Contacts of the helix formed by residues 176 - 190 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A LYS* 3.3 32.0 + - - +
134A VAL* 3.8 12.3 - - + -
135A GLY* 3.4 35.2 - - - -
138A ASN* 3.1 23.3 - - + +
171A PHE* 3.8 19.1 - + - -
172A ASP 4.1 0.7 - - - -
173A PHE* 2.9 24.2 + - - +
174A ALA 3.0 1.6 + - - -
175A PRO* 1.3 108.0 - - + +
177A PRO* 1.3 66.2 - - - +
179A VAL* 3.1 14.6 + - + -
180A ALA* 3.0 18.2 + - - +
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Residues in contact with PRO 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASN* 3.9 6.5 - - - +
173A PHE 5.1 0.2 - - - +
174A ALA 4.1 7.4 - - - +
175A PRO 3.7 7.6 - - - +
176A TYR* 1.3 87.3 - - - +
178A ASN* 1.3 64.4 + - - +
180A ALA* 3.7 7.8 - - + +
181A ALA* 2.9 31.7 + - - +
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Residues in contact with ASN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASN* 3.0 44.9 + - - +
139A THR* 5.1 0.2 - - - +
141A LEU* 3.7 16.0 - - + +
142A GLU* 3.0 40.9 + - - +
143A GLY 5.1 1.0 + - - -
177A PRO* 1.3 83.1 - - - +
179A VAL* 1.3 56.4 - - - +
181A ALA* 3.4 5.3 + - - +
182A TRP* 2.9 31.4 + - - +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.8 10.5 - - + +
137A LEU* 4.1 16.8 - - + -
138A ASN* 3.6 38.4 - - + +
141A LEU* 3.8 7.0 - - + -
163A ILE* 4.6 4.7 - - + -
173A PHE* 3.9 28.3 - - + -
176A TYR* 3.1 15.3 + - + +
178A ASN* 1.3 74.9 - - - +
180A ALA* 1.3 56.0 + - - +
182A TRP* 3.2 16.3 + - + -
183A PHE* 2.7 38.7 + - + +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 4.5 19.5 - - + +
174A ALA* 6.2 0.2 - - - -
176A TYR 3.0 11.7 + - - +
177A PRO* 3.7 11.4 - - + +
178A ASN 3.3 0.2 - - - -
179A VAL* 1.3 78.6 - - - +
181A ALA* 1.3 61.6 + - - +
183A PHE* 3.4 6.7 + - - +
184A ALA* 3.1 24.6 + - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO 2.9 19.5 + - - +
178A ASN* 3.7 6.1 - - - +
180A ALA* 1.3 78.5 - - - +
182A TRP* 1.3 59.8 + - - +
184A ALA* 3.5 6.5 + - - +
185A ARG* 3.0 31.5 + - + +
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Residues in contact with TRP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.2 9.2 - - + -
141A LEU* 3.6 34.5 - - + -
144A GLN 6.1 0.2 - - - +
145A GLU 3.7 17.9 - - - +
146A TYR* 4.0 7.0 - + - -
147A ALA 4.0 1.8 - - - +
156A ASP* 2.9 30.7 + - - -
159A LEU* 3.6 48.2 - - + -
160A ALA* 3.9 5.6 - - + -
163A ILE* 3.7 23.8 - - + -
178A ASN 2.9 17.4 + - - +
179A VAL* 3.5 14.1 - - + -
181A ALA* 1.3 74.1 - - - +
183A PHE* 1.3 91.7 + + + +
185A ARG* 3.1 11.5 + - - +
186A CYS* 3.0 42.0 + - - -
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Residues in contact with PHE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ALA* 4.3 7.4 - - - -
163A ILE* 3.7 26.5 - - + -
164A ALA* 3.6 24.9 - - - -
167A GLU* 3.6 32.8 - - + -
173A PHE* 4.8 9.4 - + - -
179A VAL* 2.7 23.3 + - + +
180A ALA* 3.7 6.7 - - - +
182A TRP* 1.3 90.1 - + + +
184A ALA* 1.3 62.5 + - - +
186A CYS* 3.2 8.8 + - + +
187A LYS* 3.2 35.1 + - - +
193A TYR* 3.0 32.1 - + - -
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ALA 3.1 17.0 + - - +
181A ALA* 3.7 7.2 - - - +
183A PHE* 1.3 76.6 - - - +
185A ARG* 1.3 64.4 + - + +
187A LYS* 3.2 23.5 + - + +
188A ALA* 3.3 13.2 + - - +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLU* 2.6 39.8 + - - +
146A TYR* 4.4 13.9 - - + +
181A ALA* 3.0 25.3 + - - +
182A TRP* 3.1 12.5 + - - +
184A ALA* 1.3 77.7 - - - +
186A CYS* 1.3 57.7 + - - +
188A ALA* 3.2 4.7 + - - -
189A ASN* 2.8 49.4 + - - +
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Residues in contact with CYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TYR* 4.3 13.7 - - - -
152A LEU* 4.4 3.6 - - - -
156A ASP* 4.4 14.8 - - - -
160A ALA* 4.4 13.2 - - + -
182A TRP* 3.0 53.5 + - - -
183A PHE* 3.2 9.6 + - + +
185A ARG* 1.3 74.7 - - - +
187A LYS* 1.3 62.7 + - - +
190A ALA* 2.6 45.9 + - + +
193A TYR* 3.9 4.4 - - + -
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Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 3.3 27.9 + - - -
183A PHE* 3.2 42.2 + - - +
184A ALA* 3.2 13.2 + - - +
186A CYS* 1.3 77.9 - - - +
188A ALA* 1.3 60.2 + - - +
190A ALA 4.6 1.0 + - - +
193A TYR* 3.4 50.0 - - + +
197A GLN* 4.5 9.2 + - - +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ALA 3.3 7.5 + - - +
185A ARG* 3.2 8.4 + - - +
186A CYS 3.1 0.6 - - - -
187A LYS* 1.3 81.3 - - - +
189A ASN* 1.3 68.8 + - - +
190A ALA 5.4 0.2 - - - -
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Residues in contact with ASN 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TYR* 3.1 25.9 + - - +
152A LEU* 3.7 10.2 - - + +
185A ARG* 2.8 37.6 + - - +
188A ALA* 1.3 88.6 - - - +
190A ALA* 1.3 64.1 + - - +
191A PRO* 3.3 10.9 - - - +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 4.5 2.7 - - - -
152A LEU* 3.7 8.4 - - + +
157A LEU* 3.9 20.9 - - + -
160A ALA* 5.6 0.7 - - + -
186A CYS* 2.6 36.4 + - + +
187A LYS 4.8 1.0 - - - +
189A ASN* 1.3 72.1 - - - +
191A PRO* 1.3 72.7 - - - +
192A GLY 3.4 0.7 + - - -
193A TYR* 3.2 30.0 + - + +
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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
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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