Contacts of the strand formed by residues 107 - 119 (chain A) in PDB entry 2OR4
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 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LYS* 5.9 1.3 - - - +
105A LEU 3.4 0.2 - - - -
106A ASP* 1.3 81.8 - - - +
108A VAL* 1.3 70.0 + - - +
109A GLU* 4.8 12.6 - - - +
359A ILE 4.5 1.0 + - - -
360A GLY* 3.3 0.3 - - - -
361A THR* 2.9 48.8 + - - +
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Residues in contact with VAL 108 (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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97A GLN* 3.0 31.1 + - + +
100A TRP* 3.8 17.3 - - + -
101A LYS* 3.4 51.3 - - + +
105A LEU* 3.9 13.5 - - + +
107A SER* 1.3 83.1 - - - +
109A GLU* 1.3 68.7 + - - +
358A VAL* 3.5 31.2 - - + -
359A ILE 3.4 7.0 - - - +
360A GLY* 4.2 2.5 - - - -
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLN* 3.8 8.0 + - - +
101A LYS* 5.2 3.7 + - - -
107A SER* 4.8 10.9 - - - +
108A VAL* 1.3 90.8 + - - +
110A LEU* 1.3 69.9 + - - +
358A VAL* 3.6 3.9 - - - +
359A ILE* 2.8 39.7 + - + +
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Residues in contact with LEU 110 (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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90A PHE* 4.1 27.8 - - + -
93A ALA* 4.1 14.1 - - + +
94A LYS* 4.2 9.6 - - + -
97A GLN* 3.7 29.0 - - + +
109A GLU* 1.3 81.6 + - - +
111A ALA* 1.3 59.2 + - - +
112A HIS* 4.1 7.0 + - + +
356A TYR* 4.1 20.2 - - + -
357A ASN 3.3 4.9 - - - +
358A VAL* 3.7 31.9 - - + -
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Residues in contact with ALA 111 (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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109A GLU 4.0 1.2 + - - -
110A LEU* 1.3 71.0 - - - +
112A HIS* 1.3 61.1 + - - +
113A TYR* 3.7 27.0 - - + +
356A TYR* 3.7 0.8 - - - -
357A ASN* 2.8 43.2 + - + +
359A ILE* 4.4 6.3 - - + +
434A TRP* 4.0 18.2 - - + +
437A GLU* 5.0 2.7 - - - +
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Residues in contact with HIS 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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110A LEU* 4.0 7.2 + - - +
111A ALA* 1.3 74.0 - - - +
113A TYR* 1.3 79.9 + - - +
114A ASP* 5.1 1.1 - - - -
274A ALA 4.8 0.3 - - - +
275A ASN* 5.3 3.3 - - - +
354A ARG* 3.5 43.4 + - + -
355A ILE 3.1 14.4 - - - +
356A TYR* 3.7 24.3 - + + -
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Residues in contact with TYR 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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111A ALA* 3.7 18.3 - - + +
112A HIS* 1.3 83.2 - - - +
114A ASP* 1.3 64.2 + - - +
115A VAL* 3.9 17.3 - - + -
273A PRO* 4.0 10.1 - - + -
274A ALA* 3.3 25.4 - - + +
275A ASN* 4.6 3.4 - - + +
354A ARG* 3.3 3.6 - - - +
355A ILE* 2.8 45.4 + - + +
357A ASN* 3.6 26.0 - - - -
433A GLU* 3.8 18.8 - - + -
434A TRP* 3.4 33.1 - - - -
437A GLU* 2.6 38.5 + - - -
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Residues in contact with ASP 114 (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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112A HIS* 5.1 1.4 - - - -
113A TYR* 1.3 72.0 - - - +
115A VAL* 1.3 61.0 + - - +
266A ASP* 4.4 0.5 - - - +
274A ALA* 2.9 16.2 + - - +
275A ASN 4.7 5.5 - - - +
276A GLU* 4.9 5.7 - - - -
280A ARG* 3.0 38.5 + - - +
352A VAL* 3.7 18.8 - - + +
353A THR 3.5 4.4 - - - +
354A ARG* 2.9 56.8 + - - +
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Residues in contact with VAL 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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113A TYR* 4.1 9.0 - - + -
114A ASP* 1.3 78.8 - - - +
116A LEU* 1.3 65.0 + - - +
117A LEU* 3.2 7.8 + - + +
266A ASP* 3.6 28.3 - - + +
274A ALA* 3.9 10.3 - - + -
352A VAL* 4.1 4.0 - - - -
353A THR* 2.8 31.8 + - - +
355A ILE* 3.7 37.5 - - + -
429A LEU* 3.8 21.1 - - + -
433A GLU* 3.9 14.1 - - + -
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Residues in contact with LEU 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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115A VAL* 1.3 71.1 - - - +
117A LEU* 1.4 71.1 + - - +
164A PHE* 3.2 32.6 - - + -
266A ASP* 2.9 18.7 + - - +
267A PRO* 4.2 21.3 - - + +
268A LEU* 4.0 25.9 - - + +
283A ILE* 3.8 27.8 - - + -
289A LEU* 4.3 5.6 - - + -
350A ASN* 3.9 20.9 - - + +
351A GLU* 3.9 17.5 - - - +
352A VAL* 4.1 7.6 - - + +
429A LEU* 3.7 7.6 - - - +
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Residues in contact with LEU 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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84A ALA* 3.6 16.4 - - + +
85A GLY* 3.8 7.6 - - - +
115A VAL* 3.2 15.2 + - + +
116A LEU* 1.4 84.5 - - - +
118A SER* 1.3 63.3 + - - +
119A TYR* 3.3 28.9 - - + +
164A PHE* 3.9 4.0 - - - -
350A ASN* 3.1 8.3 - - - +
351A GLU* 2.8 38.9 + - - +
353A THR* 3.7 17.5 - - - +
355A ILE* 4.2 8.3 - - + -
423A ALA* 4.2 4.7 - - + -
426A PHE* 3.6 29.4 - - + -
429A LEU* 3.7 15.3 - - + -
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Residues in contact with SER 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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117A LEU* 1.3 77.9 - - - +
119A TYR* 1.4 68.3 + - - +
161A PHE* 3.3 13.9 - - - -
163A ALA* 3.7 8.9 - - - -
164A PHE* 2.9 39.8 + - - -
165A SER 5.1 0.3 + - - -
348A SER* 4.4 9.2 - - - -
349A THR 3.4 6.8 + - - -
350A ASN* 3.4 16.9 + - - -
426A PHE* 3.2 21.8 - - - -
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Residues in contact with TYR 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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83A LEU* 3.6 33.9 - - + -
84A ALA 2.6 24.6 + - - -
85A GLY* 3.4 14.1 + - - -
86A THR* 4.7 6.3 - - + -
117A LEU* 3.3 21.1 - - + +
118A SER* 1.4 81.2 + - - +
120A PRO* 1.3 82.5 - - + +
122A LYS* 5.8 6.5 - - - +
158A VAL* 5.3 0.7 - - + -
161A PHE* 4.4 0.9 - + - -
348A SER* 4.1 4.5 - - - -
349A THR* 3.0 31.1 + - - +
351A GLU* 3.5 41.7 - - + +
353A THR* 3.9 11.4 - - + +
426A PHE* 4.4 4.7 - + - -
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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