Contacts of the helix formed by residues 111 - 132 (chain A) in PDB entry 3ORO
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 THR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PRO 4.1 0.4 + - - -
110A MET* 1.3 74.0 - - - +
112A PRO* 1.3 75.1 - - + +
113A LYS* 4.4 3.3 + - - +
114A ARG* 3.2 20.9 + - - +
115A ALA* 2.9 19.6 + - - +
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Residues in contact with PRO 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 MET 3.6 3.1 - - - +
111A THR* 1.3 87.9 - - + +
113A LYS* 1.3 64.1 + - + +
115A ALA* 3.3 1.9 + - - +
116A ILE* 3.0 32.8 + - + +
210A LEU* 3.8 13.2 - - + -
242A GLY* 3.5 25.1 - - - +
243A LEU* 3.7 13.7 - - + -
247A LEU* 4.2 18.4 - - + -
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Residues in contact with LYS 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 THR* 3.3 4.9 + - - +
112A PRO* 1.3 80.6 - - + +
114A ARG* 1.3 63.8 + - - +
116A ILE* 3.4 8.0 + - + +
117A GLU* 3.0 32.7 + - - +
276A VAL 5.7 0.2 - - - -
277A HIS* 3.7 51.5 + - + +
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Residues in contact with ARG 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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103A ILE* 4.4 8.1 - - - +
107A GLU* 4.1 18.2 + - - -
110A MET* 3.6 41.6 - - - +
111A THR* 3.2 24.2 + - - +
113A LYS* 1.3 74.9 - - - +
115A ALA* 1.3 66.8 + - - +
117A GLU* 3.1 17.7 + - - +
118A VAL* 2.9 33.6 + - + +
146A ILE* 4.0 25.9 - - - +
150A ASN* 4.7 8.3 + - - -
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Residues in contact with ALA 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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110A MET* 4.0 19.0 - - + -
111A THR 2.9 12.7 + - - +
112A PRO 3.6 8.1 - - - +
114A ARG* 1.3 77.3 - - - +
116A ILE* 1.3 57.1 + - - +
118A VAL* 3.3 2.4 + - - +
119A ILE* 3.0 35.9 + - - +
206A LEU* 4.5 2.5 - - + -
209A VAL* 4.0 21.1 - - + -
210A LEU* 3.6 24.2 - - + -
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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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112A PRO* 3.0 25.5 + - + +
113A LYS* 3.7 10.1 - - + +
115A ALA* 1.3 76.3 - - + +
117A GLU* 1.3 58.9 + - - +
119A ILE* 4.2 3.3 - - - +
120A ALA* 2.8 35.6 + - + +
206A LEU* 5.2 2.7 - - + -
247A LEU* 4.2 24.9 - - + -
273A LEU* 3.4 42.3 - - + +
274A VAL* 5.3 0.2 - - - -
276A VAL* 3.7 30.7 - - + +
277A HIS* 4.0 22.0 - - + +
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Residues in contact with GLU 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 LYS* 3.0 24.7 + - - +
114A ARG* 3.1 18.6 + - - +
116A ILE* 1.3 77.1 - - - +
118A VAL* 1.3 63.2 + - + +
120A ALA* 3.6 6.3 - - - +
121A ASP* 3.1 30.3 + - - +
277A HIS* 2.8 32.7 + - + +
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Residues in contact with VAL 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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100A LEU* 4.1 32.1 - - + -
110A MET* 4.1 12.6 - - + -
114A ARG* 2.9 27.7 + - + +
115A ALA* 3.7 5.8 - - - +
117A GLU* 1.3 75.7 - - + +
119A ILE* 1.3 63.4 + - + +
121A ASP* 3.2 6.8 + - - +
122A ALA* 3.0 24.5 + - + +
144A ILE* 4.9 1.8 - - + -
146A ILE* 3.8 21.5 - - + -
152A VAL* 3.8 27.7 - - + +
209A VAL* 6.4 0.9 - - + -
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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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100A LEU* 4.6 9.0 - - + -
115A ALA 3.0 20.9 + - - +
116A ILE* 4.2 2.2 - - - +
118A VAL* 1.3 76.1 - - + +
120A ALA* 1.3 59.0 + - - +
122A ALA* 3.2 6.0 + - + +
123A CYS* 2.9 27.9 + - - -
144A ILE* 5.1 0.7 - - + -
202A LEU* 3.7 33.2 - - + -
205A VAL* 3.9 28.3 - - + -
206A LEU* 3.8 31.6 - - + +
209A VAL* 4.5 7.4 - - + -
269A MET* 4.3 7.2 - - + -
273A LEU* 3.8 17.7 - - + -
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Residues in contact with ALA 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* 2.8 25.4 + - + +
117A GLU* 3.6 7.9 - - - +
119A ILE* 1.3 74.5 - - - +
121A ASP* 1.3 62.8 + - - +
123A CYS* 3.3 6.4 + - - +
124A GLN* 3.3 15.9 + - - +
270A ARG* 3.4 37.2 + - + +
273A LEU* 4.0 17.6 - - + +
274A VAL* 5.0 5.6 - - + -
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Residues in contact with ASP 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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70A ALA* 4.0 12.8 - - + +
117A GLU* 3.1 16.5 + - - +
118A VAL 3.2 9.2 + - - +
120A ALA* 1.3 77.6 - - - +
122A ALA* 1.3 61.7 + - - +
124A GLN* 3.1 20.2 + - - +
125A ALA 3.2 9.5 + - - -
150A ASN 5.4 2.1 - - - +
151A ALA* 5.8 0.2 - - - -
152A VAL* 3.7 32.6 + - + +
270A ARG* 5.3 5.4 + - - -
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Residues in contact with ALA 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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118A VAL 3.0 13.7 + - - +
119A ILE* 3.5 11.4 - - + +
