Contacts of the helix formed by residues 144 - 160 (chain A) in PDB entry 1N3Y
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 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLY 5.3 0.7 - - - -
142A SER 3.6 4.4 + - - -
143A ILE* 1.3 77.8 - - - +
145A SER* 1.3 59.3 + - - +
146A ARG* 3.6 11.4 + - - +
147A ASN* 3.0 37.8 + - - +
148A PHE* 2.8 26.5 + - - +
202A GLN* 4.4 0.2 - - - -
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Residues in contact with SER 145 (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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143A ILE 3.8 0.8 + - - -
144A SER* 1.3 73.4 - - - +
146A ARG* 1.3 62.0 + - - +
148A PHE* 3.3 2.7 + - - +
149A ALA* 3.0 24.1 + - - +
202A GLN* 4.2 13.2 + - - -
204A GLN* 5.4 4.0 + - - -
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Residues in contact with ARG 146 (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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144A SER* 3.2 8.1 + - - +
145A SER* 1.3 80.6 - - - +
147A ASN* 1.3 82.2 + - - +
149A ALA* 3.3 7.5 + - - +
150A THR* 3.0 32.9 + - - +
301A ASP* 3.6 28.7 + - - -
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Residues in contact with ASN 147 (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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143A ILE* 3.9 9.8 - - + +
144A SER* 3.0 30.1 + - - +
146A ARG* 1.3 103.2 + - - +
148A PHE* 1.3 60.9 + - - +
150A THR* 3.2 7.1 + - - -
151A MET 2.9 24.4 + - - -
300A PHE* 3.5 48.8 + - + +
301A ASP* 4.9 1.7 - - - +
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Residues in contact with PHE 148 (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 ILE* 4.4 7.6 - - + -
138A ASP 4.1 2.9 - - - -
139A GLY* 4.1 4.3 - - - -
143A ILE* 3.6 8.4 - - + +
144A SER 2.8 12.6 + - - +
145A SER* 3.7 5.4 - - - +
147A ASN* 1.3 76.3 - - - +
149A ALA* 1.3 66.3 + - - +
151A MET* 3.1 31.4 + - + +
152A MET* 3.0 35.1 + - + +
173A GLN* 3.5 35.9 - - - -
200A VAL* 3.8 28.9 - - + -
202A GLN* 3.4 49.6 - - + +
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Residues in contact with ALA 149 (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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145A SER 3.0 13.7 + - - +
146A ARG* 3.5 10.5 - - - +
147A ASN 3.2 0.2 - - - -
148A PHE* 1.3 80.9 - - - +
150A THR* 1.3 62.2 + - - +
152A MET* 3.2 8.3 + - - +
153A ASN* 3.0 31.1 + - - +
156A ARG* 4.4 0.2 + - - -
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Residues in contact with THR 150 (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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146A ARG* 3.0 19.3 + - - +
147A ASN* 3.5 12.8 + - - -
149A ALA* 1.3 77.6 - - - +
151A MET* 1.3 61.7 + - - +
153A ASN* 3.2 13.1 + - + +
154A PHE* 3.1 21.2 + - + +
300A PHE* 3.2 35.0 - - - +
301A ASP* 3.9 17.6 + - - +
303A LEU* 5.6 0.7 - - + -
304A LYS* 4.9 7.6 - - - +
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Residues in contact with MET 151 (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 ILE* 4.0 26.2 - - + -
138A ASP 3.2 27.6 - - - +
143A ILE* 4.4 7.4 - - + -
147A ASN 2.9 12.7 + - - +
148A PHE* 3.4 33.9 - - + +
150A THR* 1.3 77.2 - - - +
152A MET* 1.3 63.0 + - - +
154A PHE* 3.1 5.0 + - - +
155A VAL* 3.0 21.1 + - + +
238A ILE* 3.6 41.1 - - + +
300A PHE* 3.9 17.0 - - + -
303A LEU* 4.0 12.8 - - + -
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Residues in contact with MET 152 (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 ILE* 3.5 30.3 - - - -
148A PHE* 3.0 34.9 + - + +
149A ALA* 3.2 9.4 + - - +
151A MET* 1.3 77.9 - - - +
153A ASN* 1.3 57.1 + - - +
155A VAL* 3.3 10.1 + - + +
156A ARG* 2.9 52.6 + - - +
171A LEU* 4.2 3.4 - - + -
197A LEU* 3.7 32.3 - - + +
200A VAL* 3.7 36.8 - - + +
