Contacts of the helix formed by residues 161 - 172 (chain D) in PDB entry 6UZA
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 VAL 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D LEU* 4.2 8.5 - - + -
153D LEU* 4.2 17.7 - - + -
158D LEU* 4.2 31.2 - - + +
159D SER 4.3 3.8 - - - +
160D ARG* 1.3 75.6 - - - +
162D GLY* 1.3 61.7 + - - +
163D ASP 3.3 0.9 - - - -
164D ALA* 3.3 1.7 + - - +
165D LEU* 2.9 27.2 + - - +
180D ILE* 4.1 14.3 - - + +
183D HIS* 4.2 32.3 - - + +
186D PHE* 4.3 7.4 - - + -
206D PHE* 4.9 11.1 + - + -
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Residues in contact with GLY 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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161D VAL* 1.3 78.4 - - - +
163D ASP* 1.3 57.7 + - - +
165D LEU* 3.3 6.8 + - - +
166D LEU* 3.0 23.0 + - - +
186D PHE* 4.4 1.6 - - - -
206D PHE* 4.0 25.8 + - - -
207D TYR* 3.4 36.4 - - - -
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Residues in contact with ASP 163 (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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138D GLN* 2.4 35.1 + - - +
160D ARG* 4.2 4.0 - - + +
161D VAL 3.3 1.6 - - - +
162D GLY* 1.3 73.5 - - - +
164D ALA* 1.3 60.7 + - - +
166D LEU* 3.3 8.7 + - - +
167D LEU* 2.9 28.2 + - - +
206D PHE 4.4 0.6 + - - -
207D TYR* 4.2 13.1 - - - +
208D ALA 3.8 18.2 - - - +
209D TYR* 3.4 10.3 - - + +
215D ARG* 3.0 48.1 + - - +
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Residues in contact with ALA 164 (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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137D LEU* 3.8 25.6 - - + +
138D GLN* 5.0 6.3 - - + +
141D VAL* 3.5 20.2 - - + +
160D ARG 3.6 18.7 + - - +
161D VAL 3.3 6.0 + - - +
162D GLY 3.3 0.4 - - - -
163D ASP* 1.3 79.8 + - - +
165D LEU* 1.3 57.9 + - - +
167D LEU* 4.4 5.4 - - - -
168D ALA* 3.0 31.0 + - - +
180D ILE* 3.9 7.6 - - + +
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Residues in contact with LEU 165 (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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161D VAL 2.9 13.6 + - - +
162D GLY* 3.5 7.4 - - - +
163D ASP 3.2 0.2 - - - -
164D ALA* 1.3 77.2 - - - +
166D LEU* 1.3 57.7 + - - +
168D ALA* 3.4 2.6 + - - +
169D ILE* 2.9 47.8 + - + +
177D VAL* 4.4 10.8 - - + +
180D ILE* 3.8 28.4 - - + +
181D LEU* 3.8 30.3 - - + -
186D PHE* 3.7 28.0 - - + -
192D LEU* 4.4 0.7 - - + -
207D TYR* 4.7 4.5 - - + -
222D PRO* 3.8 29.4 - - + -
238D LEU* 6.0 0.2 - - + -
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Residues in contact with LEU 166 (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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162D GLY 3.0 17.6 + - - +
163D ASP* 3.3 10.7 + - - +
165D LEU* 1.3 76.3 - - - +
167D LEU* 1.3 58.3 + - - +
169D ILE* 3.4 1.7 + - + -
170D SER* 2.9 29.1 + - - -
207D TYR* 3.7 30.7 - - + +
214D THR* 6.4 0.9 - - - -
215D ARG* 6.0 0.7 - - + +
216D PHE* 4.1 29.4 - - + +
220D VAL* 4.4 12.8 - - + +
221D THR 4.3 3.4 - - - +
222D PRO* 4.0 39.3 - - + -
225D LEU* 3.3 21.8 - - + +
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Residues in contact with LEU 167 (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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872C ILE* 6.5 0.2 - - + -
134D GLN* 5.2 0.7 - - - +
138D GLN* 4.0 15.5 - - + +
141D VAL* 4.2 9.6 - - + -
142D ALA* 3.9 27.4 - - + +
163D ASP* 2.9 18.1 + - - +
164D ALA* 3.8 4.7 - - - +
166D LEU* 1.3 77.5 - - - +
168D ALA* 1.3 56.2 + - - +
170D SER* 3.3 7.7 + - - +
171D LYS* 3.0 53.6 + - + +
215D ARG* 4.1 39.9 - - - +
216D PHE* 4.7 3.1 - - + -
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Residues in contact with ALA 168 (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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141D VAL* 3.8 7.6 - - + +
164D ALA 3.0 19.0 + - - +
165D LEU 3.9 2.0 - - - +
167D LEU* 1.3 74.5 - - - +
169D ILE* 1.3 59.7 + - - +
171D LYS 4.5 0.2 - - - +
172D GLY* 3.0 21.8 + - - -
173D TYR* 3.1 21.7 + - + +
176D ILE* 3.8 28.3 - - + -
177D VAL* 3.7 21.0 - - + +
180D ILE* 4.6 2.2 - - + -
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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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165D LEU* 2.9 34.0 + - + +
166D LEU* 3.8 5.6 - - - +
168D ALA* 1.3 74.6 - - - +
170D SER* 1.3 63.3 + - - +
172D GLY* 3.5 10.9 + - - -
177D VAL* 3.7 19.1 - - + -
222D PRO* 3.7 34.3 - - + +
225D LEU* 3.9 11.7 - - + -
226D ALA* 3.7 34.5 - - + +
229D CYS* 4.5 2.4 - - - -
231D GLU* 4.0 13.3 - - - +
234D ILE* 3.9 12.6 - - + -
238D LEU* 4.0 13.0 - - + -
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Residues in contact with SER 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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166D LEU 2.9 17.5 + - - -
167D LEU* 3.6 10.8 - - - +
168D ALA 3.3 0.2 - - - -
169D ILE* 1.3 78.4 - - - +
171D LYS* 1.3 61.1 + - - +
216D PHE* 3.7 27.3 - - - -
225D LEU* 4.3 5.1 - - - +
229D CYS* 4.2 23.8 - - - +
231D GLU* 4.4 3.5 - - - +
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Residues in contact with LYS 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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872C ILE* 6.4 1.0 - - - +
875C GLU* 4.3 12.3 + - - -
142D ALA* 3.7 29.5 + - - +
167D LEU* 3.0 40.8 + - + +
170D SER* 1.3 79.5 - - - +
172D GLY* 1.3 60.2 + - - +
173D TYR* 3.6 45.9 + - + +
231D GLU* 4.5 1.9 - - - +
882D GLY 5.6 3.8 + - - -
885D LYS* 4.3 9.3 - - - +
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Residues in contact with GLY 172 (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 ALA 3.0 7.0 + - - -
169D ILE 3.5 2.3 + - - -
170D SER 3.4 2.8 - - - -
171D LYS* 1.3 79.0 - - - +
173D TYR* 1.3 65.0 + - - +
174D VAL* 3.4 13.0 + - - +
231D GLU* 3.6 29.6 - - - +
234D ILE* 4.4 6.5 - - - -
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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