Contacts of the helix formed by residues 171 - 184 (chain O) 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 GLN 171 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168O ILE* 3.4 27.5 - - + +
170O GLN* 1.3 95.2 - - + +
172O LYS* 1.3 59.3 + - - +
173O ALA 3.3 1.8 - - - -
174O PHE* 3.2 8.4 + - + +
175O PHE* 3.0 59.4 + - + -
206O GLU* 3.4 54.1 + - + +
375O ARG 5.5 0.5 - - - +
376O GLY* 5.7 0.5 - - - -
381O PHE* 3.9 16.7 - - - -
385O THR* 4.1 7.1 - - - +
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Residues in contact with LYS 172 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O MET* 3.7 36.9 - - + +
163O LEU* 3.6 28.4 - - + +
164O SER* 3.7 28.3 - - - -
168O ILE* 3.6 13.7 - - + +
169O SER* 3.3 32.5 - - - +
170O GLN 4.6 1.3 - - - -
171O GLN* 1.3 75.5 - - - +
173O ALA* 1.3 68.8 + - + +
175O PHE 3.8 0.2 - - - -
176O ALA* 3.2 28.4 + - - +
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Residues in contact with ALA 173 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160O MET* 4.7 12.8 - - - -
170O GLN 4.2 6.8 + - - +
171O GLN 3.3 0.4 - - - -
172O LYS* 1.3 86.6 - - + +
174O PHE* 1.3 63.2 + - - +
175O PHE 3.5 0.2 + - - -
176O ALA* 4.0 5.8 + - - +
177O LYS* 3.1 26.5 + - - +
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Residues in contact with PHE 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O GLN 4.9 1.5 + - - +
171O GLN* 3.2 13.8 + - - +
173O ALA* 1.3 79.6 - - - +
175O PHE* 1.3 75.9 + + + +
177O LYS* 4.9 6.7 + - - +
178O MET* 3.7 36.6 + - + +
206O GLU 5.0 0.2 - - - -
207O ASP* 3.3 38.1 - - + +
208O SER 3.4 22.9 - - - -
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Residues in contact with PHE 175 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O LEU* 3.7 14.4 - - + -
168O ILE* 3.6 15.7 - - + -
171O GLN* 3.0 49.7 + - + +
173O ALA 3.2 0.4 - - - -
174O PHE* 1.3 100.9 - + - +
176O ALA* 1.3 59.6 + - - +
177O LYS 3.4 1.3 - - - -
178O MET* 3.2 12.6 + - - +
179O VAL* 3.0 28.2 + - - +
206O GLU 4.2 9.2 - - - -
207O ASP* 4.0 2.2 - - - -
208O SER* 3.3 42.2 - - - -
374O LEU* 4.4 6.7 - - + -
375O ARG 5.1 0.7 - - - -
385O THR* 4.2 12.3 - - + -
389O LEU* 3.7 22.8 - - + +
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Residues in contact with ALA 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156O GLU* 4.1 27.6 - - + +
159O ALA* 4.5 3.0 - - + +
160O MET* 4.1 15.5 - - + +
163O LEU* 4.0 7.0 - - + -
172O LYS 3.2 19.3 + - - +
173O ALA* 4.0 4.4 + - - +
174O PHE 3.6 0.4 - - - -
175O PHE* 1.3 78.5 - - - +
177O LYS* 1.3 58.6 + - + +
179O VAL* 3.1 7.0 + - - +
180O VAL* 2.9 32.2 + - - +
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Residues in contact with LYS 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152O ARG* 5.2 4.5 - - - +
153O LYS* 6.2 0.7 - - - -
156O GLU* 3.3 32.3 - - - +
173O ALA* 3.1 26.4 + - - +
174O PHE* 4.9 6.1 + - - +
176O ALA* 1.3 74.2 - - + +
178O MET* 1.3 61.5 + - + +
180O VAL* 3.9 7.4 - - - +
181O ASP* 2.9 44.3 + - - +
