Contacts of the helix formed by residues 175 - 189 (chain B) 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 HIS 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B LEU* 4.5 9.4 - - + +
174B HIS* 1.3 87.4 + - + +
176B LYS* 1.3 62.6 + - - +
177B ASP 3.3 3.3 + - - +
178B HIS* 3.8 13.9 + - + +
179B PHE* 3.8 17.5 + - - -
208B SER* 6.4 1.1 - - - -
209B LEU* 3.7 54.4 + - + +
210B ALA* 5.0 6.9 + - + +
382B ILE* 5.7 4.5 - - + -
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA 4.6 0.2 - - - +
164B GLY* 3.4 29.9 - - - +
167B LEU* 3.7 28.7 - - + +
168B SER* 3.8 11.2 - - - +
172B LEU* 3.4 34.3 - - + +
173B THR* 3.8 23.7 + - - +
174B HIS 3.4 3.4 + - - +
175B HIS* 1.3 77.2 - - - +
177B ASP* 1.3 69.6 + - - +
179B PHE* 3.1 6.9 + - - +
180B THR* 2.5 43.0 + - - +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B THR 6.0 0.9 - - - -
174B HIS 5.2 0.8 + - - +
175B HIS* 3.3 1.0 - - - +
176B LYS* 1.3 98.2 + - - +
178B HIS* 1.3 64.7 + - - +
180B THR* 3.4 9.9 + - - +
181B LYS* 3.2 40.6 + - - +
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Residues in contact with HIS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B HIS* 3.8 12.6 + - + +
176B LYS 3.3 0.4 - - - -
177B ASP* 1.3 79.0 - - - +
179B PHE* 1.3 63.0 + - + +
180B THR 3.6 0.2 + - - -
181B LYS* 3.8 4.7 + - - +
182B LEU* 3.5 32.1 + - + +
209B LEU 2.9 25.2 + - - +
210B ALA* 3.0 29.6 + - + -
212B SER* 3.2 43.5 + - - -
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 4.5 13.3 - - + +
172B LEU* 3.6 21.8 - - + -
175B HIS 3.9 6.1 - - - -
176B LYS 3.1 8.9 + - - +
178B HIS* 1.3 81.9 - - - +
180B THR* 1.3 64.1 + - - +
181B LYS 3.4 0.2 - - - -
182B LEU* 3.9 7.1 - - + +
183B ALA* 3.1 29.1 + - - +
209B LEU* 3.7 40.2 - - + -
212B SER* 3.2 33.2 - - - -
373B ILE* 5.8 3.4 - - + -
375B LEU* 4.7 16.2 - - + -
376B ARG 5.0 2.9 - - - -
383B LEU* 6.5 0.2 - - + -
386B ALA* 3.8 22.7 - - + -
390B LEU* 4.5 21.8 - - + +
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B MET* 4.6 21.5 - - + +
163B ALA* 3.8 26.3 + - + -
164B GLY* 4.7 4.5 - - - +
167B LEU* 4.3 4.3 - - - +
176B LYS* 2.5 41.6 + - - +
177B ASP* 3.4 17.8 + - - +
178B HIS 3.2 0.4 - - - -
179B PHE* 1.3 81.5 - - - +
181B LYS* 1.3 68.8 + - - +
183B ALA* 5.1 0.2 - - - -
184B VAL* 3.3 25.1 + - - +
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 4.1 10.1 + - - +
160B MET* 3.8 32.0 - - + +
177B ASP* 3.2 28.9 + - - +
178B HIS* 3.8 5.6 + - - +
179B PHE 3.4 0.2 - - - -
180B THR* 1.3 82.5 - - - +
182B LEU* 1.3 66.1 + - + +
184B VAL* 3.6 14.9 - - - +
185B GLU* 3.9 12.0 + - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B HIS* 3.5 32.3 + - + +
179B PHE* 3.6 6.1 + - + +
180B THR 3.4 0.6 - - - -
181B LYS* 1.3 81.3 - - + +
183B ALA* 1.3 63.8 + - - +
