Contacts of the helix formed by residues 161 - 177 (chain E) in PDB entry 6NR8
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 161 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156E LEU* 3.1 43.9 - - + +
157E VAL 2.9 15.2 + - - +
158E ASP* 2.9 26.6 - - - +
160E LYS* 1.3 72.8 - - - +
162E THR* 1.3 66.3 + - - +
163E GLU 3.2 0.4 - - - -
164E PRO* 3.5 12.2 - - - +
165E LEU* 3.4 28.8 + - - +
202E ARG* 5.9 0.9 + - - -
412E LEU* 4.6 13.6 - - + +
416E ASN* 3.6 11.6 - - - +
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Residues in contact with THR 162 (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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158E ASP 3.4 20.2 - - - +
159E ILE* 2.9 17.7 + - - +
161E ASP* 1.3 79.8 + - - +
163E GLU* 1.3 54.2 + - - +
165E LEU* 3.1 11.0 + - + +
166E ILE* 2.5 45.0 + - - +
190E VAL* 4.2 25.4 - - + +
191E ASN* 5.5 2.9 - - - +
194E LEU* 5.0 16.2 - - + -
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Residues in contact with GLU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E ILE 5.5 0.4 - - - +
160E LYS* 3.0 14.8 + - + +
162E THR* 1.3 79.5 + - - +
164E PRO* 1.3 61.1 - - + +
166E ILE* 3.2 34.8 + - - +
167E GLN* 2.7 48.7 + - - +
187E GLU* 5.7 0.2 - - - +
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Residues in contact with PRO 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E LEU* 4.9 14.1 - - + -
160E LYS* 3.3 21.1 - - + +
161E ASP* 3.5 14.6 - - - +
163E GLU* 1.3 91.3 - - + +
165E LEU* 1.3 50.5 + - + +
167E GLN* 3.1 18.4 + - + +
168E THR* 2.5 40.4 + - - -
507E ILE* 4.4 22.0 - - + +
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Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ASP* 3.4 21.2 + - - +
162E THR* 3.1 11.5 + - + +
164E PRO* 1.3 74.7 - - + +
166E ILE* 1.3 61.4 + - - +
167E GLN 3.2 0.4 - - - -
168E THR* 3.8 17.7 - - + +
169E ALA* 2.8 32.2 + - - +
190E VAL* 3.8 15.2 - - + +
405E ALA 5.9 0.2 - - - +
408E VAL* 5.0 9.6 - - + -
409E ILE* 3.7 37.7 - - + -
412E LEU* 3.8 37.0 - - + -
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Residues in contact with ILE 166 (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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162E THR* 2.5 30.1 + - - +
163E GLU* 3.3 42.2 - - - +
165E LEU* 1.3 72.6 - - - +
167E GLN* 1.3 56.5 + - + +
170E LYS* 3.2 14.9 + - - +
183E ARG* 2.8 46.7 + - - +
186E ALA* 3.9 15.1 - - - +
187E GLU* 3.7 34.8 - - + +
190E VAL* 4.3 8.7 - - + +
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Residues in contact with GLN 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 GLU* 2.7 39.0 + - - +
164E PRO* 3.1 18.9 + - - +
166E ILE* 1.3 74.6 - - + +
168E THR* 1.3 62.5 + - - +
170E LYS* 3.3 15.0 - - + +
171E THR* 3.1 24.8 + - - -
505E HIS* 2.8 58.8 + - + +
507E ILE* 5.7 1.1 - - + +
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Residues in contact with THR 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 PRO 2.5 29.5 + - - -
165E LEU* 3.2 20.5 + - + +
167E GLN* 1.3 74.5 - - - +
169E ALA* 1.3 59.3 + - - +
171E THR* 3.1 23.0 + - - -
172E THR* 3.2 17.6 + - + +
408E VAL* 5.4 10.5 - - + -
505E HIS 5.1 3.5 + - - -
507E ILE* 3.7 30.0 + - - +
508E GLU* 5.7 4.5 - - + -
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Residues in contact with ALA 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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165E LEU 2.8 17.6 + - - +
168E THR* 1.3 73.2 - - - +
170E LYS* 1.3 60.2 + - - +
172E THR* 2.9 25.0 + - - +
173E LEU* 3.0 24.7 + - + +
186E ALA* 3.7 25.4 - - + +
189E ALA* 5.8 3.4 - - + -
190E VAL* 5.9 1.3 - - + -
405E ALA* 4.3 19.7 - - + -
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Residues in contact with LYS 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 ILE* 3.2 21.6 + - + +
