Contacts of the helix formed by residues 165 - 184 (chain A) in PDB entry 1P9B
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 ASN 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A GLY 4.5 0.2 + - - -
162A THR* 3.2 11.5 + - - +
163A LEU 3.2 1.1 - - - -
164A LYS* 1.3 78.5 - - + +
166A PHE* 1.3 57.5 + - - +
167A GLU* 2.9 27.4 + - - +
168A ASN* 3.0 25.2 + - + +
169A PHE* 2.9 23.9 + - - +
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Residues in contact with PHE 166 (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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163A LEU* 4.6 0.7 - - + -
164A LYS 3.8 3.2 - - - -
165A ASN* 1.3 73.6 + - - +
167A GLU* 1.3 60.0 + - - +
169A PHE* 4.0 18.6 - + - -
170A LYS* 2.9 42.5 + - + +
195A LEU* 3.6 33.9 - - + -
196A ASN* 5.6 1.6 - - - -
198A PHE 4.2 0.4 - - - -
199A TYR* 3.5 56.5 - + + -
202A HIS* 3.8 32.6 - - + +
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASN* 2.9 13.1 + - - +
166A PHE* 1.3 81.2 - - - +
168A ASN* 1.3 64.2 + - - +
170A LYS* 3.6 5.6 + - - +
171A ASN* 3.5 18.7 + - - +
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A THR* 3.6 25.5 + - - +
165A ASN* 3.0 29.7 + - + +
167A GLU* 1.3 76.1 - - - +
169A PHE* 1.3 66.3 + - - +
171A ASN* 3.3 13.2 + - - +
172A MET* 3.0 38.3 + - - +
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Residues in contact with PHE 169 (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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115A ILE* 3.8 22.4 - - + -
117A PHE* 3.9 20.6 - + - -
158A ILE* 4.1 15.7 - - + -
162A THR* 3.6 16.1 + - + +
163A LEU* 3.9 26.7 - - + -
165A ASN 2.9 18.0 + - - +
166A PHE* 3.7 18.2 - + - +
168A ASN* 1.3 78.0 - - - +
170A LYS* 1.3 55.8 + - - +
172A MET* 3.1 2.0 + - - +
173A TYR* 2.7 52.7 + + + +
195A LEU* 4.3 7.2 - - + -
198A PHE* 3.5 43.3 - + + -
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 2.9 33.1 + - + +
167A GLU* 3.8 7.2 - - - +
168A ASN 3.4 0.2 - - - -
169A PHE* 1.3 76.7 - - - +
171A ASN* 1.3 63.1 + - - +
173A TYR* 3.5 3.3 - - - +
174A SER* 3.1 24.1 + - - -
195A LEU* 3.6 43.5 - - + +
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Residues in contact with ASN 171 (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 3.5 9.0 + - - +
168A ASN* 3.3 20.0 + - - +
169A PHE 3.2 0.4 - - - -
170A LYS* 1.3 78.9 - - - +
172A MET* 1.3 71.4 + - - +
174A SER* 3.6 5.4 + - - -
175A LYS* 3.2 51.2 + - - +
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Residues in contact with MET 172 (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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158A ILE* 3.7 30.3 - - + +
162A THR* 3.6 29.4 - - + +
168A ASN* 3.0 35.4 + - - +
169A PHE* 3.7 3.6 - - - +
171A ASN* 1.3 81.3 - - - +
173A TYR* 1.3 66.1 + - - +
175A LYS* 3.3 8.5 + - - +
176A LEU* 3.1 23.0 + - - +
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Residues in contact with TYR 173 (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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117A PHE* 3.7 26.5 - + - -
158A ILE* 4.9 6.7 - - - +
169A PHE* 2.7 38.1 + + + +
170A LYS* 3.5 6.3 - - - +
172A MET* 1.3 73.3 - - - +
174A SER* 1.3 67.8 + - - +
176A LEU* 3.1 4.8 + - - +
177A ILE* 2.9 54.3 + - + +
189A TYR* 3.6 10.0 - - - -
191A LYS* 3.6 29.0 + - + -
194A GLU* 2.5 47.0 + - + +
195A LEU* 3.7 30.3 - - + -
198A PHE* 5.2 1.1 - + - -
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Residues in contact with SER 174 (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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170A LYS 3.1 13.6 + - - -
171A ASN* 3.8 7.0 - - - -
172A MET 3.3 0.2 - - - -
173A TYR* 1.3 87.6 - - - +
175A LYS* 1.3 59.2 + - - +
177A ILE* 3.8 0.5 - - - -
178A ASP* 2.9 41.4 + - - +
191A LYS* 2.8 30.4 + - - +
195A LEU* 6.2 1.3 - - - -
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Residues in contact with LYS 175 (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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171A ASN* 3.2 38.2 + - - +