185B GLU* 3.5 8.9 + - - +
186B ALA 3.7 1.7 + - - -
212B SER* 3.5 34.8 - - - +
213B TYR 3.9 7.0 - - - +
214B LEU* 3.3 49.0 - - + +
373B ILE* 3.8 19.7 - - + -
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA* 5.8 3.1 - - + -
167B LEU* 6.1 2.7 - - + -
179B PHE 3.1 19.8 + - - +
180B THR* 4.6 2.2 - - - +
182B LEU* 1.3 76.0 - - - +
184B VAL* 1.3 68.7 + - + +
185B GLU 3.3 0.9 + - - -
186B ALA* 3.4 5.8 + - - +
187B VAL* 3.3 26.1 + - - +
373B ILE* 5.0 6.5 - - + +
390B LEU* 5.3 13.2 - - + -
393B ALA* 6.3 1.8 - - + -
394B LEU* 4.2 20.9 - - + +
397B LEU* 5.0 3.4 - - + -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 3.2 35.9 + - - +
159B LEU* 3.4 55.4 - - + +
160B MET* 3.9 16.2 - - + +
163B ALA* 3.9 13.2 - - + -
180B THR 3.3 21.1 - - - +
181B LYS* 3.6 5.6 - - - +
183B ALA* 1.3 76.9 - - + +
185B GLU* 1.3 61.3 + - - +
187B VAL* 4.1 3.1 - - - -
188B LEU* 3.3 14.9 + - - +
397B LEU* 4.4 4.5 - - + -
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 3.4 16.3 + - - +
181B LYS 4.0 10.9 - - - +
182B LEU* 3.5 15.1 + - - +
183B ALA 3.2 0.8 - - - -
184B VAL* 1.3 81.3 - - - +
186B ALA* 1.3 63.2 + - - +
188B LEU* 3.2 19.9 + - + +
189B ARG* 2.8 44.1 + - - +
214B LEU* 3.3 16.1 - - + +
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B LEU 3.7 3.1 + - - +
183B ALA* 3.4 8.6 + - - +
185B GLU* 1.3 76.5 - - - +
187B VAL* 1.3 64.8 + - + +
189B ARG* 3.4 22.1 + - - +
190B LEU* 3.6 11.6 - - - +
199B ILE* 3.8 20.9 - - + +
214B LEU* 3.8 18.4 - - + +
371B CYS* 3.7 27.1 - - + -
373B ILE* 6.2 0.4 - - + -
394B LEU* 6.3 0.9 - - + -
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 4.8 3.0 - - + -
159B LEU* 3.8 20.4 - - + -
183B ALA 3.3 18.3 + - - +
184B VAL 4.3 4.0 - - - +
185B GLU 3.3 0.6 - - - -
186B ALA* 1.3 78.5 - - + +
188B LEU* 1.3 62.1 + - - +
190B LEU* 3.2 31.0 + - + +
191B LYS 4.3 1.4 + - - -
199B ILE* 5.6 3.4 - - + -
394B LEU* 3.8 18.8 - - + +
397B LEU* 3.7 44.2 - - + +
401B VAL* 3.7 14.6 - - + +
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU* 3.3 32.5 - - + +
155B PHE* 3.6 32.4 - - + -
156B ARG* 3.9 31.4 - - + +
159B LEU* 4.1 7.2 - - + +
184B VAL 3.3 13.4 + - - +
185B GLU* 3.2 16.0 + - + +
187B VAL* 1.3 78.5 - - - +
189B ARG* 1.3 58.9 + - + +
190B LEU 3.2 1.6 + - - -
191B LYS* 4.0 11.8 + - - +
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B GLU* 2.8 56.7 + - - +
186B ALA* 3.4 8.9 + - - +
187B VAL 3.2 1.0 - - - -
188B LEU* 1.3 77.8 - - + +
190B LEU* 1.3 63.7 + - - +
191B LYS* 3.4 8.1 - - - +
214B LEU* 3.9 8.1 - - - +
216B GLU* 4.0 26.2 - - - +
368B GLY 3.3 20.4 - - - +
369B GLU* 3.4 19.9 + - - +
371B CYS* 3.6 27.8 - - - -
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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