Contacts of the helix formed by residues 191 - 207 (chain B) in PDB entry 2PAF
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 SER 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B PRO* 3.9 24.2 - - - +
149B ASP* 4.7 1.2 + - - -
188B PRO* 3.0 13.5 + - - +
190B SER* 1.3 83.9 + - - +
192B VAL* 1.3 65.9 + - - +
193B SER* 3.2 9.7 + - - -
194B ALA* 2.9 29.7 + - - +
195B ARG* 3.3 14.7 + - - +
220B TRP* 3.7 19.6 - - - -
901B NPF 5.6 0.4 - - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PRO* 4.1 2.0 - - + +
128B LEU 3.4 28.2 - - - +
129B ASP* 4.6 3.8 - - - +
130B ASP 5.7 1.1 - - - +
149B ASP* 3.4 29.2 - - - +
150B VAL* 3.9 5.6 - - - -
151B SER* 4.2 16.8 - - - +
190B SER 3.1 5.3 + - - -
191B SER* 1.3 68.9 + - - +
193B SER* 1.3 75.1 + - - +
194B ALA 2.8 1.7 + - - -
195B ARG* 2.8 36.9 + - + +
196B LEU* 3.0 32.9 + - + +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASP* 2.6 29.5 + - - -
150B VAL 4.7 1.0 + - - -
160B ILE* 3.3 27.7 - - - +
191B SER* 3.2 5.4 + - - -
192B VAL* 1.3 81.2 - - - +
194B ALA* 1.3 61.5 + - - +
196B LEU* 3.6 10.4 + - - +
197B ARG* 3.0 34.2 + - - +
220B TRP* 5.1 3.1 - - - -
901B NPF 3.9 17.5 - - - -
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Residues in contact with ALA 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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186B ALA* 5.3 0.7 - - - +
187B GLY* 3.8 28.8 + - - +
188B PRO 3.2 28.7 - - - +
189B LEU* 4.7 3.1 - - + +
191B SER* 2.9 14.8 + - - +
192B VAL 3.0 0.2 - - - -
193B SER* 1.3 78.0 - - - +
195B ARG* 1.3 52.6 + - - +
197B ARG* 3.1 8.1 + - - +
198B LEU* 2.8 34.1 + - - +
201B TRP* 5.9 0.2 - - - -
220B TRP* 3.9 10.0 - - + -
245B ALA* 6.3 0.4 - - - -
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASP* 3.8 24.4 - - - +
189B LEU* 2.3 58.4 + - + +
190B SER* 2.9 23.1 + - - +
191B SER 3.6 2.0 - - - +
192B VAL* 2.8 31.7 + - + +
194B ALA* 1.3 76.8 - - - +
196B LEU* 1.3 65.5 - - + +
198B LEU* 3.1 7.0 + - - +
199B ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 196 (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 VAL 4.8 2.9 - - - +
151B SER* 4.0 25.8 - - - -
152B ASP* 4.7 0.4 - - - +
160B ILE* 5.6 3.6 - - + -
163B HIS* 3.4 50.8 + - + +
192B VAL* 3.0 50.6 + - + +
193B SER* 3.7 12.1 - - - +
195B ARG* 1.3 75.9 - - + +
197B ARG* 1.3 54.0 + - - +
198B LEU 2.7 1.7 + - - -
199B ALA* 4.5 4.9 - - - -
200B GLY* 2.5 37.5 + - - -
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Residues in contact with ARG 197 (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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163B HIS* 4.8 6.7 - - + +
167B THR* 3.5 11.0 - - + +
193B SER* 3.0 24.2 + - - +
194B ALA* 3.1 7.2 + - - +
196B LEU* 1.3 75.2 - - - +
198B LEU* 1.3 59.5 + - - +
200B GLY 3.8 0.7 - - - -
201B TRP* 3.2 37.6 + - + -
220B TRP* 3.5 19.7 - - - -
245B ALA* 3.2 27.6 + - + +
273B TYR* 3.3 45.8 + - + +
291B GLN* 3.1 12.9 + - - +
901B NPF 2.6 65.0 + - - -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 4.5 10.3 - - + -
186B ALA* 4.3 14.8 - - + -
189B LEU* 3.9 29.6 - - + -
194B ALA 2.8 13.1 + - - +
195B ARG* 3.5 10.3 - - - +
196B LEU 2.7 1.2 + - - -
197B ARG* 1.3 74.5 - - - +
199B ALA* 1.3 69.7 + - - +
200B GLY 2.9 0.4 - - - -
201B TRP* 2.7 38.5 + - + +
202B HIS* 3.0 24.0 + - + -
215B GLU* 3.7 26.9 - - + +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ARG 2.9 18.2 + - - +
196B LEU* 3.7 5.2 - - - +
198B LEU* 1.3 73.8 - - - +
200B GLY* 1.3 66.8 + - - +
202B HIS* 3.0 13.2 + - - +
203B LYS* 3.0 23.0 + - - +
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Residues in contact with GLY 200 (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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163B HIS* 4.7 5.2 - - - -
