Contacts of the helix formed by residues 185 - 195 (chain B) in PDB entry 1PJS
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 ASN 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B VAL* 4.3 5.2 - - - +
181B LYS* 3.4 9.4 + - - +
182B PHE* 3.3 17.0 + - - +
183B PHE 3.4 1.0 - - - -
184B VAL* 1.3 75.4 - - - +
186B ASP* 1.3 59.7 + - - +
187B ARG* 3.2 31.7 + - - +
188B LEU* 2.9 39.0 + - + +
189B ALA* 3.3 18.8 + - - +
203B THR* 3.8 9.2 - - - +
207B LEU* 3.4 28.9 - - + +
217B GLU* 5.7 3.8 - - - -
295B ARG* 4.6 2.5 - - - +
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Residues in contact with ASP 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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148B PRO* 3.7 31.5 - - - +
183B PHE 5.6 0.5 - - - +
184B VAL* 3.0 9.6 + - - +
185B ASN* 1.3 70.8 - - - +
187B ARG* 1.3 66.7 + - + +
189B ALA* 3.3 9.5 + - - +
190B GLN* 3.0 27.0 + - - +
217B GLU* 5.7 1.2 + - - -
234B LYS* 5.1 10.8 - - - -
237B GLN* 5.4 1.4 - - - +
238B GLN* 2.8 34.3 + - - +
241B GLN* 5.2 2.9 - - - +
295B ARG* 2.8 20.0 + - - +
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Residues in contact with ARG 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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453A TRP* 6.5 0.2 - - + -
185B ASN* 3.2 24.4 + - - +
186B ASP* 1.3 77.6 - - + +
188B LEU* 1.3 58.8 + - - +
190B GLN* 3.3 7.0 + - - +
191B SER* 2.9 32.9 + - - -
203B THR* 3.6 24.8 + - - +
206B ARG* 5.6 6.9 - - - +
207B LEU* 5.8 0.8 - - - +
216B GLY 4.7 2.2 + - - -
217B GLU* 3.1 38.8 + - - +
323B PRO* 3.4 41.0 - - - +
324B PHE 4.6 13.5 - - - +
325B SER* 4.7 14.4 - - - +
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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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154B VAL* 4.2 11.7 - - + -
157B TYR* 4.0 16.4 - - + -
182B PHE* 3.5 36.6 - - + -
185B ASN* 2.9 24.2 + - + +
187B ARG* 1.3 76.2 - - - +
189B ALA* 1.3 61.3 + - - +
191B SER* 3.3 4.8 + - - -
192B LEU* 3.0 26.8 + - + +
200B VAL* 4.0 33.0 - - + +
203B THR* 3.7 17.4 - - + +
204B THR* 4.0 7.2 - - - +
207B LEU* 3.9 14.4 - - + -
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Residues in contact with ALA 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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150B HIS* 3.5 31.5 - - + +
151B LEU* 5.3 0.7 - - - -
153B GLN* 3.7 12.0 - - - +
154B VAL* 3.9 19.2 - - + +
185B ASN 3.3 11.2 + - - +
186B ASP* 3.6 13.9 - - - +
187B ARG 3.3 0.2 - - - -
188B LEU* 1.3 79.3 - - - +
190B GLN* 1.3 56.2 + - - +
192B LEU* 3.5 0.6 + - - -
193B ALA* 3.1 26.2 + - - +
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Residues in contact with GLN 190 (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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227A ASP* 4.0 13.3 - - - +
412A THR 5.3 0.5 - - - +
414A VAL* 4.7 3.6 - - - +
453A TRP* 5.8 1.6 - - + -
454A PHE* 3.2 25.4 - - + -
150B HIS* 3.3 29.8 + - + +
186B ASP 3.0 16.8 + - - +
187B ARG* 3.5 7.4 - - - +
188B LEU 3.2 0.2 - - - -
189B ALA* 1.3 73.4 - - - +
191B SER* 1.3 55.1 + - - +
193B ALA* 2.9 4.8 + - - -
194B ASN* 2.7 79.1 + - - +
234B LYS* 4.6 16.9 + - - +
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Residues in contact with SER 191 (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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454A PHE 5.6 1.4 + - - -
187B ARG* 2.9 19.1 + - - +
188B LEU* 3.6 7.6 - - - -
190B GLN* 1.3 75.5 - - - +
192B LEU* 1.3 58.2 + - - +
194B ASN* 3.1 8.5 + - - +
195B ALA 2.8 24.6 + - - -
196B ASP* 3.1 15.1 + - - +
199B ALA* 3.5 22.7 + - - +
200B VAL* 3.6 27.1 - - - +
203B THR* 5.0 1.9 + - - -
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Residues in contact with LEU 192 (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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153B GLN* 3.8 32.4 + - + +
154B VAL* 4.7 2.0 - - + +
157B TYR* 3.6 47.8 - - + -
188B LEU* 3.0 26.1 + - + +
189B ALA 3.8 5.2 - - - +
190B GLN 3.2 0.2 - - - -
191B SER* 1.3 75.1 - - - +
193B ALA* 1.3 61.5 + - - +
195B ALA* 3.2 13.4 + - - +
200B VAL* 3.5 31.0 - - + -
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Residues in contact with ALA 193 (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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414A VAL* 2.7 43.0 - - + +
150B HIS* 3.7 29.6 - - + +
153B GLN* 3.8 17.4 - - - +
189B ALA 3.1 14.2 + - - +
190B GLN* 2.9 9.2 + - - +
192B LEU* 1.3 76.5 - - - +
194B ASN* 1.3 52.5 + - - +
195B ALA* 3.4 0.7 - - - +
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Residues in contact with ASN 194 (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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414A VAL* 3.4 36.7 - - - +
454A PHE* 3.4 35.6 + - - -
455A SER* 4.2 10.3 + - - +
457A HIS* 4.9 9.0 + - + -
190B GLN* 2.7 47.8 + - - +
191B SER* 3.7 7.3 - - - +
193B ALA* 1.3 76.8 - - - +
195B ALA* 1.3 72.2 + - - +
196B ASP* 4.3 10.3 + - + +
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Residues in contact with ALA 195 (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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457A HIS* 4.3 10.7 + - - -
191B SER 2.8 5.8 + - - -
192B LEU* 3.2 12.9 + - - +
193B ALA 5.1 0.7 - - - +
194B ASN* 1.3 82.2 - - - +
196B ASP* 1.3 60.2 + - - +
197B GLU* 3.4 6.6 + - - +
200B VAL* 5.5 0.9 - - - -
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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