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Residues in contact with MET 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O PHE* 3.7 39.9 - - + +
175O PHE* 3.2 12.0 + - - +
177O LYS* 1.3 76.3 - - + +
179O VAL* 1.3 62.5 + - - +
181O ASP* 4.8 0.9 - - - -
182O ALA 3.3 14.2 + - - -
208O SER* 3.3 38.6 - - - +
209O GLN* 3.9 13.0 - - + -
210O LEU* 3.3 20.6 - - + +
372O PHE* 3.2 31.2 - - + -
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Residues in contact with VAL 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159O ALA* 4.3 9.6 - - + -
163O LEU* 4.7 1.8 - - + -
175O PHE 3.0 18.4 + - - +
176O ALA* 3.1 10.5 + - - +
178O MET* 1.3 75.7 - - - +
180O VAL* 1.3 63.4 + - - +
182O ALA* 3.3 2.3 + - - +
183O VAL* 3.1 33.0 + - + +
372O PHE* 4.2 11.4 - - + -
389O LEU* 4.3 21.8 - - + +
392O ALA* 3.7 44.2 - - + +
393O ILE* 4.4 8.7 - - + +
396O VAL* 4.8 2.9 - - + -
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Residues in contact with VAL 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152O ARG* 3.6 42.6 - - + +
155O LEU* 3.8 28.9 - - + +
156O GLU* 3.7 22.4 - - + +
159O ALA* 4.8 3.4 - - + -
176O ALA 2.9 19.5 + - - +
177O LYS* 3.4 7.4 + - - +
178O MET 3.4 0.2 - - - -
179O VAL* 1.3 76.3 - - + +
181O ASP* 1.3 62.7 + - - +
183O VAL* 3.4 4.5 + - - +
184O MET* 3.3 34.2 + - + +
396O VAL* 5.4 4.9 - - + -
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Residues in contact with ASP 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152O ARG* 2.5 34.6 + - - -
177O LYS* 2.9 28.0 + - - +
178O MET* 4.8 0.8 - - - -
180O VAL* 1.3 75.6 - - - +
182O ALA* 1.3 60.4 + - - +
184O MET* 4.3 8.9 - - - +
185O MET* 3.7 31.3 + - + +
210O LEU* 3.9 14.1 - - + -
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Residues in contact with ALA 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O MET 3.3 19.3 + - - +
179O VAL* 3.7 4.0 - - - +
180O VAL 3.2 0.4 - - - -
181O ASP* 1.3 78.5 - - - +
183O VAL* 1.3 66.2 + - + +
184O MET 3.3 0.2 - - - -
185O MET 3.4 2.8 + - - -
186O LEU* 3.2 28.5 + - + +
195O ILE* 5.9 4.3 - - + -
210O LEU* 3.7 13.4 - - + +
370O CYS* 3.6 18.1 - - + -
372O PHE* 3.7 20.2 - - + -
393O ILE* 6.4 0.9 - - + -
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Residues in contact with VAL 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179O VAL* 3.1 25.6 + - + +
180O VAL 4.1 2.7 - - - +
182O ALA* 1.3 75.4 - - + +
184O MET* 1.3 59.9 + - + +
186O LEU* 2.9 22.4 + - - +
187O ASP* 3.0 21.6 + - - +
195O ILE* 5.9 2.2 - - + -
393O ILE* 4.6 16.6 - - + +
396O VAL* 4.0 22.4 - - + -
397O ARG* 3.7 32.8 - - + +
400O ILE* 3.8 25.4 - - + -
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Residues in contact with MET 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150O GLU 5.6 2.2 - - - +
152O ARG* 3.8 38.8 - - + +
155O LEU* 5.5 4.3 - - + -
180O VAL* 3.3 29.8 + - + +
181O ASP* 4.5 8.7 - - - +
182O ALA 3.3 0.2 - - - -
183O VAL* 1.3 76.6 - - + +
185O MET* 1.3 60.2 + - + +
187O ASP* 3.3 24.6 + - - +
400O ILE* 5.1 8.3 - - + -
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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