164B GLU* 5.5 4.0 - - - -
167B THR* 3.4 24.7 - - - -
196B LEU 2.5 22.5 + - - -
198B LEU 2.8 2.2 + - - -
199B ALA* 1.3 75.0 - - - +
201B TRP* 1.3 62.4 + - - -
203B LYS* 3.3 7.3 + - - +
204B TYR* 3.1 24.1 - - - -
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Residues in contact with TRP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY 5.1 1.6 + - - -
167B THR* 3.5 31.4 + - + +
170B GLY* 5.4 0.6 - - - -
171B VAL* 3.9 5.4 - - + +
184B LEU* 3.7 28.9 - - + -
185B LEU 3.3 24.7 - - - -
186B ALA* 4.2 8.5 - - + -
194B ALA 5.9 0.2 - - - -
197B ARG* 3.2 24.2 + - + -
198B LEU* 2.7 26.9 + - + +
200B GLY* 1.3 71.1 - - - -
202B HIS* 1.3 64.5 - - - +
204B TYR* 3.2 4.2 + - - -
205B LEU* 3.1 25.5 + - + +
243B LEU* 3.3 56.2 - - + +
244B VAL 4.1 2.5 - - - -
245B ALA* 3.4 22.2 - - + -
271B VAL 5.4 0.9 - - - -
273B TYR* 4.7 16.3 - + - -
289B ILE* 5.6 1.4 - - - +
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Residues in contact with HIS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 4.5 3.7 - - + +
198B LEU* 3.0 36.5 + - + +
199B ALA* 3.3 12.1 + - - +
201B TRP* 1.3 73.2 - - - +
203B LYS* 1.3 69.0 + - - +
205B LEU* 2.7 19.4 + - + +
206B THR* 2.8 22.7 + - - +
212B PRO* 4.3 22.0 - - + +
215B GLU* 2.8 42.7 + - - -
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Residues in contact with LYS 203 (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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164B GLU* 2.8 42.7 + - - +
199B ALA 3.0 10.8 + - - +
200B GLY* 3.4 12.1 - - - +
202B HIS* 1.3 73.7 - - - +
204B TYR* 1.3 68.7 + - + +
206B THR* 3.3 4.6 + - - -
207B ARG* 2.7 59.3 + - + +
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Residues in contact with TYR 204 (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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164B GLU* 2.7 47.7 + - - +
167B THR* 3.6 10.8 - - - -
168B ARG* 3.4 37.6 - - + +
171B VAL* 3.3 30.8 - - + +
172B GLU* 5.4 2.0 - - + +
200B GLY* 3.1 22.9 - - - -
201B TRP 3.2 1.0 + - - +
202B HIS 2.9 2.4 + - - -
203B LYS* 1.3 95.6 - - + +
205B LEU* 1.3 59.1 + - - +
207B ARG* 4.0 34.6 + - + +
208B ASN* 3.1 29.3 + - - +
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Residues in contact with LEU 205 (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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171B VAL* 3.9 19.3 - - + -
175B VAL* 5.5 0.2 - - + -
182B ILE* 4.4 24.0 - - + -
184B LEU* 3.7 37.2 - - + -
201B TRP* 3.1 19.4 + - + +
202B HIS* 2.7 12.4 + - + +
204B TYR* 1.3 72.2 - - - +
206B THR* 1.3 57.9 + - - +
208B ASN* 3.7 2.2 - - - -
209B GLN 2.9 4.3 + - - -
210B ILE* 2.5 76.3 + - + +
212B PRO* 4.4 13.7 - - + -
243B LEU* 4.8 1.8 - - + -
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Residues in contact with THR 206 (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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202B HIS* 2.8 22.3 + - - +
203B LYS* 3.6 4.7 - - - -
205B LEU* 1.3 76.9 - - - +
207B ARG* 1.3 61.0 + - - +
208B ASN 2.8 0.9 - - - -
209B GLN* 2.6 29.7 + - - +
210B ILE 4.4 5.9 + - - +
211B GLN* 6.0 0.3 + - - -
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Residues in contact with ARG 207 (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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203B LYS* 2.7 47.1 + - + +
204B TYR* 4.0 35.2 + - + +
206B THR* 1.3 74.7 - - - +
208B ASN* 1.3 62.1 + - - +
209B GLN* 5.0 4.0 - - - +
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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
------------------------------------------------------------
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