167E GLN* 3.3 16.8 - - + +
168E THR 3.2 0.2 - - - -
169E ALA* 1.3 78.0 - - - +
171E THR* 1.3 55.0 + - - +
174E GLY* 2.7 31.8 + - - -
180E SER 5.3 0.6 + - - -
181E CYS* 3.5 39.9 - - + +
183E ARG* 3.5 19.0 - - - +
186E ALA* 4.3 0.2 - - - +
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Residues in contact with THR 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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54E PRO* 4.7 23.7 - - + +
167E GLN 3.1 12.8 + - - -
168E THR* 3.1 13.0 + - - -
170E LYS* 1.3 82.5 - - - +
172E THR* 1.3 62.9 + - + +
174E GLY 5.7 0.2 - - - -
175E SER* 3.9 21.0 + - - -
176E LYS* 5.0 1.7 - - - +
494E LEU* 5.8 7.6 - - + -
505E HIS 5.1 5.0 + - - -
506E VAL* 5.9 10.3 - - + +
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Residues in contact with THR 172 (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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104E ASP* 4.0 21.1 - - - +
168E THR* 3.5 18.4 - - + +
169E ALA* 2.9 19.8 + - - +
171E THR* 1.3 80.2 - - + +
173E LEU* 1.3 66.0 + - - +
176E LYS* 3.6 20.2 + - - +
401E SER* 3.5 35.7 + - - +
404E ASP* 6.2 0.2 - - + -
405E ALA* 4.6 6.2 - - + +
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Residues in contact with LEU 173 (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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169E ALA* 3.0 18.9 + - + +
170E LYS* 4.3 1.3 - - - +
172E THR* 1.3 81.1 + - - +
174E GLY* 1.3 57.6 + - - +
175E SER 2.9 9.9 + - - -
176E LYS 3.4 8.0 + - - -
177E VAL* 3.6 15.9 + - + -
178E VAL* 2.8 25.6 + - + +
181E CYS* 4.8 9.4 - - - -
182E HIS* 4.1 15.9 - - + +
185E MET* 3.7 38.4 - - + -
186E ALA* 4.2 12.1 - - + +
398E ALA* 4.4 1.8 - - - +
401E SER* 3.8 16.6 - - - -
402E LEU* 3.7 26.7 - - + -
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Residues in contact with GLY 174 (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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170E LYS* 2.7 24.5 + - - -
171E THR 4.6 0.2 - - - -
172E THR 3.6 0.2 - - - -
173E LEU* 1.3 70.9 - - - +
175E SER* 1.3 58.2 + - - +
178E VAL 3.2 12.1 - - - -
179E ASN* 3.1 19.9 - - - +
180E SER* 5.0 0.2 - - - -
181E CYS* 3.8 20.2 - - - +
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Residues in contact with SER 175 (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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516B ARG* 4.7 10.0 + - - -
54E PRO* 3.5 34.8 + - - +
171E THR* 3.9 14.4 + - - -
173E LEU 2.9 1.0 + - - -
174E GLY* 1.3 79.5 - - - +
176E LYS* 1.3 70.9 + - - +
178E VAL 4.7 3.4 - - - -
179E ASN* 5.1 3.4 - - - +
494E LEU* 5.5 6.1 - - - +
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Residues in contact with LYS 176 (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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516B ARG* 4.2 11.6 - - - +
53E GLY 4.9 1.3 - - - +
54E PRO* 2.9 41.6 + - + +
56E GLY 3.0 24.2 + - - -
58E ASP* 4.2 4.2 + - - +
72E ASN* 3.1 25.1 - - + +
171E THR 5.0 1.8 - - - +
172E THR* 3.6 20.0 - - - +
173E LEU 3.4 1.4 + - - -
175E SER* 1.3 99.3 - - - +
177E VAL* 1.3 63.9 - - + +
178E VAL 3.7 0.2 - - - -
397E GLU* 3.0 17.0 - - + +
401E SER* 4.5 7.2 - - - +
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Residues in contact with VAL 177 (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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173E LEU* 3.6 32.3 + - + +
176E LYS* 1.3 77.7 - - - +
178E VAL* 1.3 74.3 + - + +
182E HIS* 6.2 0.2 - - + -
394E ILE* 3.3 39.6 - - + +
397E GLU* 3.7 27.6 - - + +
398E ALA* 3.5 21.1 - - + +
401E SER* 4.0 7.9 - - - +
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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