Contacts of the helix formed by residues 166 - 179 (chain B) in PDB entry 1JPP
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 VAL 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B ASP* 3.1 21.9 + - - +
165B GLN* 1.3 80.5 - - - +
167B VAL* 1.3 64.2 + - + +
168B VAL 3.4 0.2 - - - -
169B ASN* 3.8 4.9 - - - +
170B LYS* 3.0 31.5 + - + +
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Residues in contact with VAL 167 (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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159B LEU* 3.4 41.3 - - + +
162B ASP* 4.0 15.3 - - + +
164B ASP* 3.4 37.5 - - + +
166B VAL* 1.3 79.5 - - + +
168B VAL* 1.3 55.9 + - - +
170B LYS* 3.8 3.3 - - - +
171B ALA* 2.9 31.7 + - - +
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Residues in contact with VAL 168 (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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159B LEU 3.6 12.6 - - - +
160B LEU* 3.4 32.0 - - - +
162B ASP* 4.0 12.8 - - + +
164B ASP 3.9 6.7 - - - +
165B GLN* 3.0 39.7 - - - +
167B VAL* 1.3 73.2 - - - +
169B ASN* 1.3 84.4 + - - +
171B ALA* 4.0 2.7 - - - +
172B ALA* 3.2 23.2 + - - +
201B THR* 5.1 11.6 - - + +
210B THR* 4.8 4.1 - - + +
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Residues in contact with ASN 169 (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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165B GLN* 2.3 34.4 + - - +
166B VAL* 3.6 5.8 + - - +
167B VAL 3.3 0.4 - - - -
168B VAL* 1.3 90.8 - - - +
170B LYS* 1.3 57.9 + - - +
171B ALA 3.6 0.2 + - - -
172B ALA* 3.7 6.4 + - - +
173B VAL* 3.3 22.0 + - - +
205B THR* 4.7 2.6 + - - -
207B ASP* 3.2 28.3 + - - +
210B THR* 2.8 32.8 + - - +
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Residues in contact with LYS 170 (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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166B VAL* 3.0 22.3 + - + +
167B VAL* 4.1 3.6 - - - +
169B ASN* 1.3 75.2 - - - +
171B ALA* 1.3 63.6 + - - +
173B VAL* 3.8 10.7 + - - +
174B MET* 3.7 31.6 + - + +
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Residues in contact with ALA 171 (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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156B LEU* 4.9 5.6 - - + +
159B LEU* 3.9 28.0 - - + -
160B LEU* 3.9 19.3 - - + +
167B VAL 2.9 20.1 + - - +
168B VAL 4.0 1.3 - - - +
169B ASN 3.3 0.4 - - - -
170B LYS* 1.3 74.7 - - - +
172B ALA* 1.3 66.1 + - - +
174B MET* 3.2 13.8 + - + +
175B VAL* 3.1 26.2 + - + +
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Residues in contact with ALA 172 (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 LEU* 3.8 13.2 - - + +
168B VAL 3.2 16.7 + - - +
169B ASN 3.8 6.7 - - - +
170B LYS 3.4 0.2 - - - -
171B ALA* 1.3 77.5 - - - +
173B VAL* 1.3 62.2 + - + +
175B VAL* 3.3 5.1 + - - +
176B HIS* 2.9 25.6 + - - +
201B THR* 5.4 0.7 - - + -
210B THR* 4.3 13.0 - - + +
213B CYS* 4.7 8.4 - - + +
214B THR* 4.2 24.2 - - + -
217B THR* 5.0 0.7 + - - -
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Residues in contact with VAL 173 (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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169B ASN 3.3 19.1 - - - +
170B LYS* 4.0 10.8 - - - +
171B ALA 3.3 0.6 - - - -
172B ALA* 1.3 77.7 - - + +
174B MET* 1.3 63.1 + - + +
176B HIS* 3.6 8.7 + - + +
177B GLN* 3.5 24.8 + - + +
209B GLU* 6.3 2.0 - - + -
210B THR* 6.2 1.3 - - - -
213B CYS* 4.5 21.3 - - + +
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Residues in contact with MET 174 (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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156B LEU* 4.4 23.8 - - + -
159B LEU* 5.4 8.7 - - + -
170B LYS* 3.7 24.5 - - + +
171B ALA* 3.2 14.2 + - + +
172B ALA 3.1 0.6 - - - -
173B VAL* 1.3 75.6 - - + +
175B VAL* 1.3 67.2 + - - +
176B HIS 3.1 2.4 + - - -
177B GLN* 3.2 15.7 + - - +
178B LEU* 3.4 13.7 + - - +
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Residues in contact with VAL 175 (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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156B LEU* 3.9 30.9 - - + +
160B LEU* 4.3 18.8 - - + -
171B ALA 3.1 14.2 + - - +
172B ALA* 3.8 8.1 - - - +
174B MET* 1.3 75.8 - - - +
176B HIS* 1.3 63.4 + - - +
178B LEU* 3.2 22.6 + - - +
179B SER* 3.4 7.1 + - - -
188B ILE* 4.1 16.7 - - + +
194B MET* 4.5 5.6 - - + -
198B ILE* 4.1 26.7 - - + -
217B THR* 4.3 8.5 + - + +
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Residues in contact with HIS 176 (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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172B ALA 2.9 17.3 + - - +
173B VAL* 3.6 11.4 - - + +
175B VAL* 1.3 77.4 - - - +
177B GLN* 1.3 68.4 + - - +
179B SER* 2.7 27.0 + - - -
180B LYS* 3.9 30.5 + - - +
212B ARG* 4.5 11.8 + - - -
213B CYS* 3.7 31.1 + - + +
216B GLY* 4.3 22.0 - - - -
217B THR* 3.5 24.3 + - - +
220B ASN* 4.9 2.7 - - - -
254B TYR* 5.5 5.5 + - - -
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Residues in contact with GLN 177 (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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173B VAL* 3.5 14.9 + - + +
174B MET* 3.2 9.1 + - - +
176B HIS* 1.3 85.7 - - + +
178B LEU* 1.3 63.2 + - + +
180B LYS* 3.2 45.9 + - - +
181B LYS* 3.2 27.6 - - - +
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Residues in contact with LEU 178 (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 ALA* 5.7 5.2 - - + -
153B ILE* 4.8 11.4 - - + -
156B LEU* 3.9 27.6 - - + -
174B MET 3.4 10.9 + - - +
175B VAL* 3.2 10.9 + - - +
176B HIS 3.2 0.4 - - - -
177B GLN* 1.3 74.7 - - + +
179B SER* 1.3 53.9 + - - +
180B LYS 2.7 16.9 + - - -
181B LYS* 2.9 23.5 + - + +
184B SER* 3.1 38.2 - - - +
188B ILE* 4.4 15.3 - - + -
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Residues in contact with SER 179 (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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175B VAL 3.4 2.7 + - - -
176B HIS* 2.7 26.9 + - - -
178B LEU* 1.3 76.7 - - - +
180B LYS* 1.3 56.3 + - - +
181B LYS 3.4 0.4 - - - -
185B ARG* 3.1 37.3 + - - -
188B ILE* 4.7 7.4 - - - +
217B THR* 4.1 16.8 - - - -
220B ASN* 3.4 22.8 + - - +
221B LEU* 4.2 23.1 - - - -
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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