Contacts of the helix formed by residues 152 - 162 (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 GLU 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D TRP* 3.9 6.1 - - + +
147D SER* 3.5 11.7 + - - +
150D ALA* 3.0 17.1 + - + +
151D SER* 1.3 79.4 - - - +
153D ALA* 1.3 68.3 + - - +
154D GLU 3.2 2.0 - - - -
155D HIS* 3.0 20.7 + - - +
156D GLN* 3.3 14.5 + - + +
5F ARG* 3.1 36.2 + - - +
6F THR 3.0 23.9 - - - +
7F LEU* 3.5 27.8 - - + -
112I GLN* 3.3 15.4 + - - +
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Residues in contact with ALA 153 (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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126D LEU* 4.2 8.5 - - + +
130D LEU 4.1 1.5 - - - +
131D ARG* 3.2 39.3 - - - +
132D SER 3.9 2.0 - - - +
133D TRP* 3.3 27.0 - - + +
147D SER 4.9 0.2 + - - -
151D SER* 5.5 0.9 - - - -
152D GLU* 1.3 78.5 - - - +
154D GLU* 1.3 52.4 + - - +
156D GLN* 2.8 8.2 + - - +
157D ARG* 2.7 34.9 + - - +
137J ARG* 6.1 1.1 - - - +
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Residues in contact with GLU 154 (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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131D ARG* 5.5 6.5 + - - +
151D SER* 4.6 19.0 - - - +
152D GLU 4.4 0.6 - - - +
153D ALA* 1.3 79.0 - - - +
155D HIS* 1.3 57.9 + - + +
157D ARG* 3.3 41.2 + - - +
158D ALA* 3.1 24.8 + - - +
137J ARG* 4.2 17.8 + - - +
172J SER* 5.4 7.0 - - - +
212J GLN* 4.1 19.1 + - - +
223J SER* 4.9 6.5 + - - -
224J SER 4.4 3.5 + - - +
225J ILE* 4.0 35.2 - - + +
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Residues in contact with HIS 155 (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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151D SER 3.8 19.7 - - - -
152D GLU* 3.0 21.9 + - - +
154D GLU* 1.3 78.2 - - + +
156D GLN* 1.3 63.3 + - - +
158D ALA* 3.2 8.8 - - - +
159D TYR* 3.2 22.2 + - - +
4F PRO* 5.5 4.5 - - - +
5F ARG* 3.8 28.2 + - + +
171J PRO* 3.3 35.6 - - + +
172J SER* 2.9 35.2 + - - -
212J GLN* 5.0 13.8 - - + +
213J VAL* 5.7 8.0 - - + +
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Residues in contact with GLN 156 (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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97D TRP* 4.3 1.4 - - - -
114D GLU* 2.9 38.7 - - - +
126D LEU* 3.8 19.5 - - + -
133D TRP* 3.7 16.5 - - + -
152D GLU* 3.7 14.1 + - - +
153D ALA 2.8 6.5 + - - +
155D HIS* 1.3 75.7 - - - +
157D ARG* 1.3 57.9 + - - +
158D ALA 2.9 1.6 - - - -
159D TYR* 3.0 6.7 + - - +
160D LEU* 2.7 41.8 + - + +
3F ALA* 4.3 11.0 - - - +
4F PRO* 6.1 0.6 - - - +
5F ARG* 2.6 41.1 + - - +
6F THR* 4.4 6.9 + - - +
7F LEU* 5.9 0.4 - - - +
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Residues in contact with ARG 157 (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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126D LEU* 5.0 0.2 - - - +
129D ASP 5.1 0.7 - - - -
130D LEU* 3.3 36.8 + - + +
131D ARG* 4.0 43.5 - - - +
153D ALA 2.7 14.6 + - - +
154D GLU* 3.3 36.7 + - - +
156D GLN* 1.3 71.5 - - - +
158D ALA* 1.3 61.0 + - - +
160D LEU* 4.8 2.7 - - - -
161D GLU* 3.3 66.7 + - - +
212J GLN* 5.8 0.8 - - - +
217J LYS* 5.3 8.7 + - - +
219J ALA* 5.6 7.9 - - - +
220J GLN 6.0 0.8 - - - +
223J SER* 4.9 5.3 + - - -
225J ILE* 6.0 0.4 - - - +
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Residues in contact with ALA 158 (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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154D GLU 3.1 14.2 + - - +
155D HIS* 3.2 16.4 - - - +
156D GLN 2.9 1.2 - - - -
157D ARG* 1.3 75.6 - - - +
159D TYR* 1.3 65.4 + - - +
162D ASP* 3.1 30.0 + - - +
163D THR* 3.4 3.8 + - - +
212J GLN* 3.5 25.8 - - - +
217J LYS* 4.2 13.2 - - - +
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Residues in contact with TYR 159 (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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7D TYR* 4.0 4.3 - - - -
99D HIS* 3.4 32.2 + + - -
155D HIS 3.2 9.8 + - - +
156D GLN* 3.0 14.1 + - - +
158D ALA* 1.3 78.2 - - - +
160D LEU* 1.3 77.9 + - + +
163D THR* 3.1 31.1 + - + -
164D CYS* 2.6 62.9 + - + +
1F VAL* 2.7 25.7 + - + -
2F MET 3.6 5.6 - - - -
3F ALA* 3.4 37.8 + - + -
4F PRO* 3.6 17.0 - - + -
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Residues in contact with LEU 160 (chain D).
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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99D HIS* 4.7 0.4 - - + -
100D GLY 4.0 19.7 - - - +
101D CYS* 3.7 12.9 - - + +
109D PHE* 3.9 7.6 - - + -
112D GLY* 5.0 0.9 - - - -
113D TYR 3.5 31.2 - - - +
114D GLU* 4.4 10.3 - - + +
126D LEU* 4.0 15.7 - - + -
130D LEU* 3.9 37.2 - - + -
156D GLN 2.7 22.3 + - - +
157D ARG 4.5 0.2 - - - +
159D TYR* 1.3 98.7 - - + +
161D GLU* 1.3 57.6 + - - +
164D CYS* 3.8 2.8 - - - +
165D VAL* 3.2 21.5 - - - +
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Residues in contact with GLU 161 (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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109D PHE* 3.9 40.1 - - + +
129D ASP 5.4 0.9 - - - +
130D LEU* 3.9 14.7 - - + +
131D ARG* 5.9 0.2 + - - -
157D ARG* 3.3 54.1 + - - +
158D ALA 4.8 0.2 - - - +
160D LEU* 1.3 77.0 - - - +
162D ASP* 1.3 59.5 + - + +
165D VAL* 3.4 15.5 - - - +
217J LYS* 6.0 1.3 - - - +
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Residues in contact with ASP 162 (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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158D ALA 3.1 12.8 + - - +
160D LEU 3.2 1.2 - - - -
161D GLU* 1.3 82.0 - - + +
163D THR* 1.3 68.9 + - - +
164D CYS 3.6 1.1 - - - -
165D VAL* 3.6 4.3 - - - +
166D GLU* 3.0 33.7 + - - +
199J LYS* 4.7 16.0 + - - +
217J LYS* 3.5 35.6 - - - +
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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