Contacts of the helix formed by residues 168 - 179 (chain D) in PDB entry 3COG
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 ASP 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D CYS 5.2 0.8 + - - -
138D SER* 5.7 1.4 + - - +
140D ILE* 3.9 20.7 - - + +
166D VAL 4.2 0.4 + - - -
167D ILE* 1.3 70.3 - - - +
169D ILE* 1.3 60.1 + - - +
170D GLU* 3.4 8.0 + - - +
171D GLY* 3.1 22.4 + - - -
172D CYS* 2.9 31.8 + - - -
302D LEU* 3.8 30.1 - - + +
305D ARG* 5.2 3.1 + - - -
306D GLN* 3.8 5.9 - - - +
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Residues in contact with ILE 169 (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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156D ILE* 4.3 4.7 - - + -
158D THR* 3.7 33.2 - - + -
167D ILE* 3.9 2.0 - - - +
168D ASP* 1.3 71.9 + - - +
170D GLU* 1.3 57.6 + - - +
172D CYS* 3.3 5.5 + - - +
173D ALA* 2.8 28.8 + - - +
184D LEU* 4.1 3.6 - - + +
186D VAL* 4.0 31.6 - - + -
196D GLN* 3.9 19.1 - - + +
198D PRO* 4.1 11.4 - - + +
201D LEU* 3.5 42.6 - - + +
203D ALA* 4.4 5.8 - - + +
306D GLN* 3.1 14.5 + - - +
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Residues in contact with GLU 170 (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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168D ASP* 3.4 6.8 + - - +
169D ILE* 1.3 76.3 - - - +
171D GLY* 1.3 59.1 + - - +
173D ALA* 3.3 2.4 + - + +
174D HIS* 2.9 30.2 + - + +
200D ALA 4.4 3.6 - - - +
201D LEU* 3.1 46.2 + - + +
306D GLN* 4.7 1.0 + - - -
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Residues in contact with GLY 171 (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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140D ILE* 3.5 25.2 - - - +
168D ASP* 3.1 15.2 + - - -
170D GLU* 1.3 77.6 - - - +
172D CYS* 1.3 60.3 + - - +
174D HIS* 3.5 6.5 + - - +
175D ILE* 3.2 27.0 + - - +
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Residues in contact with CYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D CYS* 3.9 15.0 - - - -
140D ILE* 4.1 11.2 - - - -
143D LEU* 3.8 26.9 - - + -
156D ILE* 5.4 3.4 - - + -
167D ILE* 3.4 24.5 - - + -
168D ASP 2.9 21.8 + - - +
169D ILE* 3.7 4.3 - - - +
171D GLY* 1.3 72.2 - - - +
173D ALA* 1.3 56.6 - - - +
175D ILE* 3.2 4.1 + - - +
176D VAL* 2.8 41.9 + - - +
184D LEU* 4.2 13.2 - - + -
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Residues in contact with ALA 173 (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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169D ILE 2.8 17.9 + - - +
170D GLU* 3.4 5.6 - - + +
172D CYS* 1.3 75.8 - - - +
174D HIS* 1.3 57.4 + - - +
176D VAL* 4.6 0.7 - - - -
177D HIS* 2.9 42.1 + - - +
184D LEU* 3.6 12.7 - - + +
201D LEU 3.8 6.1 - - - +
202D GLY* 3.5 33.4 - - - +
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Residues in contact with HIS 174 (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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170D GLU* 2.9 16.5 + - + +
171D GLY* 3.7 7.6 - - - +
173D ALA* 1.3 74.5 - - - +
175D ILE* 1.3 74.0 + - + +
177D HIS* 3.9 2.9 - - - +
178D LYS* 3.1 63.4 + - + +
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Residues in contact with ILE 175 (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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140D ILE* 3.7 24.5 - - + -
143D LEU* 4.2 8.5 - - + -
144D GLU* 3.7 47.8 - - + +
147D ILE* 3.5 27.9 - - + +
171D GLY 3.2 12.3 + - - +
172D CYS* 3.2 9.3 + - - +
174D HIS* 1.3 92.6 - - + +
176D VAL* 1.3 62.8 + - - +
178D LYS* 3.4 23.8 + - + +
179D HIS 4.5 1.4 + - - -
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Residues in contact with VAL 176 (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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143D LEU* 3.8 22.4 - - + -
147D ILE* 4.2 10.1 - - + -
154D VAL* 3.9 22.4 - - + -
172D CYS 2.8 24.5 + - - +
173D ALA* 4.0 4.5 - - - +
175D ILE* 1.3 73.4 - - - +
177D HIS* 1.3 64.2 + - + +
179D HIS 3.4 18.4 - - - +
182D ILE* 3.5 51.4 + - + +
184D LEU* 4.2 17.5 - - + +
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Residues in contact with HIS 177 (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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173D ALA* 2.9 26.3 + - + +
174D HIS* 3.9 2.9 - - - +
176D VAL* 1.3 81.0 - - + +
178D LYS* 1.3 65.9 + - - +
179D HIS* 3.3 7.1 + - - +
180D GLY 4.7 4.8 - - - +
182D ILE 3.5 19.9 + - - +
184D LEU* 4.4 2.9 - - + +
202D GLY* 3.0 28.3 + - - -
204D ASP* 2.7 35.1 + - - -
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Residues in contact with LYS 178 (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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144D GLU* 5.8 1.8 - - - -
174D HIS* 3.1 49.3 + - + +
175D ILE* 3.5 17.7 - - + +
176D VAL 3.4 1.2 - - - -
177D HIS* 1.3 78.4 - - - +
179D HIS* 1.3 95.9 + - + +
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Residues in contact with HIS 179 (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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147D ILE* 5.8 1.9 - - + +
175D ILE 4.5 1.4 + - - -
176D VAL 3.4 16.9 + - - +
177D HIS 4.2 1.5 - - - -
178D LYS* 1.3 111.9 + - + +
180D GLY* 1.3 68.9 + - - +
182D ILE* 3.8 9.4 - - - +
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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