Contacts of the helix formed by residues 128 - 142 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ARG 3.9 0.2 + - - -
127A LEU* 1.3 75.0 - - - +
129A GLY* 1.3 69.5 + - - +
130A GLY* 3.5 4.3 + - - -
131A GLU* 2.5 50.9 + - - +
132A ARG* 2.9 10.3 + - - +
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 4.6 1.1 - - - -
127A LEU 4.1 0.2 + - - -
128A SER* 1.3 74.0 - - - +
130A GLY* 1.3 53.8 + - - +
132A ARG* 3.1 20.1 + - - +
133A GLN* 2.7 32.0 + - - +
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A SER* 3.1 5.2 + - - -
129A GLY* 1.3 75.9 - - - +
131A GLU* 1.3 61.3 + - - +
133A GLN* 2.8 26.4 + - - +
134A ARG* 3.1 31.7 + - - +
165A LEU* 5.4 0.4 - - - -
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 4.8 1.3 - - + +
118A HIS* 4.5 2.6 + - - -
119A LEU* 2.9 44.1 - - + +
122A ARG* 4.0 6.3 + - - -
126A ARG 3.8 5.2 - - - +
127A LEU* 3.4 16.2 - - + -
128A SER* 2.5 58.2 + - - +
130A GLY* 1.3 71.2 - - - +
132A ARG* 1.3 56.5 + - - +
134A ARG* 3.3 10.5 + - - +
135A VAL* 2.7 35.5 + - - +
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 3.9 21.8 + - + -
81A LEU* 3.8 26.9 - - + +
124A PRO* 3.3 43.3 + - - +
125A ALA* 3.9 10.3 + - - +
127A LEU* 4.0 16.6 + - + -
128A SER 2.9 16.5 + - - +
129A GLY* 3.2 13.9 - - - +
131A GLU* 1.3 72.7 - - - +
133A GLN* 1.3 58.0 + - - +
135A VAL* 2.9 6.1 + - - +
136A ALA* 2.6 36.9 + - - +
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Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 3.1 36.3 + - + +
129A GLY* 2.7 21.2 - - - +
130A GLY* 2.8 25.9 + - - +
132A ARG* 1.3 72.5 - - - +
134A ARG* 1.3 59.9 + - + +
136A ALA* 3.3 4.9 - - - +
137A LEU* 3.0 32.6 + - - +
153A PRO 4.3 3.2 - - - +
154A LEU* 5.2 0.4 - - - +
157A VAL* 4.2 13.3 - - - +
161A THR* 5.7 1.6 - - - +
165A LEU* 3.3 46.6 - - + +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.2 36.8 + - + +
115A GLY* 3.6 14.1 + - - -
116A ILE* 3.5 20.9 - - + -
130A GLY* 3.1 18.5 + - - +
131A GLU* 3.5 9.0 - - - +
132A ARG 3.0 0.6 - - - -
133A GLN* 1.3 75.2 - - + +
135A VAL* 1.3 56.8 + - - +
137A LEU* 3.0 9.4 + - + +
138A ALA* 2.6 37.4 + - - +
165A LEU* 6.2 1.2 - - - +
168A GLU* 3.5 32.7 + - - +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 4.2 19.1 - - + -
87A VAL* 3.7 45.3 - - + +
90A ASN* 4.3 9.0 - - + +
91A ILE* 4.3 3.4 - - + -
116A ILE* 4.1 9.2 - - + +
119A LEU* 5.6 1.1 - - + -
127A LEU* 3.6 24.7 - - + -
131A GLU* 2.7 25.4 - - + +
132A ARG 2.9 5.5 + - - +
134A ARG* 1.3 70.4 - - - +
136A ALA* 1.3 63.6 + - - +
138A ALA* 3.1 7.0 + - - +
139A ARG* 2.8 25.5 + - + +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 4.6 11.4 - - + +
79A TYR* 3.9 34.1 - - + -
