Contacts of the helix formed by residues 128 - 142 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126F ARG 4.0 0.2 + - - -
127F LEU* 1.3 75.6 - - - +
129F GLY* 1.3 67.8 + - - +
130F GLY* 3.5 4.7 + - - -
131F GLU* 2.5 50.3 + - - +
132F ARG* 3.0 10.5 + - - +
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Residues in contact with GLY 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F TYR* 4.6 1.4 - - - -
127F LEU 4.1 0.2 + - - -
128F SER* 1.3 75.4 - - - +
130F GLY* 1.3 54.1 + - - +
132F ARG* 3.1 18.8 + - - +
133F GLN* 2.7 32.6 + - - +
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Residues in contact with GLY 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F SER* 3.1 5.0 + - - -
129F GLY* 1.3 77.3 - - - +
131F GLU* 1.3 61.2 + - - +
133F GLN* 2.8 25.4 + - - +
134F ARG* 3.1 31.6 + - - +
165F LEU* 5.4 0.7 - - - -
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Residues in contact with GLU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE* 4.8 1.6 - - + +
118F HIS* 4.5 2.4 + - - -
119F LEU* 2.9 45.4 - - + +
122F ARG* 4.0 6.6 + - - -
126F ARG 3.8 5.2 - - - +
127F LEU* 3.4 16.0 - - + -
128F SER* 2.5 57.6 + - - +
130F GLY* 1.3 68.8 - - - +
132F ARG* 1.3 58.7 + - - +
134F ARG* 3.3 10.3 + - - +
135F VAL* 2.7 36.7 + - - +
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Residues in contact with ARG 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F TYR* 3.9 21.3 + - + -
81F LEU* 3.9 27.8 - - + +
124F PRO* 3.3 42.7 + - - +
125F ALA* 3.9 9.9 + - - +
127F LEU* 4.0 17.1 + - + +
128F SER 3.0 15.9 + - - +
129F GLY* 3.2 14.1 - - - +
131F GLU* 1.3 76.5 - - - +
133F GLN* 1.3 54.9 + - - +
135F VAL* 2.9 5.6 + - - +
136F ALA* 2.6 38.8 + - - +
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Residues in contact with GLN 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F TYR* 3.0 36.9 + - + +
129F GLY* 2.7 20.5 - - - +
130F GLY* 2.8 25.8 + - - +
132F ARG* 1.3 73.2 - - - +
134F ARG* 1.3 59.4 + - + +
136F ALA* 3.3 4.3 - - - +
137F LEU* 2.9 33.7 + - + +
153F PRO 4.3 3.0 - - - +
154F LEU* 5.9 0.2 - - - -
157F VAL* 4.2 13.5 - - - +
161F THR* 5.7 1.8 - - - +
165F LEU* 3.3 46.8 - - + +
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Residues in contact with ARG 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LEU* 3.2 37.0 + - + +
115F GLY* 3.6 14.1 + - - -
116F ILE* 3.5 20.2 - - + -
130F GLY* 3.1 18.2 + - - +
131F GLU* 3.5 8.3 - - - +
132F ARG 3.0 0.6 - - - -
133F GLN* 1.3 75.1 - - + +
135F VAL* 1.3 56.0 + - - +
137F LEU* 3.0 9.5 + - - +
138F ALA* 2.6 37.4 + - - +
165F LEU* 6.2 1.2 - - - +
168F GLU* 3.5 32.9 + - - +
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Residues in contact with VAL 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F LEU* 4.2 18.8 - - + -
87F VAL* 3.7 44.0 - - + +
90F ASN* 4.4 7.2 - - + +
91F ILE* 4.3 4.9 - - + -
116F ILE* 4.1 9.8 - - + +
119F LEU* 5.5 1.3 - - + -
127F LEU* 3.6 24.0 - - + -
131F GLU* 2.7 26.4 + - + +
132F ARG 2.9 5.5 + - - +
134F ARG* 1.3 71.5 - - + +
136F ALA* 1.3 64.1 + - - +
138F ALA* 3.2 7.2 + - - +
