Contacts of the helix formed by residues 148 - 160 (chain A) in PDB entry 2CND
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 ILE 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A CYS* 3.6 22.2 - - - -
145A GLY 3.3 17.1 + - - +
146A SER* 2.8 6.0 - - - +
147A GLY* 1.3 76.9 - - - +
149A THR* 1.3 62.7 + - + +
150A PRO 3.3 0.7 - - - -
151A MET* 3.1 12.7 + - + -
152A TYR* 2.7 37.0 + - + +
155A ILE* 5.3 0.7 - - + -
171A LEU* 4.2 13.0 - - + -
173A TYR* 3.6 27.4 - - + +
182A LEU* 4.2 7.9 - - + -
183A LEU* 3.9 27.4 - - + -
187A LEU* 4.2 21.1 - - + -
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Residues in contact with THR 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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65A THR* 3.3 15.8 + - - +
66A PRO 5.0 2.1 - - - +
67A THR* 3.7 27.8 - - + -
79A LEU* 4.4 10.5 - - + -
146A SER* 3.2 5.2 + - - +
148A ILE* 1.3 88.0 - - + +
150A PRO* 1.3 80.1 - - - +
152A TYR* 3.9 7.2 - - - +
153A GLN* 3.2 20.8 + - - +
182A LEU* 5.8 0.7 - - + -
183A LEU* 4.4 4.3 - - + -
271A FAD 2.6 38.9 + - + +
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Residues in contact with PRO 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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46A GLY* 5.8 0.5 - - - -
65A THR* 3.7 24.5 - - + +
146A SER 4.0 1.8 - - - +
147A GLY 3.5 15.9 - - - +
149A THR* 1.3 99.3 - - - +
151A MET* 1.3 62.1 + - - +
153A GLN* 3.3 17.9 + - - +
154A ILE* 3.6 10.7 + - - +
242A CYS* 3.8 19.3 - - - -
270A PHE* 3.5 32.4 - - + -
271A FAD 3.9 15.3 - - + -
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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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141A MET* 3.9 37.0 - - + +
142A ILE 4.0 6.5 - - - +
143A CYS* 4.1 13.2 - - + -
147A GLY 3.7 13.2 - - - +
148A ILE* 3.1 14.8 + - + +
150A PRO* 1.3 71.9 - - - +
152A TYR* 1.3 57.4 + - - +
153A GLN 3.0 5.4 + - - -
154A ILE* 3.1 7.1 + - - +
155A ILE* 2.9 32.5 + - + +
171A LEU* 4.5 3.1 - - + -
240A LEU* 3.6 9.2 - - - +
241A ALA* 3.5 20.0 - - - +
242A CYS* 3.3 38.4 - - + +
270A PHE* 3.9 17.7 - - + -
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Residues in contact with TYR 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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66A PRO 5.5 0.7 - - - -
67A THR* 3.8 26.3 + - + -
148A ILE* 2.7 23.1 + - + +
149A THR* 3.3 5.4 + - - +
151A MET* 1.3 72.5 - - - +
153A GLN* 1.3 57.4 + - - +
155A ILE* 3.9 10.0 - - - +
156A GLN* 3.1 46.7 + - - +
183A LEU* 3.8 39.9 - - + +
186A GLU* 3.6 31.7 - - + +
187A LEU* 4.4 10.5 - - + -
189A ARG* 4.7 1.2 + - - -
190A TRP* 3.1 41.4 - + - -
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Residues in contact with GLN 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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43A LEU* 4.2 13.7 + - - +
44A PRO 3.8 12.7 + - - -
45A ILE* 3.8 21.6 - - + +
46A GLY* 2.8 30.0 + - - -
47A LYS 3.4 16.5 + - - +
65A THR* 3.6 21.6 - - + +
66A PRO* 4.8 11.2 + - - +
68A SER 6.2 0.2 - - - +
149A THR 3.2 10.8 + - - +
150A PRO* 3.3 12.5 - - - +
151A MET 3.0 0.6 + - - -
152A TYR* 1.3 75.7 - - - +
154A ILE* 1.3 66.4 + - - +
156A GLN* 3.3 9.0 + - - +
157A ALA* 3.0 21.1 + - - +
