Contacts of the helix formed by residues 174 - 187 (chain B) in PDB entry 3PII
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 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY 3.3 6.7 + - - -
173B ILE* 1.3 77.3 - - - +
175B GLY* 1.3 58.3 + - - -
176B PHE 3.3 2.0 - - - -
177B GLY* 3.9 1.4 - - - +
178B HIS* 2.7 35.5 + - - -
195B ASP* 4.6 0.2 + - - -
200B LYS* 4.4 11.0 - - - +
237B THR* 5.0 0.2 + - - -
330B GLY* 4.9 6.3 - - - -
342B SO4 3.3 17.6 + - - -
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Residues in contact with GLY 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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149B ALA* 4.1 7.5 - - - +
174B GLY* 1.3 70.7 - - - -
176B PHE* 1.3 63.7 + - - +
178B HIS* 3.2 23.0 + - - -
179B VAL* 3.8 9.2 - - - +
328B ILE 5.8 0.6 + - - -
330B GLY* 3.9 22.7 + - - +
331B ARG* 4.4 8.9 - - - +
342B SO4 3.0 21.6 + - - -
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Residues in contact with PHE 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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38B CYS* 5.8 2.5 - - - -
148B CYS* 4.4 11.7 - - - -
149B ALA* 3.4 39.7 - - + -
152B THR* 4.4 14.6 - - + -
153B THR* 3.6 9.6 + - - +
175B GLY* 1.3 73.2 - - - +
177B GLY* 1.3 57.6 + - - +
179B VAL* 3.0 9.0 + - - +
180B ALA* 2.7 33.9 + - - +
237B THR* 3.8 29.4 - - + -
260B VAL* 3.8 32.1 - - + -
261B GLY* 5.6 1.6 - - - -
285B ILE* 5.6 5.6 - - + -
331B ARG* 3.5 18.2 - - - -
342B SO4 3.9 15.3 + - - +
500B BMD 5.4 2.0 - - - -
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Residues in contact with GLY 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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170B ILE* 3.6 10.6 - - - +
172B GLY 3.0 28.4 + - - -
173B ILE* 3.8 7.9 - - - -
174B GLY 3.3 4.0 + - - +
176B PHE* 1.3 78.9 - - - +
178B HIS* 1.3 56.5 + - - +
180B ALA* 3.1 4.6 + - - +
181B VAL* 3.0 32.7 + - - +
237B THR* 4.1 3.8 + - - -
342B SO4 5.1 0.2 + - - -
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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
----------------------------------------------------------
173B ILE* 3.9 19.8 - - + +
174B GLY 2.7 28.1 + - - +
175B GLY* 3.2 19.9 + - - -
177B GLY* 1.3 72.3 - - - +
179B VAL* 1.3 76.2 + - + +
181B VAL* 3.8 3.2 + - - +
182B GLN* 2.8 36.0 + - - +
203B LEU* 4.3 9.9 - - + -
207B LEU* 3.4 23.9 - - + +
306B THR* 3.9 5.6 - - + -
307B ILE* 3.1 46.7 + - + +
330B GLY* 3.9 23.0 - - - -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 5.7 1.3 - - + -
149B ALA* 3.5 34.8 - - + +
150B GLY* 4.2 5.8 - - - +
153B THR* 3.8 5.6 - - + -
175B GLY 3.8 7.0 - - - +
176B PHE 3.0 9.8 + - - +
178B HIS* 1.3 102.3 - - + +
180B ALA* 1.3 66.5 + - - +
182B GLN* 2.9 22.1 + - - +
183B TYR* 3.1 21.3 + - + -
304B VAL* 4.9 6.1 - - + -
305B LYS 4.7 0.7 - - - +
306B THR* 3.7 27.8 - - + +
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Residues in contact with ALA 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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153B THR* 3.2 31.2 - - + +
157B LEU* 3.2 13.4 - - + +
170B ILE* 3.9 24.2 - - + +
176B PHE 2.7 14.1 + - - +
177B GLY* 3.1 10.7 + - - +
179B VAL* 1.3 71.6 - - - +
181B VAL* 1.3 55.3 + - - +
183B TYR 3.4 0.3 + - - -
184B ALA* 3.0 26.3 + - - +
235B VAL* 5.2 4.5 - - + -
237B THR* 4.9 4.0 - - + -
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 4.2 26.2 - - + -
173B ILE* 4.2 12.6 - - + -
177B GLY 3.0 16.4 + - - +
178B HIS* 3.9 10.5 - - - +
