Contacts of the helix formed by residues 154 - 171 (chain B) in PDB entry 1PVR
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 ARG 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B SER* 3.3 3.1 + - - +
153B ASP* 1.3 77.7 - - - +
155B CYS* 1.3 65.3 + - - +
156B GLN* 3.2 28.5 + - - +
157B ASP* 2.8 46.9 + - - +
158B ILE* 2.8 26.9 + - - +
4C A 3.7 22.6 + - - -
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Residues in contact with CYS 155 (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 ASP 3.5 2.4 + - - -
154B ARG* 1.3 70.7 - - - +
156B GLN* 1.3 63.7 + - - +
158B ILE* 3.0 11.8 + - - +
159B ARG* 2.8 24.4 + - - +
224B TRP* 4.2 7.3 - - - -
227B VAL* 4.1 34.3 - - + +
242B VAL* 3.4 16.2 - - + -
246B GLY* 3.1 34.3 - - - +
248B ALA* 4.1 18.2 - - - -
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Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ARG* 3.2 31.9 + - + +
155B CYS* 1.3 78.2 - - - +
157B ASP* 1.3 57.4 + - - +
159B ARG* 3.0 24.7 + - - +
160B ASN* 2.8 47.3 + - - +
242B VAL* 3.8 15.7 - - + +
246B GLY* 5.7 0.2 - - - -
4C A 2.9 41.7 + - - +
5C C 3.5 17.1 + - - +
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Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B MET* 3.7 28.0 - - + +
152B SER* 2.3 44.5 + - - +
154B ARG* 2.8 42.5 + - - +
155B CYS 3.4 0.2 - - - -
156B GLN* 1.3 76.0 - - - +
158B ILE* 1.3 63.9 + - - +
160B ASN* 4.4 4.3 + - - -
161B LEU* 2.9 27.8 + - - +
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B SER 3.7 6.7 - - - +
153B ASP* 3.0 28.5 - - - +
154B ARG 2.8 28.7 + - - +
155B CYS* 3.4 7.4 - - - +
157B ASP* 1.3 77.1 - - - +
159B ARG* 1.3 62.0 + - - +
161B LEU* 3.5 5.3 + - - +
162B ALA* 3.2 21.0 + - - +
220B LEU 4.7 2.5 - - - +
223B ARG* 3.6 41.1 - - + +
224B TRP* 3.5 33.9 - - + +
227B VAL* 3.8 20.4 - - + -
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B CYS 2.8 12.6 + - - +
156B GLN* 3.4 16.0 + - - +
158B ILE* 1.3 73.8 - - - +
160B ASN* 1.3 73.3 + - - +
162B ALA* 2.9 7.3 + - - +
163B PHE* 2.8 33.0 + - + +
224B TRP* 3.3 39.7 - - + -
239B PHE* 3.6 23.0 - - + -
240B CYS 2.7 39.7 + - - +
241B ARG* 3.7 1.2 - - - +
242B VAL* 3.6 11.2 - - + +
256B LEU* 3.8 14.8 - - - +
260B ALA* 6.2 0.8 - - - +
264B ILE* 4.4 12.4 - - + +
5C C 2.4 44.2 + - - -
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B MET* 3.8 17.5 - - + +
156B GLN* 2.8 38.9 + - - +
157B ASP* 4.9 3.0 + - - +
159B ARG* 1.3 99.9 + - - +
161B LEU* 1.3 57.5 + - - +
163B PHE* 3.3 4.3 + - - +
164B LEU* 3.0 34.6 + - + +
264B ILE* 3.4 35.0 + - + +
267B ALA* 5.5 5.7 - - - +
268B THR* 5.4 1.4 + - - +
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Residues in contact with LEU 161 (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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142B PHE* 4.3 8.1 - - + -
145B VAL* 4.7 8.1 - - + -
146B ARG* 3.8 33.7 - - + +
149B MET* 3.8 19.0 - - + +
150B GLU* 3.5 36.6 - - - +
157B ASP 2.9 17.9 + - - +
158B ILE* 3.9 5.6 - - - +
160B ASN* 1.3 76.6 - - - +
162B ALA* 1.3 56.8 + - - +
164B LEU* 4.0 3.5 - - + -
165B GLY 3.0 20.4 + - - -
220B LEU* 3.6 34.0 - - + +
223B ARG* 6.3 0.4 - - - +
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Residues in contact with ALA 162 (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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158B ILE 3.2 11.8 + - - +
159B ARG 2.9 9.1 + - - +
161B LEU* 1.3 75.8 - - - +
163B PHE* 1.3 64.3 + - - +
165B GLY* 3.1 1.9 + - - -
166B ILE* 3.0 26.5 + - - +
220B LEU* 3.8 32.2 - - - +
221B VAL* 4.2 8.6 - - + +
224B TRP* 3.9 14.1 - - + -
239B PHE* 4.0 12.1 - - + -
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Residues in contact with PHE 163 (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 ARG 2.8 12.2 + - - +
160B ASN 3.3 6.0 + - - +
162B ALA* 1.3 77.4 - - - +
164B LEU* 1.3 77.3 + - + +
166B ILE* 3.1 1.9 + - - +
167B ALA* 2.8 21.7 + - + +
174B LEU* 3.7 12.8 - - + -
177B ILE* 3.7 37.0 - - + -
239B PHE* 3.5 19.5 - + + -
