Contacts of the helix formed by residues 167 - 177 (chain X) in PDB entry 6JM9
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 GLY 167 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164X SER* 3.3 18.9 + - - -
165X GLY 3.2 5.5 + - - -
166X VAL* 1.4 78.8 - - - +
168X GLN* 1.4 63.2 + - - +
169X VAL 3.3 3.9 + - - -
170X VAL* 3.7 2.5 - - - +
171X LEU* 3.4 24.0 + - - +
195X ALA* 4.9 0.4 - - - -
218X LEU* 3.5 30.1 - - - +
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Residues in contact with GLN 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X LEU* 3.7 23.4 - - + +
115X TYR* 5.7 0.7 - - + -
138X GLU* 3.5 32.2 + - + +
139X THR 2.9 30.3 + - - +
141X PHE* 5.4 4.4 - - - +
144X VAL* 4.5 1.2 - - - +
164X SER 4.6 0.8 + - - -
166X VAL* 3.4 8.1 - - + -
167X GLY* 1.4 76.0 - - - +
169X VAL* 1.4 83.2 + - - +
170X VAL 3.4 0.2 - - - -
171X LEU* 3.6 4.2 + - - -
172X GLN* 3.1 43.2 + - - +
198X MET* 3.9 23.6 - - + -
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Residues in contact with VAL 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139X THR* 3.2 20.4 - - - +
144X VAL* 3.7 24.1 - - + +
147X MET* 3.8 19.1 - - + -
159X PHE* 4.5 4.7 - - + -
161X ASP* 3.5 17.3 - - - +
164X SER 5.3 1.3 - - - +
167X GLY 3.3 0.6 - - - -
168X GLN* 1.4 94.1 - - + +
170X VAL* 1.3 54.1 - - - +
172X GLN* 3.3 8.1 - - - +
173X VAL* 3.0 31.1 + - - +
239X PHE* 4.1 14.6 - - + -
500X SAM 4.1 13.9 - - - +
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Residues in contact with VAL 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159X PHE* 4.0 12.3 - - + -
161X ASP* 3.4 28.3 - - + +
164X SER* 4.3 2.5 - - - -
167X GLY 3.7 9.2 - - - +
169X VAL* 1.3 71.1 - - - +
171X LEU* 1.3 57.4 - - + +
173X VAL* 3.4 4.3 + - - +
174X ALA* 2.9 27.6 + - - +
182X HIS* 3.7 14.3 - - + +
183X TYR* 3.4 49.1 - - - +
184X GLY* 4.0 7.0 - - - +
216X TYR* 4.9 5.6 - - + -
217X THR 4.8 0.4 - - - +
218X LEU* 4.0 13.2 - - + -
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Residues in contact with LEU 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X LEU* 4.0 5.6 - - + -
167X GLY 3.4 17.5 + - - +
168X GLN* 3.6 6.9 + - - +
169X VAL 3.4 0.2 - - - -
170X VAL* 1.3 74.7 - - + +
172X GLN* 1.4 60.3 + - - +
174X ALA* 3.3 5.7 + - - +
175X ALA* 3.1 24.3 + - - +
198X MET* 3.8 31.9 - - + +
199X ASP* 4.3 2.9 - - - -
202X PHE* 3.6 46.8 - - + -
216X TYR* 3.4 40.2 - - + -
218X LEU* 4.0 20.4 - - + -
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Residues in contact with GLN 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X LEU* 3.9 24.4 - - + +
111X LEU* 3.3 23.5 - - + +
141X PHE* 3.1 57.9 + - - -
144X VAL* 3.5 23.3 - - + +
145X ALA* 3.9 6.7 - - - +
148X ILE* 4.1 6.1 - - + +
168X GLN* 3.1 22.1 + - - +
169X VAL 3.3 10.1 - - - +
171X LEU* 1.4 75.4 - - - +
173X VAL* 1.3 65.0 + - - +
174X ALA 3.5 0.2 + - - -
175X ALA 3.6 0.2 + - - -
176X ALA* 3.3 24.6 + - - +
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Residues in contact with VAL 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144X VAL* 4.5 0.4 - - + -
147X MET* 4.0 9.0 - - + -
148X ILE* 3.8 26.2 - - + -
153X MET* 4.2 9.6 - - + -
159X PHE* 3.7 39.0 - - + -
169X VAL 3.0 18.8 + - - +
170X VAL 3.6 8.1 - - - +
171X LEU 3.4 0.2 - - - -
172X GLN* 1.3 78.2 - - - +
174X ALA* 1.3 50.1 + - - +
177X THR* 2.8 55.7 + - - +
182X HIS* 3.6 20.0 - - + +
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Residues in contact with ALA 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ARG* 4.1 1.4 + - - -
170X VAL 2.9 13.9 + - - +
171X LEU 3.3 4.9 + - - +
173X VAL* 1.3 78.5 - - - +
175X ALA* 1.4 57.5 + - - +
177X THR 3.0 11.4 - - - +
182X HIS* 3.3 37.7 - - + -
213X HIS* 4.0 0.4 - - - -
214X ALA* 3.0 24.2 + - + +
216X TYR* 3.7 28.5 - - + -
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Residues in contact with ALA 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ARG* 3.4 22.9 + - - -
102X PRO* 3.6 7.9 - - + +
107X LEU* 4.1 19.3 - - + -
171X LEU 3.1 15.9 + - - +
172X GLN 3.6 1.8 + - - +
173X VAL 3.3 0.2 - - - -
174X ALA* 1.4 75.4 - - - +
176X ALA* 1.4 57.2 + - - +
202X PHE* 4.2 7.6 - - + -
206X MET* 3.9 26.5 - - + -
212X LYS 3.5 9.2 - - - +
213X HIS* 3.9 11.8 - - - +
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Residues in contact with ALA 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ARG* 3.2 18.9 + - - +
102X PRO* 5.3 4.9 - - - +
107X LEU* 4.2 14.1 - - + -
148X ILE* 4.3 23.2 - - + +
172X GLN 3.3 17.4 + - - +
173X VAL 4.1 1.3 - - - +
175X ALA* 1.4 76.9 - - - +
177X THR* 1.4 62.1 - - - +
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Residues in contact with THR 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ARG* 3.0 9.4 - - - +
148X ILE* 3.8 20.4 - - + +
152X LYS* 6.0 0.2 - - - -
153X MET* 3.4 49.5 - - + +
173X VAL* 2.8 32.8 + - - +
174X ALA 3.0 15.2 - - - +
176X ALA* 1.4 75.0 - - - +
178X ASN* 1.4 60.5 + - - +
182X HIS* 3.6 4.3 + - - -
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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