Contacts of the helix formed by residues 139 - 149 (chain J) 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 THR 139 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138J ARG* 1.3 72.3 - - - +
140J TRP* 1.3 54.9 + - - +
141J GLU* 4.1 9.6 + - + +
142J GLU* 2.8 40.8 + - + +
143J SER* 2.6 38.5 + - - -
221J CYS 2.7 26.0 + - - -
222J GLY* 3.5 15.1 - - - -
223J SER 3.8 9.0 - - - -
224J SER* 5.4 2.0 - - - -
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Residues in contact with TRP 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J THR* 1.3 74.1 + - - +
141J GLU* 1.3 81.3 + - + +
143J SER* 3.1 7.2 + - - -
144J LEU* 2.8 49.3 + - + +
154J LEU* 3.6 20.7 - - + +
174J TRP* 3.3 46.4 - + + +
175J ILE 3.3 21.6 + - - -
176J GLY* 4.4 0.4 - - - -
177J VAL 4.6 0.6 + - - -
178J PHE* 3.7 36.3 - + + -
189J MET* 4.0 14.4 - - + -
208J CYS* 3.5 34.8 - - + +
221J CYS* 3.5 13.2 + - + +
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Residues in contact with GLU 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J THR* 4.1 11.1 + - + +
140J TRP* 1.3 99.1 - - + +
142J GLU* 1.3 64.9 + - + +
144J LEU* 2.9 14.9 + - - +
145J LEU* 3.0 27.6 + - + +
221J CYS* 4.7 4.0 + - + +
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Residues in contact with GLU 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ARG* 3.4 30.7 - - + +
139J THR* 2.8 34.3 + - + +
141J GLU* 1.3 77.7 - - + +
143J SER* 1.3 54.1 + - - +
145J LEU* 3.0 13.7 + - + +
146J ALA* 2.7 38.9 + - + +
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Residues in contact with SER 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J ARG* 3.7 10.2 - - - +
139J THR 2.6 30.0 + - - -
140J TRP* 3.2 12.6 - - - -
142J GLU* 1.3 72.6 - - - +
144J LEU* 1.3 60.2 + - - +
146J ALA* 4.0 2.3 - - - +
147J CYS* 3.3 20.8 + - - -
154J LEU* 3.5 17.8 - - - +
174J TRP* 3.3 16.6 + - - -
227J TYR* 3.6 32.2 - - - +
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Residues in contact with LEU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J TRP* 2.8 41.8 + - + +
141J GLU* 3.4 10.5 - - - +
143J SER* 1.3 73.8 - - - +
145J LEU* 1.3 64.3 + - + +
147J CYS* 3.6 2.1 + - - +
148J THR* 2.9 37.8 + - - +
153J SER* 5.9 0.9 - - - -
154J LEU* 4.0 32.5 - - + +
189J MET* 4.3 25.1 - - + -
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Residues in contact with LEU 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J GLU* 3.0 33.0 + - + +
142J GLU* 3.0 15.6 + - + +
144J LEU* 1.3 76.5 - - + +
146J ALA* 1.3 54.0 + - - +
148J THR* 2.9 9.1 + - - -
149J SER* 2.8 36.4 + - - -
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Residues in contact with ALA 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J ARG* 5.2 8.7 - - + +
142J GLU 2.7 21.0 + - - +
143J SER 4.0 1.1 - - - +
145J LEU* 1.3 71.7 - - - +
147J CYS* 1.3 62.4 + - - +
149J SER* 3.3 17.1 + - - -
150J LYS* 3.4 23.3 + - - +
227J TYR* 3.9 31.6 - - + +
229J CYS* 4.8 0.4 - - - -
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Residues in contact with CYS 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J SER 3.3 17.4 + - - +
144J LEU 3.8 4.3 - - - +
145J LEU 3.2 0.8 - - - -
146J ALA* 1.3 77.3 - - - +
148J THR* 1.3 58.8 + - - +
150J LYS* 2.9 22.7 + - - +
152J SER* 2.9 16.2 + - - +
153J SER* 3.6 20.9 - - - +
154J LEU* 3.8 17.9 - - - +
227J TYR* 4.1 3.8 - - - -
228J HIS 3.9 1.3 - - - -
229J CYS* 2.0 57.4 - - - -
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Residues in contact with THR 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J LEU* 2.9 26.4 + - - +
145J LEU* 2.9 7.4 + - - -
147J CYS* 1.3 73.0 - - - +
149J SER* 1.3 60.6 + - - +
150J LYS 3.0 6.3 + - - -
151J ASN* 3.5 11.7 + - - +
152J SER 3.4 12.9 + - - +
153J SER* 5.2 1.9 - - - -
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Residues in contact with SER 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J LEU* 2.8 13.0 + - - -
146J ALA* 3.5 14.6 - - - -
147J CYS 3.2 0.2 - - - -
148J THR* 1.3 76.0 - - - +
150J LYS* 1.3 59.7 + - - +
151J ASN* 3.5 3.2 + - - -
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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