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Residues in contact with ILE 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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45A ILE* 4.0 18.6 - - + -
46A GLY* 5.1 8.1 - - - +
119A VAL* 5.4 0.7 - - + -
121A TYR* 4.3 17.0 - - + -
127A PHE* 4.0 15.5 - - + -
139A LEU* 4.3 8.3 - - + -
141A MET* 3.9 18.2 - - + -
150A PRO 3.6 11.0 + - - +
151A MET* 3.1 7.1 + - - +
153A GLN* 1.3 74.8 - - + +
155A ILE* 1.3 66.6 + - - +
157A ALA* 2.9 3.1 + - - +
158A VAL* 2.9 39.0 + - + +
240A LEU* 3.6 30.5 - - + -
270A PHE* 4.5 9.6 - - + -
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Residues in contact with ILE 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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141A MET* 3.7 24.5 - - + -
148A ILE* 5.3 0.9 - - + -
151A MET* 2.9 25.6 + - + +
152A TYR* 4.0 7.9 - - - +
154A ILE* 1.3 77.3 - - - +
156A GLN* 1.3 60.7 + - - +
158A VAL* 4.0 0.7 - - - +
159A LEU* 3.2 30.0 + - + +
169A MET* 3.8 24.0 - - + -
171A LEU* 4.5 10.8 - - + -
187A LEU* 4.0 18.4 - - + -
190A TRP* 3.5 29.8 - - + -
198A LEU* 3.9 22.0 - - + -
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Residues in contact with GLN 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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67A THR 4.1 8.9 + - - +
68A SER 3.9 13.9 - - - +
69A MET* 2.9 44.9 - - + +
70A VAL 4.8 0.9 + - - -
152A TYR* 3.1 46.4 + - - +
153A GLN* 3.6 7.1 - - - +
154A ILE 3.1 0.2 - - - -
155A ILE* 1.3 77.0 - - - +
157A ALA* 1.3 56.8 + - - +
159A LEU* 3.9 2.2 - - - +
160A ARG* 2.9 31.8 + - + +
190A TRP* 3.6 24.9 - - + -
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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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45A ILE* 4.0 27.8 - - + -
121A TYR* 4.2 13.0 - - + -
153A GLN 3.0 12.3 + - - +
154A ILE* 2.9 10.5 + - - +
156A GLN* 1.3 73.9 - - - +
158A VAL* 1.3 66.8 + - - +
160A ARG* 2.8 18.8 + - - +
161A ASP* 3.0 14.2 + - - +
165A ASP* 4.6 0.9 - - - -
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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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121A TYR* 3.6 20.9 - - + +
139A LEU* 5.1 0.7 - - + -
154A ILE* 2.9 27.8 + - + +
155A ILE 4.0 3.1 - - - +
157A ALA* 1.3 70.5 - - - +
159A LEU* 1.3 59.0 + - + +
161A ASP* 2.9 12.3 + - - +
162A GLN* 2.6 27.7 + - - +
165A ASP* 3.1 40.8 + - - +
167A THR* 3.9 25.8 - - + +
169A MET* 4.0 24.2 - - + -
197A ARG* 4.8 1.6 - - - -
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Residues in contact with LEU 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 ILE* 3.2 25.5 + - + +
156A GLN* 4.2 2.7 - - - +
158A VAL* 1.3 79.2 - - + +
160A ARG* 1.3 63.3 + - - +
162A GLN* 3.0 22.2 + - + +
169A MET* 4.1 9.9 - - + -
190A TRP* 3.7 35.7 - - + +
194A TYR* 3.4 59.4 + - + -
197A ARG* 3.7 22.9 - - + -
198A LEU* 4.8 4.3 - - + -
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Residues in contact with ARG 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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69A MET* 3.3 31.9 - - + +
70A VAL* 5.0 10.5 - - - -
71A ASP* 3.1 29.4 + - - +
156A GLN* 2.9 19.1 + - + +
157A ALA* 2.8 9.6 + - - +
159A LEU* 1.3 78.3 - - - +
161A ASP* 1.3 58.2 + - - +
162A GLN 2.9 10.9 + - - +
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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