Contacts of the helix formed by residues 140 - 150 (chain D) in PDB entry 3CII
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 ALA 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D TYR* 3.4 52.0 - - + +
124D LEU* 4.5 1.1 - - + -
135D ALA* 3.8 4.7 - - + -
136D VAL 3.9 7.4 - - - +
137D ASP 2.7 22.3 + - - +
139D ALA* 1.3 70.1 - - - +
141D GLN* 1.3 65.2 + - - +
142D ILE 2.9 5.3 + - - -
143D SER* 2.9 15.1 + - - -
144D GLU* 2.9 10.7 + - - +
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Residues in contact with GLN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLU* 5.5 1.2 + - - -
213A ILE 4.1 13.7 + - - -
214A THR* 3.8 29.4 - - + +
215A LEU 4.4 5.5 + - - +
230A LEU* 3.7 24.8 - - + +
243A LYS* 4.2 14.2 - - - +
135D ALA* 3.6 20.9 - - + +
137D ASP 4.9 0.7 - - - +
138D THR* 4.1 23.4 + - - +
139D ALA 3.4 1.0 - - - -
140D ALA* 1.3 77.5 - - - +
142D ILE* 1.3 55.8 + - + +
144D GLU* 3.4 9.1 - - - +
145D GLN* 3.0 32.6 + - - +
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A THR* 3.8 28.7 - - - +
228A THR* 3.8 33.2 - - + -
229A GLU* 4.1 7.9 - - - +
230A LEU* 4.4 19.5 - - + +
84D TYR* 3.4 48.9 - - + +
139D ALA 4.8 7.6 - - - +
140D ALA 2.9 0.6 + - - -
141D GLN* 1.3 76.7 - - + +
143D SER* 1.3 53.9 + - - +
145D GLN* 3.1 14.4 + - - +
146D LYS* 2.7 36.4 + - - +
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Residues in contact with SER 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.1 6.1 - - - -
123D TYR* 2.7 43.7 + - - -
124D LEU* 4.3 7.2 - - - +
140D ALA 2.9 3.1 + - - -
142D ILE* 1.3 73.8 - - - +
144D GLU* 1.3 63.8 + - - +
146D LYS* 4.0 3.5 - - - +
147D SER* 2.9 28.8 + - - -
8F PHE 5.2 0.2 - - - +
9F LEU* 2.5 40.5 + - - -
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Residues in contact with GLU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A THR* 5.8 3.5 - - - +
124D LEU* 3.8 12.4 - - + +
133D TRP* 3.5 27.5 - - - +
134D THR* 3.6 4.0 - - - +
135D ALA* 3.2 41.6 + - + +
140D ALA 2.9 6.5 + - - -
141D GLN* 3.4 16.0 - - - +
143D SER* 1.3 74.3 - - - +
145D GLN* 1.3 63.7 + - - +
146D LYS 3.1 0.2 - - - -
147D SER* 2.8 21.1 + - - -
148D ASN* 2.8 24.2 + - - +
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Residues in contact with GLN 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU 4.6 2.3 - - - +
216A THR* 3.7 37.0 - - + +
217A TRP 4.7 3.6 + - - -
223A GLY 5.2 2.4 + - - -
225A THR* 3.3 31.2 + - + +
228A THR* 6.0 1.2 - - - +
141D GLN* 3.0 16.2 + - - +
142D ILE* 3.3 18.1 - - - +
144D GLU* 1.3 84.2 - - - +
146D LYS* 1.3 61.9 + - - +
147D SER 3.2 0.2 - - - -
148D ASN* 4.1 9.9 - - - -
149D ASP* 3.0 45.6 + - - +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A THR* 3.2 40.7 + - - +
226A GLN* 4.3 12.5 - - - +
80D THR* 5.3 4.1 - - - +
84D TYR* 3.4 23.5 + - - -
142D ILE* 2.7 19.0 + - - +
143D SER* 4.0 6.7 - - - +
144D GLU 3.1 0.2 + - - -
145D GLN* 1.3 74.2 - - - +
147D SER* 1.3 60.9 + - - +
149D ASP* 4.4 2.1 - - - +
150D ALA* 3.8 20.1 + - - +
8F PHE* 3.5 25.6 - - + +
9F LEU* 3.4 13.2 - - - +
158I ASN* 5.6 4.3 - - - +
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D TRP* 3.8 17.6 - - - -
143D SER 2.9 18.2 + - - -
144D GLU 2.8 3.0 + - - -
146D LYS* 1.3 79.5 - - - +
148D ASN* 1.3 65.8 + - - +
149D ASP 3.2 1.1 - - - -
150D ALA* 3.5 1.5 + - - +
151D SER 3.5 15.1 + - - -
152D GLU* 3.5 15.4 + - - -
7F LEU* 3.5 38.6 - - - +
8F PHE 4.1 10.7 + - - -
9F LEU* 5.5 0.5 - - - +
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Residues in contact with ASN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D SER* 4.0 18.8 - - - -
133D TRP* 2.9 46.6 + - - +
144D GLU* 2.8 21.7 + - - +
145D GLN* 4.3 8.1 - - - -
147D SER* 1.3 77.8 - - - +
149D ASP* 1.3 65.2 + - - +
151D SER* 3.6 9.7 + - - -
137J ARG* 5.5 6.8 + - - -
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Residues in contact with ASP 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLU 5.2 4.3 - - - +
223A GLY 4.7 8.7 - - - +
225A THR* 5.8 0.5 - - - +
145D GLN* 3.0 37.0 + - - +
146D LYS* 4.7 2.2 - - - +
147D SER 3.2 0.6 - - - -
148D ASN* 1.3 83.3 - - - +
150D ALA* 1.3 57.8 + - + +
151D SER* 3.3 7.3 + - - -
137J ARG* 5.6 3.6 - - - +
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS 3.8 16.1 + - - +
147D SER* 3.5 6.0 + - - +
148D ASN 3.4 0.2 - - - -
149D ASP* 1.3 77.7 - - + +
151D SER* 1.3 69.7 + - - +
152D GLU* 3.0 17.8 + - + +
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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