Contacts of the helix formed by residues 146 - 158 (chain D) in PDB entry 3CJC
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 SER 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D SER* 3.8 20.0 - - - -
109D PHE* 3.6 27.3 - - - -
142D ALA 2.8 21.1 + - - -
143D GLU* 3.3 2.7 + - - -
144D ILE 3.3 0.4 - - - -
145D ASN* 1.3 74.8 + - - +
147D LEU* 1.3 64.2 + - - +
148D TYR 3.2 2.5 - - - -
149D ASP* 3.2 27.8 + - - +
150D VAL* 3.3 13.0 + - - +
185D ARG* 4.7 1.9 + - - +
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Residues in contact with LEU 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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109D PHE* 4.4 2.5 - - + -
113D PRO* 4.5 1.6 - - + -
131D VAL* 4.3 24.7 - - + -
133D LEU* 3.3 29.8 - - + -
143D GLU 3.3 9.3 + - - +
144D ILE* 3.4 23.1 - - - +
145D ASN 3.3 0.6 - - - -
146D SER* 1.3 75.3 - - - +
148D TYR* 1.3 65.8 + - - +
150D VAL* 3.0 23.4 + - + +
151D TYR* 3.0 14.2 + - - +
165D LEU* 4.1 17.2 - - + +
169D PHE* 3.3 37.9 - - + -
186D LEU* 4.1 11.0 - - + -
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Residues in contact with TYR 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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145D ASN 3.6 14.8 + - - +
147D LEU* 1.3 78.7 - - - +
149D ASP* 1.3 69.7 + - - +
151D TYR* 3.6 6.1 + + - +
152D LEU* 3.0 45.7 + - + +
185D ARG* 4.0 43.1 - - + -
186D LEU* 4.2 16.5 - - + +
189D SER* 4.5 15.7 + - - -
191D THR* 5.5 1.8 - - - -
192D PHE* 3.7 31.4 - + - -
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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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97D TYR* 3.9 14.6 + - + +
146D SER* 3.2 17.4 + - - +
147D LEU 3.1 0.4 - - - -
148D TYR* 1.3 84.1 - - - +
150D VAL* 1.3 56.4 + - - +
152D LEU* 3.1 13.5 + - + +
153D ASP* 2.7 35.5 + - - +
185D ARG* 3.2 32.0 + - - -
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Residues in contact with VAL 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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95D TYR* 4.4 0.6 + - - +
97D TYR* 3.8 40.4 + - + -
109D PHE* 4.0 11.0 - - + -
113D PRO* 4.4 7.4 - - + -
115D VAL* 4.1 13.5 - - + -
131D VAL* 3.8 36.3 - - + -
146D SER 3.5 13.9 - - - +
147D LEU* 3.0 16.7 + - + +
149D ASP* 1.3 76.7 - - - +
151D TYR* 1.3 57.2 + - - +
153D ASP* 3.1 5.9 + - - +
154D VAL* 3.0 26.4 + - - +
165D LEU* 5.5 0.4 - - + -
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Residues in contact with TYR 151 (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 VAL* 5.6 0.4 - - - -
147D LEU 3.0 11.0 + - - +
148D TYR* 3.8 10.1 - + - +
150D VAL* 1.3 73.7 - - - +
152D LEU* 1.3 67.7 + - + +
154D VAL* 3.2 17.9 + - - +
155D GLN* 3.0 41.3 + - - +
160D LEU 4.7 0.7 - - - -
161D ASN* 2.7 41.6 + - - +
163D VAL* 3.4 32.5 - - + -
165D LEU* 4.4 8.5 - - + +
191D THR* 4.3 20.9 - - + +
192D PHE* 3.9 24.5 - + + -
217D ALA* 3.6 23.1 - - + +
218D GLY* 4.3 2.1 + - - -
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Residues in contact with LEU 152 (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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148D TYR* 3.0 43.9 + - + +
149D ASP* 3.1 15.5 + - + +
151D TYR* 1.3 76.5 - - + +
153D ASP* 1.3 55.8 + - - +
155D GLN* 3.1 33.6 + - - +
156D GLN* 2.6 48.8 + - - +
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Residues in contact with ASP 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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95D TYR* 3.6 6.9 + - - +
97D TYR* 3.4 28.5 - - + +
149D ASP 2.7 15.3 + - - +
150D VAL 3.1 9.8 + - - +
152D LEU* 1.3 71.3 - - - +
154D VAL* 1.3 63.9 + - - +
155D GLN 3.2 1.6 - - - -
156D GLN* 3.1 14.8 + - - +
157D LYS* 2.7 52.6 + - - +
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Residues in contact with VAL 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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95D TYR* 3.7 16.6 - - + +
115D VAL* 4.2 19.5 - - + -
129D ALA* 4.4 2.5 - - + -
131D VAL* 4.7 8.5 - - + -
150D VAL 3.0 21.2 + - - +
151D TYR* 3.2 13.9 + - - +
153D ASP* 1.3 76.2 - - - +
155D GLN* 1.3 57.7 + - - +
157D LYS* 4.5 3.4 - - - +
158D TRP* 2.9 48.2 + - + -
159D HIS 3.4 2.9 + - - -
160D LEU* 3.7 22.9 - - + +
163D VAL* 3.9 14.6 - - + -
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Residues in contact with GLN 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 TYR* 3.0 43.1 + - + +
152D LEU* 3.1 42.3 - - - +
153D ASP 3.2 0.4 - - - -
154D VAL* 1.3 78.6 - - - +
156D GLN* 1.3 62.1 + - - +
159D HIS* 2.9 38.2 + - - +
160D LEU 4.6 4.7 - - - +
161D ASN* 3.9 23.1 + - - +
191D THR* 5.8 0.2 - - - +
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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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152D LEU* 2.6 50.0 + - - +
153D ASP* 3.1 18.4 + - - +
155D GLN* 1.3 84.0 - - - +
157D LYS* 1.3 61.1 + - + +
159D HIS* 3.8 12.9 - - - -
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Residues in contact with LYS 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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95D TYR* 3.4 44.7 - - + -
153D ASP* 2.7 47.1 + - - +
154D VAL* 3.3 4.5 + - - +
156D GLN* 1.3 82.7 - - - +
158D TRP* 1.3 80.6 + - + +
159D HIS* 3.5 4.4 + - - -
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Residues in contact with TRP 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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93D ASP* 3.7 40.1 + - + -
95D TYR* 3.4 39.3 - + - -
115D VAL* 3.5 23.3 - - + -
116D VAL 4.3 0.2 - - - -
117D LYS* 3.6 57.4 + - + +
129D ALA* 3.9 13.9 - - + -
154D VAL* 2.9 23.7 + - + +
157D LYS* 1.3 92.1 - - + +
159D HIS* 1.3 72.7 - - - +
160D LEU* 3.2 14.0 + - + +
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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