Contacts of the helix formed by residues 176 - 190 (chain B) in PDB entry 1PN9
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 TYR 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B LYS* 3.2 35.7 + - + +
134B VAL* 3.4 15.0 - - + -
135B GLY* 3.7 29.4 - - - -
138B ASN* 3.0 24.0 - - + +
171B PHE* 3.6 22.7 - + - -
172B ASP 3.9 8.1 - - - -
173B PHE* 2.9 16.7 + - - +
174B ALA 3.1 0.2 - - - -
175B PRO* 1.3 108.3 - - + +
177B PRO* 1.3 63.2 - - - +
179B VAL* 3.1 14.8 + - + -
180B ALA* 3.1 18.4 + - - +
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Residues in contact with PRO 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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138B ASN* 3.9 7.0 - - - +
173B PHE 4.9 0.2 - - - +
174B ALA 4.0 7.2 - - - +
175B PRO 3.3 9.6 - - - +
176B TYR* 1.3 88.0 - - - +
178B ASN* 1.3 68.6 + - - +
180B ALA* 3.5 7.4 + - + +
181B ALA* 3.1 24.8 + - - +
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Residues in contact with ASN 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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138B ASN* 2.8 44.1 + - - +
141B LEU* 3.6 17.6 - - + +
142B GLU* 3.3 35.6 + - - +
143B GLY 4.8 2.8 + - - -
177B PRO* 1.3 83.3 - - - +
179B VAL* 1.3 57.5 + - - +
181B ALA* 3.5 4.9 + - - +
182B TRP* 2.9 30.7 + - - +
185B ARG* 5.0 1.2 + - - -
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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
----------------------------------------------------------
134B VAL* 3.7 12.6 - - + +
137B LEU* 4.2 17.0 - - + -
138B ASN* 3.6 38.6 - - + +
141B LEU* 3.8 7.6 - - + -
163B ILE* 4.6 3.8 - - + -
173B PHE* 3.9 27.6 - - + -
176B TYR* 3.1 14.3 + - + +
178B ASN* 1.3 73.7 - - - +
180B ALA* 1.3 56.8 + - - +
182B TRP* 3.5 16.1 - - + -
183B PHE* 2.7 38.6 + - + +
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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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173B PHE* 4.3 21.3 - - + +
174B ALA* 6.1 0.2 - - - -
176B TYR 3.1 12.7 + - - +
177B PRO* 3.8 11.2 - - + +
178B ASN 3.4 0.2 - - - -
179B VAL* 1.3 77.7 - - - +
181B ALA* 1.3 61.6 + - - +
183B PHE* 3.7 7.6 - - - +
184B ALA* 3.0 23.2 + - - +
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Residues in contact with ALA 181 (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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177B PRO 3.1 17.6 + - - +
178B ASN* 3.8 5.2 - - - +
180B ALA* 1.3 73.4 - - - +
182B TRP* 1.3 67.4 + - - +
184B ALA* 3.0 10.1 + - - +
185B ARG* 2.9 42.5 + - - +
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Residues in contact with TRP 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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137B LEU* 4.0 7.6 - - + -
141B LEU* 3.5 33.9 - - + -
145B GLU 4.2 0.9 - - - -
146B TYR* 4.1 14.8 - + - -
147B ALA* 4.1 2.7 - - + +
156B ASP* 2.8 33.5 + - - -
159B LEU* 3.6 48.0 - - + -
160B ALA* 3.7 6.3 - - + -
163B ILE* 3.6 25.1 - - + -
178B ASN 2.9 19.3 + - - +
179B VAL* 3.5 14.4 - - + -
181B ALA* 1.3 73.9 - - - +
183B PHE* 1.3 90.6 - + + +
185B ARG* 2.8 32.1 + - - +
186B CYS* 2.9 33.4 + - - -
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Residues in contact with PHE 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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160B ALA* 4.2 7.0 - - - -
163B ILE* 3.7 28.7 - - + -
164B ALA* 3.7 24.2 - - - -
167B GLU* 3.4 33.4 - - + -
173B PHE* 4.6 11.2 - + - -
179B VAL* 2.7 23.6 + - + +
180B ALA* 3.7 7.9 - - - +
182B TRP* 1.3 90.0 - + + +
184B ALA* 1.3 62.2 + - - +
186B CYS* 3.0 9.2 + - + +
187B LYS* 3.0 36.8 + - - +
193B TYR* 3.2 29.6 - + - -
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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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180B ALA 3.0 13.5 + - - +
181B ALA* 3.0 13.1 + - - +
183B PHE* 1.3 76.2 - - - +
185B ARG* 1.3 64.6 + - + +
186B CYS 3.1 0.7 + - - -
187B LYS* 3.1 22.8 + - - +
188B ALA* 3.2 13.7 + - - +
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Residues in contact with ARG 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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141B LEU* 6.2 0.2 - - - +
144B GLN 3.6 15.4 + - - -
145B GLU* 2.9 61.0 + - - +
146B TYR* 4.0 17.9 + - + +
178B ASN 5.0 1.2 + - - -
181B ALA* 2.9 27.8 + - - +
182B TRP* 2.8 28.2 + - - +
184B ALA* 1.3 78.0 - - + +
186B CYS* 1.3 56.1 + - - +
188B ALA* 4.7 2.7 - - - +
189B ASN* 3.0 42.9 + - - +
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Residues in contact with CYS 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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146B TYR* 4.5 7.4 - - - -
152B LEU* 5.1 4.0 - - - -
156B ASP* 4.3 13.2 - - - -
160B ALA* 4.2 21.3 - - + -
182B TRP* 2.9 52.8 + - - -
183B PHE* 3.0 13.2 + - + +
185B ARG* 1.3 74.9 - - - +
187B LYS* 1.3 61.9 + - - +
188B ALA 3.0 1.8 - - - -
190B ALA* 2.9 39.5 + - + +
193B TYR* 3.6 3.8 - - + -
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Residues in contact with LYS 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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167B GLU* 2.8 28.8 + - - -
183B PHE* 3.0 48.1 + - + +
184B ALA* 3.1 12.5 + - - +
186B CYS* 1.3 76.0 - - - +
188B ALA* 1.3 59.5 + - - +
190B ALA 5.2 0.2 - - - +
193B TYR* 3.5 50.3 - - + +
197B GLN* 4.9 5.7 + - - +
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Residues in contact with ALA 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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184B ALA 3.2 14.0 + - - +
185B ARG* 4.0 5.2 - - - +
186B CYS 3.0 0.4 - - - -
187B LYS* 1.3 79.8 - - + +
189B ASN* 1.3 68.8 + - - +
190B ALA 5.6 0.4 - - - -
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Residues in contact with ASN 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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146B TYR* 3.3 21.8 + - - +
152B LEU* 3.9 10.4 - - + +
185B ARG* 3.0 33.8 + - - +
188B ALA* 1.3 90.8 - - - +
190B ALA* 1.3 63.5 + - - +
191B PRO* 3.2 11.3 - - - +
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Residues in contact with ALA 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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17B MET* 4.3 4.9 - - - -
152B LEU* 3.9 10.6 - - + +
156B ASP 6.4 0.2 - - - -
157B LEU* 3.6 22.4 - - + -
160B ALA* 5.6 1.3 - - + -
186B CYS* 2.9 26.6 + - + +
187B LYS 4.8 0.5 - - - +
188B ALA 5.6 0.2 - - - -
189B ASN* 1.3 76.8 - - - +
191B PRO* 1.3 69.2 - - - +
192B GLY 3.3 0.3 + - - -
193B TYR* 3.1 29.2 + - + +
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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