Contacts of the helix formed by residues 110 - 124 (chain A) in PDB entry 1OPT
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 ILE 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLY* 3.4 27.5 + - - +
108A TYR 3.4 0.6 - - - -
109A PHE* 1.3 82.5 - - - +
111A GLY* 1.4 64.7 + - - +
112A PHE 3.6 2.2 - - - -
113A PHE* 3.3 32.9 + - + +
114A SER* 4.0 6.8 + - - +
161A LEU* 4.7 11.9 - - + -
164A ILE* 5.8 6.7 - - + -
194A GLN* 4.8 15.9 - - - +
196A LEU 5.1 2.9 - - - +
197A LYS* 4.0 50.5 - - + +
255A LEU* 6.4 0.9 - - + -
258A ASN* 5.3 2.9 - - - +
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 3.0 18.2 + - - -
108A TYR 4.4 0.2 + - - -
110A ILE* 1.4 75.5 - - - +
112A PHE* 1.3 62.0 + - - +
113A PHE 3.5 0.3 + - - -
114A SER* 3.5 8.4 + - - -
115A GLY* 3.2 15.9 + - - -
157A VAL* 4.0 8.4 - - - +
158A PHE* 5.6 4.5 - - - -
161A LEU* 3.6 31.5 - - - +
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Residues in contact with PHE 112 (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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76A ASP* 3.5 38.1 - - - +
79A PHE* 3.6 38.1 - + + -
80A LEU* 3.8 35.2 - - + -
83A VAL* 6.1 0.2 - - + -
84A PRO* 3.9 18.4 - - + -
108A TYR* 3.3 50.5 - + - -
110A ILE 3.4 1.2 + - - -
111A GLY* 1.3 73.4 - - - +
113A PHE* 1.3 62.6 + - + +
115A GLY* 3.2 8.2 + - - -
116A ILE* 3.2 26.3 + - + +
158A PHE* 5.9 8.1 - + - -
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Residues in contact with PHE 113 (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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80A LEU* 4.9 13.9 - - + -
109A PHE* 3.3 30.3 - + - -
110A ILE* 3.3 21.4 + - + +
112A PHE* 1.3 80.1 - - + +
114A SER* 1.4 59.8 + - - +
116A ILE* 3.9 2.8 + - - +
117A PHE* 3.3 22.1 + - - +
247A PHE* 3.5 14.7 - - + -
251A TYR* 3.1 42.0 - + + -
254A VAL* 4.5 17.9 - - + -
255A LEU* 6.4 1.3 - - + -
283A GLU* 5.9 0.7 - - - -
286A GLY* 3.3 32.1 - - - -
287A MET* 4.5 9.2 - - + -
289A HIS* 6.1 1.1 - - - -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 4.0 6.9 + - - +
111A GLY* 3.5 13.7 + - - -
113A PHE* 1.4 73.9 - - - +
115A GLY* 1.3 61.8 + - - +
117A PHE* 3.5 9.1 - - - +
118A PHE* 3.3 30.4 + - - -
157A VAL* 3.6 19.4 - - - +
161A LEU* 5.1 7.0 - - - +
206A PRO* 3.8 29.4 + - - +
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Residues in contact with GLY 115 (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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76A ASP* 3.9 16.2 - - - -
111A GLY 3.2 12.6 + - - -
112A PHE 3.2 7.7 + - - -
114A SER* 1.3 75.3 - - - +
116A ILE* 1.3 60.6 + - - +
118A PHE 3.8 0.3 + - - -
119A ILE* 3.4 26.8 + - - +
153A TRP* 4.3 0.9 + - - -
157A VAL* 3.6 22.4 - - - +
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Residues in contact with ILE 116 (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 ALA* 4.4 17.9 - - + -
76A ASP* 3.6 13.0 - - - +
77A LEU* 3.9 39.5 - - + -
112A PHE 3.2 20.7 + - - +
113A PHE* 3.9 3.1 + - - +
115A GLY* 1.3 70.2 - - - +
117A PHE* 1.4 59.0 + - - +
119A ILE* 3.2 9.8 + - + -
120A ILE* 2.9 40.0 + - + +
289A HIS* 3.9 23.6 - - + +
293A ASN* 3.7 25.4 - - - +
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Residues in contact with PHE 117 (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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113A PHE 3.3 20.4 + - - +
114A SER* 3.5 8.5 - - - +
115A GLY 3.5 0.2 - - - -
116A ILE* 1.4 74.0 - - - +
118A PHE* 1.3 69.8 + + - +
120A ILE* 3.5 1.3 + - - -
121A LEU* 3.1 18.4 + - + +
206A PRO 3.1 27.8 - - - -
207A LEU* 3.9 22.2 - - + -