261B LEU* 3.2 49.6 - - + -
264B ILE* 3.6 33.9 - - + -
265B PHE* 3.5 33.7 - + - -
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE* 4.2 19.6 - - + -
142B PHE* 4.4 7.2 - - + -
145B VAL* 4.0 23.6 - - + -
149B MET* 4.8 2.2 - - + -
160B ASN 3.0 21.0 + - - +
161B LEU* 4.1 6.5 - - + +
163B PHE* 1.3 87.0 - - + +
165B GLY* 1.3 57.5 + - - +
167B ALA* 3.3 5.5 + - - +
168B TYR* 2.9 33.8 + - - +
264B ILE* 4.4 3.4 - - + -
265B PHE* 3.4 46.7 - - + -
268B THR* 3.3 28.7 - - + +
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Residues in contact with GLY 165 (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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142B PHE* 3.7 23.0 - - - -
161B LEU 3.0 16.7 + - - -
162B ALA 3.5 4.0 - - - -
163B PHE 3.1 0.4 - - - -
164B LEU* 1.3 76.4 - - - +
166B ILE* 1.3 56.8 + - - +
168B TYR* 4.0 1.9 - - - +
169B ASN* 2.9 30.8 + - - +
217B VAL* 3.4 17.1 - - - +
220B LEU* 4.4 1.6 - - - -
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Residues in contact with ILE 166 (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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162B ALA 3.0 8.4 + - - +
163B PHE* 3.7 6.3 - - - +
165B GLY* 1.3 71.5 - - - +
167B ALA* 1.3 59.0 + - - +
169B ASN* 4.3 3.1 - - - -
170B THR* 2.5 57.1 + - + +
172B LEU* 4.6 3.8 - - + -
177B ILE* 4.2 23.6 - - + -
180B ILE* 4.8 2.5 - - + -
195B ILE* 3.7 22.0 - - + -
213B LEU* 3.7 21.3 - - + -
217B VAL* 3.7 2.7 - - + +
221B VAL* 3.9 20.0 - - + -
238B LEU* 4.2 9.0 - - + -
239B PHE* 3.9 27.4 - - + -
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Residues in contact with ALA 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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163B PHE* 2.8 18.0 + - + +
164B LEU* 3.5 6.7 - - - +
166B ILE* 1.3 77.1 - - - +
168B TYR* 1.3 56.8 + - - +
170B THR* 4.3 0.7 - - - -
171B LEU* 2.9 30.9 + - - +
172B LEU 4.7 2.6 - - - +
177B ILE* 3.9 22.4 - - + +
265B PHE* 3.8 31.6 - - + -
291B ALA* 3.8 8.8 - - + +
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Residues in contact with TYR 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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137B PHE* 3.6 39.5 - + + -
138B GLU 4.5 1.1 - - - -
139B ARG* 3.4 34.3 + - + +
142B PHE* 4.2 22.9 - + + -
164B LEU 2.9 16.5 + - - +
165B GLY 4.1 1.3 - - - +
167B ALA* 1.3 76.4 - - - +
169B ASN* 1.3 74.1 + - + +
171B LEU* 3.6 13.0 - - - +
291B ALA* 3.7 12.9 - - - +
295B ALA* 3.8 21.0 - - + +
298B ASP* 2.5 38.2 + - - +
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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 GLY 2.9 20.7 + - - +
166B ILE* 3.8 4.3 - - - +
168B TYR* 1.3 86.6 - - + +
170B THR* 1.3 62.0 + - - +
171B LEU* 3.5 8.3 - - - +
212B ALA 3.4 21.6 + - - -
213B LEU* 3.6 6.8 - - + +
214B SER* 3.0 31.8 + - - +
217B VAL* 3.3 18.2 - - + +
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Residues in contact with THR 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 ILE* 2.5 39.9 + - + +
169B ASN* 1.3 71.7 - - - +
171B LEU* 1.3 67.2 + - - +
172B LEU* 3.0 32.8 + - + +
195B ILE* 4.7 2.0 - - + -
211B LYS* 3.0 51.1 + - + +
212B ALA 4.5 2.2 - - - +
213B LEU* 3.4 30.7 - - + -
312B ALA 3.5 1.6 - - - +
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Residues in contact with LEU 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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167B ALA 2.9 20.6 + - - -
168B TYR 3.6 9.6 - - - +
169B ASN 3.5 13.7 - - - +
170B THR* 1.3 76.9 - - - +
172B LEU* 1.3 69.2 + - - +
291B ALA 4.5 0.2 - - - +
292B ARG* 3.0 44.1 + - + +
295B ALA* 3.6 26.2 - - + -
296B ALA* 4.3 5.6 - - - +
299B MET* 5.3 3.8 - - - -
312B ALA* 3.9 22.9 - - + +
313B GLY* 3.9 14.1 - - - +
315B TRP* 3.9 28.5 - - + -
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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
------------------------------------------------------------
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