Contacts of the helix formed by residues 132 - 144 (chain A) in PDB entry 1N0W
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 GLY 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG 3.0 5.8 - - - -
131A THR* 1.3 81.0 - - - +
133A LYS* 1.3 59.1 + - - +
134A THR 3.3 2.7 - - - -
135A GLN* 3.1 2.4 + - - +
136A ILE* 2.8 35.3 + - - +
302A LEU* 3.9 6.5 - - - -
327A PHE* 4.5 4.5 - - - -
329A ILE* 4.2 21.8 - - - -
501A CL 3.3 8.4 - - - +
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Residues in contact with LYS 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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125A MSE 3.3 16.9 - - + +
127A GLY* 3.7 21.5 - - - +
128A GLU* 3.8 9.6 - - - +
129A PHE* 3.7 29.9 - - - +
131A THR* 3.9 1.1 - - - +
132A GLY* 1.3 76.6 - - - +
134A THR* 1.3 86.3 + - - +
136A ILE* 4.6 0.4 - - - -
137A CYS* 3.1 27.6 + - - -
163A GLU* 4.1 20.0 + - - +
222A ASP* 2.6 29.5 + - - +
223A SER* 4.9 2.6 - - - -
266A THR* 3.7 23.4 + - + -
302A LEU* 3.4 22.7 - - + +
501A CL 4.4 1.1 - - + -
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Residues in contact with THR 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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129A PHE* 3.7 11.5 - - + -
133A LYS* 1.3 96.9 + - - +
135A GLN* 1.3 62.5 + - - +
137A CYS* 3.3 4.0 + - - +
138A HIS* 2.9 57.9 + - + +
159A TYR* 3.7 7.4 - - - +
165A THR* 4.0 10.9 + - - +
222A ASP* 2.9 20.8 + - - +
501A CL 3.2 11.7 - - - +
506A EDO 3.9 14.6 - - - +
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Residues in contact with GLN 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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129A PHE* 4.1 3.8 - - - -
130A ARG* 5.7 0.6 - - - -
132A GLY* 3.1 6.2 + - - +
134A THR* 1.3 73.5 - - - +
136A ILE* 1.3 66.9 + - - +
138A HIS* 3.3 5.1 + - - +
139A THR* 3.0 27.3 + - - +
170A ARG* 3.8 16.0 - - - +
329A ILE* 3.9 40.6 - - + +
330A ASN 5.0 5.3 + - - -
333A GLY* 5.3 3.3 - - - -
334A VAL* 4.0 7.4 - - + +
501A CL 3.6 19.6 - - + +
506A EDO 3.1 45.4 + - - -
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Residues in contact with ILE 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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104A THR* 5.1 12.1 - - + +
109A LEU* 4.2 14.8 - - + -
117A ILE* 5.6 1.3 - - + -
125A MSE 3.8 22.4 - - + -
132A GLY 2.8 19.3 + - - +
133A LYS 3.7 4.5 - - - +
135A GLN* 1.3 76.7 - - - +
137A CYS* 1.3 57.5 + - - +
139A THR* 3.2 3.4 + - - -
140A LEU* 2.9 50.0 + - + +
300A LEU* 5.6 2.2 - - + -
302A LEU* 3.9 25.4 - - + -
327A PHE* 4.0 18.4 - - + -
334A VAL* 3.8 22.0 - - + -
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Residues in contact with CYS 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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125A MSE 3.6 16.8 - - - -
133A LYS 3.1 20.8 + - - -
134A THR 3.5 8.5 - - - +
135A GLN 3.2 0.2 - - - -
136A ILE* 1.3 79.8 - - - +
138A HIS* 1.3 62.2 + - - +
140A LEU* 3.4 4.8 + - - +
141A ALA* 3.1 18.7 + - - +
159A TYR* 3.7 15.9 - - + +
220A ILE* 3.2 44.1 - - + +
222A ASP* 4.3 4.3 - - - -
264A VAL* 4.3 7.2 - - - -
266A THR* 3.9 14.6 - - - -
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Residues in contact with HIS 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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134A THR* 2.9 34.8 + - + +
135A GLN* 3.3 6.0 + - - +
137A CYS* 1.3 76.9 - - - +
139A THR* 1.3 63.6 + - - +
141A ALA* 3.3 9.7 + - - +
142A VAL* 3.6 5.2 + - - +