81A LEU* 3.9 13.1 - - + +
132A ARG 2.6 21.0 + - - +
133A GLN* 3.3 8.7 - - - +
135A VAL* 1.3 73.6 - - - +
137A LEU* 1.3 62.6 + - - +
139A ARG* 3.3 10.1 + - - +
140A ALA* 3.0 23.3 + - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 5.3 1.3 - - - +
114A LEU* 4.4 12.8 - - + -
133A GLN* 3.0 13.9 + - + +
134A ARG* 3.4 9.2 - - + +
136A ALA* 1.3 75.6 - - + +
138A ALA* 1.3 67.8 + - - +
140A ALA* 2.9 7.5 + - + -
141A LEU* 2.9 45.2 + - + +
148A LEU* 4.0 25.1 - - + -
150A LEU* 5.2 8.7 - - + -
168A GLU* 6.5 0.7 - - + -
169A LEU* 4.5 19.3 - - + -
172A VAL* 4.1 27.6 - - + -
180A ILE* 6.2 0.2 - - + -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 3.8 15.7 - - + -
110A MET* 4.4 9.2 - - + +
114A LEU* 3.5 16.9 - - + +
116A ILE* 3.7 23.3 - - + -
134A ARG 2.6 17.8 + - - +
135A VAL 3.2 9.2 - - - +
137A LEU* 1.3 76.2 - - - +
139A ARG* 1.3 60.9 + - - +
141A LEU* 3.1 6.8 + - - +
142A VAL* 2.9 25.7 + - - +
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE 5.7 2.2 + - - -
75A VAL* 5.7 5.3 - - - +
76A PRO* 5.5 1.2 - - - +
79A TYR* 4.8 2.6 - - - +
80A ALA* 2.4 51.4 + - - +
81A LEU* 3.3 19.3 - - - +
82A PHE* 3.5 17.1 - - - +
90A ASN* 3.3 33.4 + - + +
91A ILE* 3.7 32.2 - - - +
93A TYR 4.8 1.5 - - - +
135A VAL 2.8 16.5 + - - +
136A ALA* 3.7 7.8 + - - +
138A ALA* 1.3 73.8 - - - +
140A ALA* 1.3 64.1 + - + +
141A LEU 3.6 0.2 + - - -
142A VAL* 4.2 3.4 + - - +
143A ILE* 4.2 9.5 - - - +
161C VAL* 3.9 13.4 - - - +
165C LEU* 3.5 38.1 - - + +
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY* 4.4 8.2 - - - -
74A PHE 4.8 5.2 - - - +
75A VAL* 4.3 16.4 - - + -
136A ALA 3.0 13.4 + - - +
137A LEU* 2.9 14.3 + - + +
139A ARG* 1.3 82.2 - - + +
141A LEU* 1.3 61.1 + - + +
143A ILE* 4.1 8.3 - - - +
145A PRO* 3.6 20.1 - - - +
148A LEU* 4.1 21.1 - - + -
165C LEU* 4.6 7.9 - - + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A MET* 3.6 20.4 - - - -
114A LEU* 4.4 6.7 - - + -
137A LEU* 2.9 31.1 + - + +
140A ALA* 1.3 76.6 - - - +
142A VAL* 1.3 52.7 + - - +
143A ILE 2.7 5.6 + - - -
144A GLN* 2.6 30.1 + - - +
145A PRO* 3.1 19.3 - - + +
148A LEU* 4.1 24.7 - - + -
172A VAL* 3.9 27.6 - - + -
176A PHE* 4.1 22.7 - - + -
178A VAL* 4.4 13.9 - - + -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 3.4 28.0 - - + +
95A LEU* 3.3 41.5 - - + +
106A ARG* 3.7 29.4 + - + +
107A VAL 4.5 0.2 - - - +
110A MET* 3.6 22.8 - - + -
138A ALA 2.9 18.5 + - - +
139A ARG* 4.2 4.5 + - - +
140A ALA 3.8 0.2 - - - -
141A LEU* 1.3 73.2 - - - +
143A ILE* 1.3 59.0 + - + +
144A GLN* 3.2 15.5 + - - +
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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