179B VAL 3.3 0.2 - - - -
180B ALA* 1.3 74.4 - - - +
182B GLN* 1.3 63.0 + - - +
184B ALA* 3.3 3.0 + - - +
185B LYS* 3.1 22.6 + - + +
191B VAL* 4.1 10.3 - - + -
193B ALA* 4.9 4.7 - - + -
204B ALA* 4.3 9.4 - - + +
207B LEU* 4.2 13.0 - - + +
208B GLY 4.6 1.1 - - - -
209B ALA* 3.9 34.8 - - + +
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Residues in contact with GLN 182 (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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178B HIS* 2.8 30.6 + - - +
179B VAL* 2.9 13.3 + - - +
181B VAL* 1.3 76.1 - - - +
183B TYR* 1.3 57.8 + - - +
185B LYS* 3.3 5.7 + - - +
186B ALA* 3.0 29.3 + - - +
207B LEU* 3.8 43.2 - - + +
303B LYS 3.7 9.8 - - - +
304B VAL* 3.3 17.5 - - + -
305B LYS* 2.7 48.3 + - - +
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Residues in contact with TYR 183 (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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146B ILE* 3.7 17.7 - - - +
150B GLY* 3.8 21.3 - - - -
153B THR* 3.5 20.4 - - + -
154B TYR* 3.6 21.5 - + + -
157B LEU* 3.7 17.7 - - + -
179B VAL* 3.1 17.3 + - + -
180B ALA 3.9 2.2 - - - +
182B GLN* 1.3 71.8 - - - +
184B ALA* 1.3 67.3 + - - +
186B ALA* 3.3 3.2 + - - +
187B MET* 2.8 32.6 + - - +
295B ALA* 2.6 46.7 + - + +
298B PHE* 3.7 26.9 - + + -
299B ALA* 4.8 0.2 - - - +
304B VAL* 3.6 26.8 - - + +
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Residues in contact with ALA 184 (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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157B LEU* 3.3 23.7 - - + +
168B VAL* 4.0 7.4 - - + -
170B ILE* 4.2 2.5 - - + -
180B ALA 3.0 19.0 + - - +
181B VAL 3.4 6.5 - - - +
182B GLN 3.3 0.2 - - - -
183B TYR* 1.3 76.5 - - - +
185B LYS* 1.3 56.6 + - - +
187B MET 3.1 13.5 + - - -
189B LEU* 3.1 31.2 + - + +
191B VAL* 3.5 22.2 - - + -
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Residues in contact with LYS 185 (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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303A LYS* 5.1 6.7 - - - +
181B VAL* 3.1 17.4 + - + +
182B GLN* 3.7 7.4 - - - +
184B ALA* 1.3 70.5 - - - +
186B ALA* 1.3 62.4 + - - +
187B MET 3.0 5.6 + - - -
188B GLY* 3.2 13.3 + - - -
189B LEU 3.1 21.8 + - - +
190B ASN* 3.6 6.5 + - - -
191B VAL* 3.8 15.0 - - + -
207B LEU 4.3 3.8 - - - +
208B GLY* 3.6 36.1 - - - +
210B ASP* 2.5 34.1 + - - +
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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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164A PRO* 4.3 0.2 - - - +
188A GLY* 3.8 17.3 - - - +
182B GLN 3.0 16.7 + - - +
183B TYR* 3.6 8.3 - - - +
185B LYS* 1.3 77.0 - - - +
187B MET* 1.3 59.6 + - - +
188B GLY 3.3 1.1 + - - -
298B PHE* 3.9 33.7 - - + -
303B LYS* 4.2 25.7 + - + +
304B VAL* 5.1 0.9 - - + -
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Residues in contact with MET 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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164A PRO* 3.6 40.0 - - + +
188A GLY* 4.7 2.7 - - - -
154B TYR* 3.8 28.0 - - + -
157B LEU* 3.8 24.2 - - + +
158B LYS* 3.8 39.3 - - + +
162B ALA 5.9 2.0 - - - +
164B PRO* 3.9 12.5 - - - +
183B TYR* 2.8 26.6 + - - +
184B ALA* 3.5 5.8 - - - +
185B LYS 3.0 1.0 - - - -
186B ALA* 1.3 80.9 - - - +
188B GLY* 1.3 56.6 + - - +
189B LEU* 3.3 18.9 + - + +
298B PHE* 4.5 5.2 - - + -
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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