210A MET* 3.6 34.8 - - + -
211A VAL* 3.9 14.4 - - + -
214A TYR* 2.6 55.2 + + - -
247A PHE* 3.7 29.0 - + + -
248A TRP* 4.0 2.9 - + - -
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Residues in contact with PHE 118 (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 SER* 3.3 22.2 + - - -
117A PHE* 1.3 81.7 - + - +
119A ILE* 1.3 58.6 + - - +
121A LEU* 3.6 18.0 + - + +
122A LEU* 3.1 26.5 + - - +
153A TRP* 3.6 24.7 - - + +
156A ALA* 3.7 39.0 - - + -
157A VAL* 3.8 24.2 - - + -
205A LEU* 4.1 7.2 - - + -
206A PRO* 4.0 18.6 - - + -
210A MET* 3.6 37.0 - - + -
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Residues in contact with ILE 119 (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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69A LEU* 3.7 41.4 - - + +
72A LEU* 3.9 13.5 - - + +
73A ALA* 3.8 37.5 - - + +
76A ASP* 5.3 4.5 - - + -
115A GLY 3.4 19.2 + - - +
116A ILE* 3.2 13.1 + - + +
118A PHE* 1.3 72.8 - - - +
120A ILE* 1.4 62.6 + - + +
122A LEU* 3.4 7.3 + - + +
123A THR* 3.3 22.2 + - - +
153A TRP* 3.2 26.0 - - + +
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Residues in contact with ILE 120 (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* 2.9 34.9 + - + +
117A PHE 3.6 0.4 - - - +
119A ILE* 1.4 71.0 - - - +
121A LEU* 1.3 55.4 + - - +
123A THR* 3.3 12.2 - - + +
124A ILE* 3.0 42.1 + - + +
214A TYR* 3.6 26.9 - - + +
243A VAL* 3.6 41.5 - - + +
244A TYR* 4.2 16.6 - - - +
247A PHE* 3.8 28.7 - - + -
289A HIS* 4.7 2.2 - - + -
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Residues in contact with LEU 121 (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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117A PHE* 3.1 15.3 + - + +
118A PHE* 3.6 26.9 - - + +
119A ILE 3.4 0.2 - - - -
120A ILE* 1.3 73.5 - - - +
122A LEU* 1.3 59.6 + - - +
124A ILE 2.9 26.2 - - - +
125A ASP* 3.0 24.4 - - - +
210A MET* 3.6 40.2 - - + +
213A CYS* 4.0 20.6 - - + -
214A TYR* 3.6 19.8 - - + -
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Residues in contact with LEU 122 (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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69A LEU* 3.8 24.2 - - + -
72A LEU* 5.2 1.1 - - + -
118A PHE 3.1 11.9 + - - +
119A ILE* 3.4 11.6 + - - +
121A LEU* 1.3 73.4 - - - +
123A THR* 1.3 56.5 + - - +
125A ASP* 3.3 21.6 - - - +
126A ARG* 3.8 27.9 + - - +
144A PHE* 5.4 0.9 - - + -
145A GLY 5.1 1.6 - - - +
149A SER* 3.5 39.7 - - - +
150A VAL* 4.6 6.1 - - + -
153A TRP* 3.8 36.3 - - + +
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Residues in contact with THR 123 (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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67A ILE* 5.5 2.5 - - - +
69A LEU* 3.9 19.8 - - + +
119A ILE 3.3 12.6 + - - +
120A ILE* 3.3 21.8 - - - +
122A LEU* 1.3 73.2 - - - +
124A ILE* 1.4 58.9 + - + +
125A ASP 3.0 7.4 + - - -
126A ARG* 3.7 21.1 + - - +
236A LEU* 4.6 10.4 - - - +
240A ILE* 3.2 45.3 - - + +
243A VAL* 4.8 9.0 - - + -
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Residues in contact with ILE 124 (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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120A ILE* 3.0 42.3 + - + +
121A LEU* 2.9 12.3 + - - +
123A THR* 1.4 65.3 - - + +
125A ASP* 1.3 70.9 + - - +
213A CYS* 4.1 17.4 - - - +
214A TYR* 4.1 29.6 - - + +
217A ILE* 3.8 32.6 - - + +
218A LEU* 5.5 4.7 - - + -
240A ILE* 4.0 26.2 - - + +
241A MET* 6.0 5.2 - - + -
244A TYR* 4.2 19.7 - - + -
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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