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Residues in contact with ASN 153 (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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149A ALA* 3.0 20.5 + - - +
150A THR* 3.2 14.0 + - - +
152A MET* 1.3 75.9 - - - +
154A PHE* 1.3 57.6 + - - +
156A ARG* 3.0 29.3 + - - +
157A ALA* 2.9 29.7 + - - +
307A GLN* 5.4 0.2 - - - -
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Residues in contact with PHE 154 (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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135A PHE* 4.6 3.4 - + - -
150A THR 3.1 11.9 + - - +
151A MET 3.2 8.5 - - - +
153A ASN* 1.3 75.5 - - - +
155A VAL* 1.3 68.5 + - - +
157A ALA* 3.2 2.1 + - - +
158A VAL* 2.9 46.3 + - + +
238A ILE* 3.9 30.3 - - + -
267A ILE* 4.0 10.8 - - + -
303A LEU* 3.2 53.4 - - + -
304A LYS 4.2 0.7 - - - +
306A ILE* 3.9 17.7 - - + -
307A GLN* 3.5 32.8 - - + +
310A LEU* 3.9 15.9 - - + -
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Residues in contact with VAL 155 (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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135A PHE* 4.0 41.7 - - + -
137A ILE* 4.2 19.7 - - + -
151A MET* 3.0 20.3 + - + +
152A MET* 3.6 17.3 - - + +
154A PHE* 1.3 80.2 - - - +
156A ARG* 1.3 62.3 + - - +
158A VAL* 3.8 1.6 - - - +
159A ILE* 3.0 42.8 + - + +
171A LEU* 4.9 4.0 - - + -
197A LEU* 4.1 16.8 - - + -
238A ILE* 4.2 7.0 - - + -
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Residues in contact with ARG 156 (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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149A ALA 4.4 0.2 + - - -
152A MET* 2.9 50.7 + - - +
153A ASN* 3.0 34.8 - - - +
155A VAL* 1.3 77.3 - - - +
157A ALA* 1.3 56.6 + - - +
159A ILE* 3.4 3.9 + - - +
160A SER* 3.0 30.8 + - - -
194A LEU* 3.9 23.4 + - + +
197A LEU* 2.8 52.2 + - + +
198A ALA* 4.2 10.3 + - - +
200A VAL* 5.8 0.2 - - - +
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Residues in contact with ALA 157 (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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153A ASN 2.9 15.9 + - - +
154A PHE 3.2 3.1 + - - +
156A ARG* 1.3 76.6 - - - +
158A VAL* 1.3 62.2 + - - +
160A SER* 2.7 24.0 + - - -
161A GLN* 3.3 14.1 + - - +
307A GLN* 3.4 36.1 + - - +
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Residues in contact with VAL 158 (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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135A PHE* 3.8 21.8 - - + -
154A PHE* 2.9 52.8 + - + +
155A VAL 3.8 3.1 - - - +
157A ALA* 1.3 72.9 - - - +
159A ILE* 1.3 67.3 + - - +
161A GLN* 3.0 19.1 + - - +
162A PHE* 3.2 32.5 - - + -
169A PHE* 5.2 1.1 - - + -
307A GLN* 4.5 13.7 - - + +
310A LEU* 4.2 20.4 - - + -
311A LYS* 5.6 4.3 - - + +
314A ILE* 4.9 4.0 - - + -
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Residues in contact with ILE 159 (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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135A PHE* 3.9 6.5 - - + -
155A VAL* 3.0 37.6 + - + +
156A ARG* 3.8 4.5 - - - +
158A VAL* 1.3 76.0 - - - +
160A SER* 1.3 61.5 - - - +
161A GLN 3.0 1.6 + - - -
162A PHE* 3.1 21.3 + - - +
169A PHE* 3.8 46.8 - - + -
182A PHE* 4.5 7.2 - - + -
187A PHE* 3.8 26.7 - - + -
193A PRO* 6.3 0.2 - - + -
194A LEU* 4.0 16.6 - - + -
197A LEU* 4.4 20.2 - - + -
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Residues in contact with SER 160 (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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156A ARG 3.0 14.7 + - - -
157A ALA* 2.7 24.1 + - - -
159A ILE* 1.3 76.6 - - - +
161A GLN* 1.3 69.7 + - - +
162A PHE 3.2 7.1 + - - +
194A LEU* 4.4 19.3 - - - +
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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