139F ARG* 2.8 25.1 + - - +
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F VAL* 4.6 12.2 - - + +
79F TYR* 4.0 35.0 - - + -
81F LEU* 3.9 12.5 - - + +
132F ARG 2.6 20.4 + - - +
133F GLN 3.3 7.6 - - - +
135F VAL* 1.3 74.9 - - - +
137F LEU* 1.3 63.6 + - - +
139F ARG* 3.3 11.1 + - - +
140F ALA* 3.0 22.4 + - - +
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F VAL* 5.3 2.0 - - + +
114F LEU* 4.3 13.2 - - + -
133F GLN 2.9 13.4 + - - +
134F ARG* 3.4 8.3 - - + +
136F ALA* 1.3 75.3 - - - +
138F ALA* 1.3 69.9 + - - +
140F ALA* 2.9 7.4 + - + -
141F LEU* 2.9 43.8 + - + +
148F LEU* 4.0 25.1 - - + -
150F LEU* 5.2 8.1 - - + -
168F GLU* 6.5 0.9 - - + -
169F LEU* 4.5 18.6 - - + -
172F VAL* 4.1 29.4 - - + -
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Residues in contact with ALA 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ILE* 3.9 15.5 - - + -
110F MET* 4.4 9.4 - - + +
114F LEU* 3.5 17.7 - - + +
116F ILE* 3.7 23.8 - - + -
134F ARG 2.6 16.5 + - - +
135F VAL 3.3 8.7 - - - +
137F LEU* 1.3 76.4 - - - +
139F ARG* 1.3 62.5 + - - +
141F LEU* 3.1 6.8 + - - +
142F VAL* 2.9 24.2 + - - +
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Residues in contact with ARG 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F PHE 5.7 1.6 + - - -
75F VAL* 5.7 5.7 - - - +
76F PRO* 5.5 1.0 - - - +
79F TYR* 4.6 2.8 - - - +
80F ALA* 2.5 47.2 + - - +
81F LEU* 3.4 19.9 - - - +
82F PHE* 3.5 15.4 - - - +
90F ASN* 3.3 33.3 + - + +
91F ILE* 3.8 32.5 - - + +
93F TYR 4.9 1.9 - - - +
135F VAL 2.8 17.3 + - - +
136F ALA* 3.7 8.1 + - - +
138F ALA* 1.3 75.0 - - - +
140F ALA* 1.3 63.4 + - - +
142F VAL* 4.2 5.5 + - - +
143F ILE* 4.2 8.1 - - - +
161H VAL* 3.7 18.0 - - - +
165H LEU* 3.4 36.6 - - + +
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Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F GLY* 4.3 8.9 - - - -
74F PHE 4.8 5.4 - - - +
75F VAL* 4.2 17.3 - - + -
136F ALA 3.0 12.8 + - - +
137F LEU* 2.9 13.0 + - + +
139F ARG* 1.3 81.8 - - + +
141F LEU* 1.3 63.0 + - + +
143F ILE* 4.1 8.5 - - - +
145F PRO* 3.6 20.5 - - - +
148F LEU* 4.1 20.4 - - + -
165H LEU* 4.6 7.0 - - - -
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Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F MET* 3.6 24.9 - - - -
114F LEU* 4.4 6.7 - - + -
137F LEU* 2.9 27.6 + - + +
140F ALA* 1.3 76.3 - - - +
142F VAL* 1.3 53.2 + - - +
143F ILE 2.7 5.8 + - - -
144F GLN* 2.6 30.5 + - - +
145F PRO* 3.1 17.5 - - + +
148F LEU* 4.1 24.9 - - + -
172F VAL* 3.9 27.6 - - + -
176F PHE* 4.1 19.1 - - + -
178F VAL* 4.4 14.6 - - + -
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Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ILE* 3.6 27.4 - - + +
95F LEU* 3.8 31.2 - - + +
106F ARG* 3.4 45.8 + - + +
107F VAL* 4.6 0.7 - - - +
110F MET* 3.6 24.0 - - + -
138F ALA 2.9 19.0 + - - +
139F ARG* 4.5 4.5 - - - +
140F ALA 3.8 0.4 - - - -
141F LEU* 1.3 73.6 - - - +
143F ILE* 1.3 58.4 + - + +
144F GLN* 3.2 6.6 + - - +
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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