Contacts of the helix formed by residues 148 - 160 (chain A) in PDB entry 3NC0
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A TRP* 3.3 11.1 + - - -
147A PRO* 1.3 88.2 - - + +
149A PHE* 1.3 65.4 + - - +
150A ILE 3.5 0.7 - - - -
151A SER* 3.3 12.2 + - - -
152A ASP* 2.8 47.2 + - - +
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Residues in contact with PHE 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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107A VAL* 6.5 0.2 - - + -
134A LEU* 4.7 14.1 - - + -
138A LEU* 3.4 43.7 - - + -
142A TRP* 3.5 24.5 - + + -
146A TRP* 3.1 52.0 + + + +
147A PRO 3.1 3.2 - - - -
148A THR* 1.3 81.0 - - - +
150A ILE* 1.3 85.6 + - + +
152A ASP* 3.6 0.7 - - - +
153A ILE* 3.1 64.3 + - + +
170A ILE* 4.5 10.5 - - + -
171A LEU* 5.3 0.4 - - + -
174A LEU* 4.5 7.0 - - + -
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Residues in contact with ILE 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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142A TRP* 4.3 18.0 - - + +
147A PRO 4.5 3.5 + - - +
149A PHE* 1.3 98.6 - - + +
151A SER* 1.3 72.5 + - - +
153A ILE* 3.2 12.9 - - + +
154A VAL* 2.9 25.6 - - - +
171A LEU* 4.5 2.9 - - + -
174A LEU* 5.2 4.7 - - + -
198A MET* 5.5 2.7 - - - -
201A GLU* 3.0 38.8 - - + +
204A GLN* 3.7 17.9 - - - +
205A ILE* 3.4 38.8 - - + -
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Residues in contact with SER 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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147A PRO 5.3 0.7 + - - -
148A THR* 3.3 13.6 + - - -
149A PHE 3.1 0.6 - - - -
150A ILE* 1.3 82.5 - - - +
152A ASP* 1.3 66.4 + - - +
154A VAL* 3.0 16.2 + - - +
155A GLY* 3.1 11.1 + - - -
204A GLN* 3.6 20.8 + - - +
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Residues in contact with ASP 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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146A TRP* 3.5 14.3 - - + -
148A THR* 2.8 49.4 + - - +
149A PHE* 3.6 4.3 - - - +
151A SER* 1.3 78.7 - - - +
153A ILE* 1.3 58.9 + - + +
154A VAL 3.3 0.2 + - - -
155A GLY* 3.3 2.3 + - - -
156A ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 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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146A TRP* 6.2 0.7 - - + -
149A PHE* 3.1 58.2 + - + +
150A ILE* 3.2 24.2 - - + +
152A ASP* 1.3 78.6 - - + +
154A VAL* 1.3 57.3 + - + +
156A ALA* 3.9 4.7 - - - +
157A SER* 2.7 33.6 + - - -
167A ASN* 3.4 23.5 - - + +
170A ILE* 5.6 6.1 - - + -
171A LEU* 3.9 26.9 - - + -
205A ILE* 5.2 1.1 - - + -
208A LEU* 5.3 0.4 - - - -
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Residues in contact with VAL 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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150A ILE 2.9 25.8 - - - +
151A SER* 3.0 9.1 + - - +
153A ILE* 1.3 77.8 - - + +
155A GLY* 1.3 66.6 + - - +
157A SER* 2.9 15.4 + - - -
158A ARG* 3.1 41.9 + - - +
204A GLN* 4.4 20.2 - - + +
205A ILE* 4.6 16.6 - - + -
208A LEU* 4.1 22.0 - - + -
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A SER 3.1 9.5 + - - -
152A ASP* 3.3 3.1 + - - -
154A VAL* 1.3 79.4 - - - +
156A ALA* 1.3 61.5 - - - +
158A ARG* 3.0 18.8 + - - +
159A THR* 3.1 17.9 + - - -
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Residues in contact with ALA 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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152A ASP 2.9 17.4 + - - +
153A ILE* 3.9 8.7 - - - +
154A VAL 3.2 0.2 - - - -
155A GLY* 1.3 75.6 - - - +
157A SER* 1.3 60.8 + - - +
159A THR* 3.5 5.1 + - - -
160A SER* 3.3 21.5 + - - +
163A LEU* 3.7 35.9 - - + +
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Residues in contact with SER 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 ILE 2.7 18.7 + - - -
154A VAL 2.9 12.1 + - - -
156A ALA* 1.3 78.3 - - - +
158A ARG* 1.3 58.2 + - - +
159A THR 3.2 0.7 - - - -
160A SER 3.0 16.3 - - - +
161A GLU* 4.7 0.9 - - - -
163A LEU 4.0 0.2 - - - -
164A CYS* 3.2 32.9 - - - +
167A ASN* 3.2 22.9 + - - +
168A MET* 5.9 0.2 - - - +
208A LEU* 3.7 23.6 - - - +
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Residues in contact with ARG 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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154A VAL* 3.6 31.5 - - - +
155A GLY* 3.0 12.0 + - - +
157A SER* 1.3 75.6 - - - +
159A THR* 1.3 61.4 + - - +
204A GLN 4.3 1.2 + - - -
207A GLN* 3.9 32.1 + - - +
208A LEU* 4.1 21.8 - - + +
211A PHE* 3.9 44.2 - - + +
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Residues in contact with THR 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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155A GLY 3.1 15.2 + - - -
156A ALA* 4.1 5.0 - - - -
157A SER 3.2 0.2 - - - -
158A ARG* 1.3 81.7 - - - +
160A SER* 1.3 61.9 + - - +
161A GLU 4.1 0.9 + - - -
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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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115A SER* 5.5 1.2 + - - -
156A ALA 3.3 6.0 + - - +
157A SER 3.0 15.7 - - - +
159A THR* 1.3 80.9 - - - +
161A GLU* 1.3 63.9 + - - +
162A SER* 3.5 9.7 + - - -
163A LEU* 3.2 35.5 + - - +
164A CYS 3.1 11.3 + - - -
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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