - - +
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TYR* 3.2 35.5 + - + +
129B GLY* 2.7 19.9 - - - +
130B GLY* 2.8 26.1 + - - +
132B ARG* 1.3 72.7 - - - +
134B ARG* 1.3 59.1 + - + +
136B ALA* 3.3 4.3 - - - +
137B LEU* 2.9 33.6 + - + +
153B PRO 4.3 3.7 - - - +
154B LEU* 5.9 0.2 - - - -
157B VAL* 4.2 12.3 - - - +
161B THR* 5.7 1.6 - - - +
165B LEU* 3.3 47.0 - - + +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 3.2 37.5 + - + +
115B GLY* 3.6 14.1 + - - -
116B ILE* 3.5 20.9 - - + -
130B GLY* 3.1 17.8 + - - +
131B GLU* 3.5 9.4 - - - +
132B ARG 2.9 0.8 + - - -
133B GLN* 1.3 74.8 - - + +
135B VAL* 1.3 55.9 + - - +
137B LEU* 3.0 9.3 + - + +
138B ALA* 2.6 37.7 + - - +
165B LEU* 6.2 1.2 - - - +
168B GLU* 3.5 32.2 + - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU* 4.2 18.8 - - + -
87B VAL* 3.6 45.3 - - + +
90B ASN* 4.5 7.0 - - + +
91B ILE* 4.4 4.7 - - + -
116B ILE* 4.1 9.6 - - + +
119B LEU* 5.6 1.3 - - + -
127B LEU* 3.6 24.7 - - + -
131B GLU* 2.7 25.5 + - - +
132B ARG 3.4 3.1 - - - +
134B ARG* 1.3 74.1 - - + +
136B ALA* 1.3 63.9 + - - +
138B ALA* 3.1 7.2 + - - +
139B ARG* 2.8 25.5 + - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 4.6 11.4 - - + +
79B TYR* 3.9 35.2 - - + -
81B LEU* 3.9 13.0 - - + +
132B ARG 2.6 15.9 + - - +
133B GLN 3.3 11.9 - - - +
135B VAL* 1.3 74.7 - - - +
137B LEU* 1.3 63.6 + - - +
139B ARG* 3.3 10.4 + - - +
140B ALA* 3.0 22.9 + - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 5.4 1.5 - - + +
114B LEU* 4.3 12.8 - - + -
133B GLN 2.9 12.9 + - - +
134B ARG* 3.4 8.5 - - + +
136B ALA* 1.3 75.5 - - + +
138B ALA* 1.3 69.3 + - - +
140B ALA* 2.9 8.3 + - + -
141B LEU* 2.9 45.0 + - + +
148B LEU* 4.0 24.9 - - + -
150B LEU* 5.2 8.5 - - + -
168B GLU* 6.2 0.9 - - + -
169B LEU* 4.5 19.7 - - + -
172B VAL* 4.1 28.3 - - + -
180B ILE* 6.1 0.2 - - + -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 3.9 14.6 - - + -
110B MET* 4.1 10.0 - - + +
114B LEU* 3.5 17.0 - - + +
116B ILE* 3.7 24.5 - - + -
134B ARG 2.6 16.7 + - - +
135B VAL 3.2 9.0 - - - +
137B LEU* 1.3 75.3 - - - +
139B ARG* 1.3 63.4 + - - +
141B LEU* 3.1 6.2 + - - +
142B VAL* 3.0 23.9 + - - +
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B PHE 5.8 3.0 + - - -
75B VAL* 5.7 6.3 - - - +
76B PRO* 5.6 1.8 - - - +
79B TYR* 4.5 3.2 - - - +
80B ALA* 2.5 49.8 + - - +
81B LEU* 3.3 21.6 - - - +
82B PHE* 3.5 14.5 - - - +
90B ASN* 3.3 37.6 + - + +
91B ILE* 3.7 33.1 - - - +
93B TYR 4.9 1.2 - - - +
135B VAL* 2.8 17.9 + - + +
136B ALA* 3.7 7.0 + - - +
138B ALA* 1.3 74.4 - - - +
140B ALA* 1.3 64.5 + - + +
141B LEU 3.6 0.2 + - - -
142B VAL* 4.2 3.1 + - - +
143B ILE* 4.2 15.6 - - - +
161D VAL* 4.3 12.4 - - - +
165D LEU* 4.2 25.7 - - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLY* 4.5 8.9 - - - -
74B PHE 4.9 4.9 - - - +
75B VAL* 4.2 17.0 - - + -
136B ALA 3.0 11.7 + - - +
137B LEU* 2.9 13.7 + - + +
139B ARG* 1.3 82.3 - - + +
141B LEU* 1.3 63.2 + - + +
143B ILE* 4.1 8.2 - - - +
145B PRO* 3.6 20.8 - - - +
148B LEU* 4.1 20.9 - - + -
165D LEU* 5.5 4.3 - - - -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B MET* 3.6 23.8 - - - -
114B LEU* 4.4 6.5 - - + -
137B LEU* 2.9 29.2 + - + +
140B ALA* 1.3 76.7 - - - +
142B VAL* 1.3 52.7 + - - +
143B ILE 2.7 6.0 + - - -
144B GLN* 2.6 31.2 + - - +
145B PRO* 3.1 18.7 - - + +
148B LEU* 4.1 24.2 - - + -
172B VAL* 3.9 27.1 - - + -
176B PHE* 4.1 18.2 - - + -
178B VAL* 4.4 14.4 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 3.4 27.4 - - + +
95B LEU* 3.2 42.1 - - + +
106B ARG* 3.8 29.2 + - + +
107B VAL* 4.4 0.9 - - - +
110B MET* 3.6 24.4 - - + -
138B ALA 3.0 18.8 + - - +
139B ARG* 4.5 4.7 - - - +
140B ALA 3.8 0.6 - - - -
141B LEU* 1.3 72.6 - - - +
143B ILE* 1.3 58.4 + - + +
144B GLN* 3.2 14.2 + - - +
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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