159A TYR* 3.2 27.5 + + - -
165A THR 3.3 19.4 + - - -
166A PHE* 3.6 8.3 - + - -
167A ARG* 2.9 43.5 + - - +
170A ARG* 3.9 28.5 - - + -
171A LEU* 3.4 30.2 - - + +
174A VAL* 4.7 2.0 - - - +
506A EDO 4.1 5.0 + - - -
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Residues in contact with THR 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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104A THR 3.3 27.6 - - - +
105A GLY* 4.5 4.0 - - - -
135A GLN 3.0 16.9 + - - -
136A ILE 3.2 4.9 + - - -
138A HIS* 1.3 77.0 - - - +
140A LEU* 1.3 57.6 + - - +
142A VAL* 3.0 7.6 + - - +
143A THR* 2.9 40.1 + - + +
174A VAL* 4.4 15.9 - - + +
177A ARG* 4.5 4.5 - - - +
333A GLY* 3.4 8.1 - - - -
334A VAL* 3.0 28.4 + - - +
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Residues in contact with LEU 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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102A ILE* 4.0 11.4 - - + -
103A THR 3.4 23.6 - - - +
104A THR* 4.0 9.0 - - + -
117A ILE* 3.7 37.0 - - + -
136A ILE* 2.9 37.0 + - + +
137A CYS* 3.8 4.9 - - - +
139A THR* 1.3 71.5 - - - +
141A ALA* 1.3 61.1 + - - +
142A VAL 3.0 5.2 - - - -
143A THR* 3.4 5.2 - - - +
144A CYS* 3.0 30.0 + - - +
218A LEU* 3.4 15.6 - - + +
220A ILE* 5.8 0.2 - - + -
264A VAL* 4.0 26.0 - - + -
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Residues in contact with ALA 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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137A CYS 3.1 14.5 + - - +
138A HIS* 3.5 11.7 - - - +
139A THR 3.2 0.6 - - - -
140A LEU* 1.3 75.2 - - - +
142A VAL* 1.3 59.0 + - - +
144A CYS* 3.6 9.1 - - - -
145A GLN* 3.0 21.1 + - - -
157A ALA* 3.6 24.0 - - + +
159A TYR* 4.6 4.7 - - + -
171A LEU* 4.1 14.1 - - + -
189A VAL* 3.6 14.1 - - + +
218A LEU* 3.8 2.2 - - - +
220A ILE* 4.1 8.3 - - + -
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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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138A HIS 3.8 12.1 - - - +
139A THR 3.0 1.7 + - - +
140A LEU 3.0 0.2 - - - -
141A ALA* 1.3 80.7 - - - +
143A THR* 1.3 61.3 + - - +
144A CYS 3.1 1.8 - - - -
145A GLN* 2.9 31.0 + - - +
146A LEU 3.9 1.7 + - - -
171A LEU* 3.7 29.2 - - + +
174A VAL* 3.5 29.2 - - + +
175A ALA* 3.9 19.5 - - - +
178A TYR* 5.1 2.2 - - + -
180A LEU* 4.1 17.8 - - + +
185A VAL* 3.8 19.1 - - + -
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Residues in contact with THR 143 (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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102A ILE* 3.5 3.9 - - - +
103A THR* 2.8 40.6 + - + +
105A GLY 5.0 0.2 - - - +
139A THR* 2.9 22.9 + - + +
140A LEU* 3.4 14.7 - - - -
142A VAL* 1.3 75.3 - - - +
144A CYS* 1.3 63.5 + - - +
145A GLN 3.0 1.9 + - - -
146A LEU* 3.1 16.8 + - + +
152A GLY* 3.1 21.3 - - - -
174A VAL* 4.8 0.9 - - + -
178A TYR* 3.7 37.7 - - + +
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Residues in contact with CYS 144 (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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102A ILE* 3.7 29.6 - - + -
140A LEU 3.0 24.8 + - - +
141A ALA 3.6 15.3 - - - -
142A VAL 3.1 0.2 - - - -
143A THR* 1.3 77.2 + - - +
145A GLN* 1.3 59.0 + - - +
153A GLY 2.9 21.7 + - - +
154A GLU 3.0 8.5 + - - -
155A GLY 3.2 18.9 + - - -
156A LYS 4.1 4.7 - - - -
157A ALA* 3.6 20.0 - - - -
217A ALA* 4.1 4.6 - - + +
218A LEU* 4.1 12.1 - - + -
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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