121A ASP* 1.3 75.9 - - - +
123A CYS* 1.3 54.5 + - - +
125A ALA* 3.3 3.3 + - - +
126A LEU* 3.0 36.6 + - + +
144A ILE* 4.4 11.0 - - + -
152A VAL* 4.2 5.3 - - + +
154A VAL* 4.1 22.6 - - + +
202A LEU* 3.9 22.7 - - + -
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Residues in contact with CYS 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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119A ILE 2.9 20.3 + - - -
120A ALA 3.4 8.7 - - - +
122A ALA* 1.3 77.1 - - - +
124A GLN* 1.3 56.7 + - - +
126A LEU* 4.5 3.6 - - - -
127A ASN* 2.9 30.3 + - - +
202A LEU* 3.4 22.6 - - - +
266A ALA* 3.6 31.9 - - - +
269A MET* 4.0 13.5 - - - -
270A ARG* 3.6 22.4 - - + -
273A LEU* 4.0 9.0 - - - -
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Residues in contact with GLN 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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68A HIS* 3.7 18.1 + - - +
70A ALA* 5.4 0.7 - - + -
120A ALA 3.3 4.4 + - - +
121A ASP* 3.1 14.6 + - - +
123A CYS* 1.3 73.9 - - - +
125A ALA* 1.3 66.3 + - - +
127A ASN* 3.4 13.3 + - - +
128A PHE* 3.1 24.3 + - - +
270A ARG* 3.3 45.3 + - - +
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Residues in contact with ALA 125 (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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68A HIS* 3.9 13.3 + - - -
70A ALA* 3.4 33.0 - - + +
71A ILE* 3.6 17.1 - - + +
121A ASP 3.2 3.7 + - - +
122A ALA 3.5 8.5 - - - +
124A GLN* 1.3 77.8 - - - +
126A LEU* 1.3 57.5 + - - +
128A PHE* 3.3 5.9 + - - +
129A SER* 3.0 24.2 + - - -
154A VAL* 3.6 16.8 - - + -
157A PHE* 5.2 0.9 - - - -
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Residues in contact with LEU 126 (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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122A ALA* 3.0 20.6 + - + +
123A CYS* 3.8 3.8 - - - +
125A ALA* 1.3 78.7 - - + +
127A ASN* 1.3 52.9 + - - +
129A SER* 3.3 5.3 + - - -
130A HIS* 2.7 51.3 + - + +
136A HIS* 3.8 34.3 - - + -
139A VAL* 4.1 18.6 - - + -
154A VAL* 5.0 6.5 - - + -
157A PHE* 4.6 8.3 - - + -
198A ASP* 3.9 20.9 - - + +
199A VAL* 5.9 0.2 - - - -
202A LEU* 4.0 31.4 - - + -
266A ALA* 4.2 6.3 - - + -
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Residues in contact with ASN 127 (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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123A CYS 2.9 21.8 + - - +
124A GLN* 3.8 16.4 - - - +
125A ALA 3.4 0.2 - - - -
126A LEU* 1.3 71.8 - - - +
128A PHE* 1.3 54.3 + - - +
130A HIS* 3.7 7.3 + - - +
131A GLN* 2.8 59.8 + - - +
265A THR* 5.1 3.6 - - - -
266A ALA* 4.0 11.4 + - + +
267A ALA* 3.7 29.5 + - + +
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Residues in contact with PHE 128 (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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66A LEU* 4.1 13.0 - - + -
67A ASN* 3.2 39.7 - - + -
68A HIS* 3.2 37.2 - + + +
71A ILE* 4.0 7.9 - - + -
124A GLN 3.1 13.4 + - - +
125A ALA 3.4 8.7 - - - +
127A ASN* 1.3 75.9 - - - +
129A SER* 1.3 64.8 + - - +
131A GLN* 3.2 7.1 + - + +
132A ASN* 2.9 49.6 + - - -
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Residues in contact with SER 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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66A LEU* 4.1 16.4 - - - -
125A ALA 3.0 11.2 + - - -
126A LEU* 3.4 10.1 - - - -
128A PHE* 1.3 77.3 - - - +
130A HIS* 1.3 60.7 + - - +
132A ASN* 3.1 11.1 + - - +
133A GLY 3.3 0.3 + - - -
134A ILE* 2.6 54.6 + - - +
135A ILE 4.7 0.3 - - - -
136A HIS 4.7 0.2 + - - -
157A PHE* 3.2 34.3 - - - -
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Residues in contact with HIS 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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126A LEU* 2.7 40.6 + - + +
127A ASN* 3.7 7.7 + - - +
129A SER* 1.3 73.7 - - - +
131A GLN* 1.3 58.5 + - + +
133A GLY* 3.0 19.6 + - - -
134A ILE 3.4 17.9 - - - +
135A ILE* 4.2 6.5 - - + -
195A ALA* 3.5 41.7 - - + +
198A ASP* 2.8 33.5 + - + -
199A VAL* 5.5 1.1 - - + -
265A THR* 5.9 0.4 - - - -
266A ALA* 4.1 19.1 + - + +
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Residues in contact with GLN 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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127A ASN* 2.8 44.7 + - - +
128A PHE* 3.2 8.9 + - + +
130A HIS* 1.3 72.9 - - + +
132A ASN* 1.3 64.4 + - - +
133A GLY 3.2 2.5 + - - -
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Residues in contact with ASN 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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66A LEU* 4.3 18.1 - - + +
128A PHE* 2.9 58.0 + - - +
129A SER 3.1 4.0 + - - +
131A GLN* 1.3 81.8 - - - +
133A GLY* 1.3 59.8 + - - +
134A ILE* 3.4 12.6 + - + +
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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