Contacts of the helix formed by residues 161 - 172 (chain E) in PDB entry 3UNF
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 ARG 161 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LEU* 6.0 2.2 - - - +
48E ARG* 3.2 28.5 - - - +
159E GLY 3.6 2.0 + - - -
160E ALA* 1.3 82.7 - - + +
162E SER* 1.3 59.0 + - - +
163E GLN* 3.2 8.8 + - - +
164E SER* 3.4 18.6 + - - +
195E THR* 2.9 50.7 + - - +
196E LEU* 3.8 7.9 - - - +
197E PRO* 3.3 30.7 - - - +
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Residues in contact with SER 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ALA* 5.0 1.1 - - - -
157E SER* 3.4 29.4 - - - -
158E ILE* 3.7 10.6 - - - -
159E GLY 2.9 23.8 + - - -
160E ALA 3.2 2.1 - - - -
161E ARG* 1.3 74.6 - - - +
163E GLN* 1.3 59.0 + - - +
164E SER 3.3 0.2 - - - -
165E ALA* 3.4 3.5 + - - +
166E ARG* 2.8 54.8 + - - +
195E THR* 4.5 4.7 - - - -
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Residues in contact with GLN 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ARG* 3.2 2.7 - - - -
162E SER* 1.3 76.4 + - - +
164E SER* 1.3 61.7 + - - +
166E ARG* 3.3 31.8 + - - +
167E THR* 3.0 43.2 + - + +
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Residues in contact with SER 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ARG* 3.4 18.5 + - - +
162E SER 3.3 0.2 - - - -
163E GLN* 1.3 80.1 - - - +
165E ALA* 1.3 59.9 + - - +
167E THR* 2.7 23.2 + - - -
168E TYR* 3.2 10.4 + - - +
194E GLU* 3.7 40.1 + - - +
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Residues in contact with ALA 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 4.1 2.7 - - + -
157E SER* 3.4 25.8 - - - +
161E ARG 4.1 0.8 + - - -
162E SER 3.4 3.6 + - - +
163E GLN 3.3 0.4 - - - -
164E SER* 1.3 77.7 - - - +
166E ARG* 1.3 62.9 + - - +
168E TYR* 3.3 3.2 + - - +
169E LEU* 3.1 31.8 + - + +
191E ALA* 3.2 38.2 + - + +
195E THR* 3.8 10.5 - - + +
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Residues in contact with ARG 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E MET* 3.9 20.4 - - + +
157E SER* 3.6 19.5 + - - +
158E ILE* 5.0 2.0 - - - +
162E SER* 2.8 46.3 + - - +
163E GLN* 3.4 33.9 - - - +
165E ALA* 1.3 77.3 - - - +
167E THR* 1.3 56.2 + - - +
169E LEU* 3.6 3.1 + - - -
170E GLU* 3.1 34.6 + - - +
55F SER* 4.9 8.1 - - - +
57F LEU* 3.8 26.2 - - + +
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Residues in contact with THR 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLN* 3.0 34.2 + - + +
164E SER* 2.7 24.6 + - - -
166E ARG* 1.3 75.9 - - - +
168E TYR* 1.3 64.0 + - - +
170E GLU* 3.3 12.4 + - - +
171E ARG* 3.0 35.3 + - - +
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Residues in contact with TYR 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E SER 3.2 8.6 + - - +
165E ALA 3.3 8.7 + - - +
167E THR* 1.3 81.4 + - - +
169E LEU* 1.3 69.5 + - + +
171E ARG* 3.3 12.0 + - - +
172E HIS* 3.3 49.0 + + + -
176E PHE* 5.2 0.2 - + - -
187E HIS* 3.1 39.1 + - + -
190E ARG* 3.0 61.8 + - + +
191E ALA* 3.8 21.5 - - + -
194E GLU* 4.5 15.9 - - + +
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Residues in contact with LEU 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.9 22.2 - - + -
35E LEU* 3.7 29.4 - - + -
155E ALA* 4.1 17.0 - - + -
156E MET 4.2 16.8 - - - +
157E SER* 4.5 0.7 - - - -
165E ALA 3.1 21.4 + - - +
166E ARG* 3.9 3.6 - - - +
168E TYR* 1.3 84.3 - - + +
170E GLU* 1.3 58.7 + - - +
172E HIS 3.2 1.4 + - - -
173E MET* 2.8 34.1 + - - +
176E PHE* 3.8 13.8 - - + -
187E HIS 4.5 0.4 - - - +
191E ALA* 3.9 17.5 - - + -
57F LEU* 3.9 19.3 - - + -
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Residues in contact with GLU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E ARG* 3.1 26.2 + - - +
167E THR* 3.6 12.4 - - - +
168E TYR 3.2 0.2 - - - -
169E LEU* 1.3 76.2 - - - +
171E ARG* 1.3 61.5 + - + +
173E MET* 3.9 16.7 - - - +
55F SER* 3.8 19.2 + - - -
56F LYS* 3.5 47.4 + - + +
57F LEU* 3.9 12.8 - - + +
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Residues in contact with ARG 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E THR* 3.0 25.5 + - - +
168E TYR* 3.5 9.4 - - - +
169E LEU 3.2 0.4 - - - -
170E GLU* 1.3 80.0 - - + +
172E HIS* 1.3 73.3 + - + +
173E MET* 3.5 1.1 + - - +
174E SER* 4.6 7.4 + - - -
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Residues in contact with HIS 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E TYR* 3.3 45.4 + + + +
169E LEU 3.2 4.6 + - - -
171E ARG* 1.3 94.0 + - + +
173E MET* 1.3 61.6 + - - +
174E SER* 3.3 2.7 - - - -
175E GLU* 3.2 32.9 + - + +
176E PHE* 3.3 23.4 - - + -
187E HIS* 3.8 26.6 - + + +
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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