172A MET* 3.3 10.0 + - - +
173A TYR 3.2 0.6 - - - -
174A SER* 1.3 76.0 - - - +
176A LEU* 1.3 64.8 + - - +
178A ASP* 4.1 6.0 - - - +
179A HIS* 3.1 24.8 + - - +
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Residues in contact with LEU 176 (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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117A PHE* 3.9 33.2 - - + -
120A HIS* 4.7 7.4 - - + +
151A THR* 4.9 1.6 - - + +
156A ILE* 3.5 45.3 - - + +
157A GLY* 4.7 2.7 - - - -
158A ILE* 4.2 13.7 - - + +
172A MET 3.1 13.7 + - - +
173A TYR 3.7 6.5 - - - +
175A LYS* 1.3 75.8 - - - +
177A ILE* 1.3 61.5 + - + +
179A HIS* 3.2 5.9 + - + +
180A LEU* 2.9 54.6 + - + +
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Residues in contact with ILE 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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117A PHE* 4.6 7.9 - - + -
119A ILE* 4.5 10.3 - - + -
173A TYR* 2.9 64.8 + - + +
174A SER 3.9 2.7 - - - +
176A LEU* 1.3 90.1 - - + +
178A ASP* 1.3 58.2 + - - +
180A LEU* 3.2 6.0 + - - +
181A MET* 2.8 59.7 + - + +
189A TYR* 3.7 17.0 - - + -
191A LYS* 3.6 24.2 - - + -
194A GLU* 4.6 0.2 - - - +
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A SER* 2.9 27.7 + - - +
175A LYS* 4.1 6.1 + - - +
177A ILE* 1.3 75.7 - - - +
179A HIS* 1.3 63.1 + - - +
181A MET* 3.8 10.0 - - - +
182A ASP* 3.1 24.1 + - - +
191A LYS* 2.9 31.6 + - - +
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Residues in contact with HIS 179 (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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156A ILE* 3.6 33.6 - - + +
175A LYS 3.1 19.3 + - - +
176A LEU* 3.4 5.4 - - - +
178A ASP* 1.3 78.4 - - - +
180A LEU* 1.3 61.2 + - + +
182A ASP* 3.4 8.5 + - - +
183A LEU* 2.9 54.5 + - + +
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Residues in contact with LEU 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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119A ILE* 3.8 38.6 - - + -
120A HIS* 4.6 7.0 - - + +
123A ILE* 5.3 4.5 - - + -
151A THR* 4.1 25.6 - - + -
156A ILE* 4.5 2.9 - - + -
176A LEU* 2.9 45.2 + - + +
179A HIS* 1.3 88.8 - - + +
181A MET* 1.3 65.9 + - - +
183A LEU* 4.2 4.3 - - + -
184A TYR* 3.0 51.2 + - + +
186A ILE* 3.8 0.9 - - - +
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Residues in contact with MET 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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119A ILE* 3.7 15.9 - - + -
177A ILE* 2.8 47.4 + - + +
178A ASP* 3.8 9.9 - - - +
180A LEU* 1.3 72.3 - - - +
182A ASP* 1.3 57.7 + - - +
185A ASN* 2.8 26.5 + - - -
186A ILE* 2.8 43.7 + - + +
187A THR 3.9 10.5 - - - +
188A GLU* 4.0 0.4 - - - -
189A TYR* 3.6 35.9 - - + +
191A LYS* 4.4 11.0 - - + -
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Residues in contact with ASP 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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178A ASP 3.1 15.1 + - - +
179A HIS* 3.6 8.2 - - - +
181A MET* 1.3 79.0 - - - +
183A LEU* 1.3 66.2 + - - +
185A ASN* 3.2 19.9 + - - +
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Residues in contact with LEU 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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179A HIS* 2.9 42.4 + - + +
180A LEU* 3.3 9.6 + - + +
182A ASP* 1.3 81.8 - - - +
184A TYR* 1.3 89.3 + - + +
185A ASN* 3.8 4.9 + - - -
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Residues in contact with TYR 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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123A ILE* 3.7 40.2 - - + +
126A ILE* 4.2 25.0 - - + +
127A GLN* 4.1 19.7 + - + -
150A SER* 5.9 2.9 - - - -
180A LEU* 3.0 29.3 + - + -
183A LEU* 1.3 107.6 - - + +
185A ASN* 1.3 74.8 + - - +
186A ILE* 3.1 23.2 + - + +
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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
------------------------------------------------------------
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