Contacts of the helix formed by residues 190 - 206 (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 ASP 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A TYR* 1.3 69.7 - - - +
191A LYS* 1.3 61.6 + - - +
192A GLU* 3.5 9.7 + - - +
193A LYS* 3.0 44.6 + - + +
194A GLU* 3.3 11.6 + - - +
1604A NO3 3.1 34.1 + - - +
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Residues in contact with LYS 191 (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 TYR* 3.6 20.5 + - + +
174A SER* 2.8 40.0 + - - +
177A ILE* 3.6 26.0 - - + -
178A ASP* 2.9 31.0 + - - +
181A MET* 4.4 6.3 - - - -
189A TYR* 3.0 19.3 + - + +
190A ASP* 1.3 71.2 - - - +
192A GLU* 1.3 59.9 + - + +
194A GLU 3.5 0.2 + - - -
195A LEU* 2.9 36.0 + - + +
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Residues in contact with GLU 192 (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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190A ASP* 3.3 7.8 + - - +
191A LYS* 1.3 79.3 - - + +
193A LYS* 1.3 62.0 - - - +
195A LEU* 3.7 7.2 - - + +
196A ASN* 2.9 39.5 + - - +
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Residues in contact with LYS 193 (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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90A LYS* 5.9 2.4 - - - +
118A ASP* 5.4 1.4 + - - -
190A ASP* 3.0 41.0 + - - +
192A GLU* 1.3 78.4 - - - +
194A GLU* 1.3 63.4 + - - +
196A ASN* 3.4 6.1 + - - +
197A LEU* 3.0 44.8 + - + +
1604A NO3 4.3 17.7 + - - -
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Residues in contact with GLU 194 (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 12.5 - - - +
118A ASP* 3.0 37.4 + - - +
173A TYR* 2.5 39.1 + - + +
189A TYR* 2.5 23.7 + - - -
190A ASP 3.3 9.7 + - - +
193A LYS* 1.3 79.1 - - - +
195A LEU* 1.3 62.7 - - - +
197A LEU* 3.2 13.8 + - + +
198A PHE* 2.9 41.5 + - + -
1604A NO3 4.0 7.8 + - - +
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Residues in contact with LEU 195 (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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166A PHE* 3.6 29.1 - - + -
169A PHE* 4.3 11.0 - - + -
170A LYS* 3.6 46.9 - - + +
173A TYR* 3.7 24.8 + - + -
174A SER* 6.2 1.3 - - - -
191A LYS* 2.9 21.3 + - + +
192A GLU* 3.7 7.0 - - + +
194A GLU* 1.3 76.9 - - - +
196A ASN* 1.3 65.4 + - - +
198A PHE* 2.9 14.5 + - - +
199A TYR 3.1 9.4 + - - -
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Residues in contact with ASN 196 (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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166A PHE* 5.6 1.8 - - - -
192A GLU* 2.9 33.2 + - - +
193A LYS* 3.9 5.6 - - - +
195A LEU* 1.3 77.6 - - - +
197A LEU* 1.3 62.3 + - + +
199A TYR* 3.2 22.2 + - - +
200A ASN* 3.4 13.2 + - - -
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Residues in contact with LEU 197 (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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90A LYS* 5.3 11.7 - - + +
118A ASP* 6.0 1.3 - - - +
193A LYS* 3.0 40.5 + - + +
194A GLU* 3.4 15.5 - - + +
196A ASN* 1.3 77.1 - - + +
198A PHE* 1.3 59.0 + - + +
200A ASN* 3.0 34.0 + - + +
201A TYR* 3.0 42.0 + - + +
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Residues in contact with PHE 198 (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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88A HIS* 6.5 0.2 - + - -
89A VAL* 3.8 28.0 - - + -
90A LYS* 5.2 2.5 - - + -
115A ILE* 3.7 22.7 - - + -
116A LEU 4.9 4.3 - - - -
117A PHE* 3.5 32.3 - + - -
163A LEU* 3.9 18.5 - - + +
166A PHE* 4.2 1.8 - - - -
169A PHE* 3.5 32.5 - + + -
173A TYR* 5.2 0.9 - + - -
194A GLU* 2.9 41.6 + - + +
195A LEU* 2.9 10.3 + - - +
197A LEU* 1.3 73.5 - - - +
199A TYR* 1.3 56.5 + - - +
200A ASN 3.2 0.2 - - - -
201A TYR* 3.4 23.1 - + - +
202A HIS* 2.7 33.4 + - - +
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Residues in contact with TYR 199 (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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166A PHE* 3.5 46.4 - + + -
195A LEU 3.1 5.7 + - - -
196A ASN* 3.3 16.2 - - - +
197A LEU 3.1 0.4 - - - -
198A PHE* 1.3 76.5 - - - +
200A ASN* 1.3 69.7 + - - +
202A HIS* 3.1 11.6 + + - +
203A ILE* 2.9 62.4 + - + +
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Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ASN* 3.4 17.2 + - - +
197A LEU* 3.0 24.6 + - - +
199A TYR* 1.3 89.1 - - - +
201A TYR* 1.3 66.4 + - + +
203A ILE* 3.3 7.7 + - - +
204A LYS* 3.1 45.7 + - - +
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Residues in contact with TYR 201 (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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89A VAL* 3.4 26.2 - - + -
90A LYS* 3.3 41.7 - - + +
93A MET* 3.2 35.4 - - + -
163A LEU* 4.3 8.5 - - + -
197A LEU* 3.0 36.5 + - + +
198A PHE* 3.2 46.4 + + - +
200A ASN* 1.3 77.8 - - + +
202A HIS* 1.3 67.6 + - - +
204A LYS* 5.5 2.2 - - - -
205A LEU* 2.8 34.5 + - + +
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Residues in contact with HIS 202 (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* 2.7 36.3 + - + +
164A LYS 3.0 28.0 - - - -
166A PHE* 3.8 26.5 + - + +
198A PHE 2.7 17.9 + - - +
199A TYR* 3.1 19.1 - + - +
201A TYR* 1.3 72.2 - - - +
203A ILE* 1.3 76.7 + - + +
206A ARG* 2.9 61.0 + - + +
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Residues in contact with ILE 203 (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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199A TYR* 2.9 55.3 + - + +
200A ASN* 3.6 9.0 - - - +
202A HIS* 1.3 92.2 - - + +
204A LYS* 1.3 67.8 + - + +
205A LEU 3.7 0.2 + - - -
206A ARG* 3.4 29.3 + - - +
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Residues in contact with LYS 204 (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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93A MET* 3.8 30.5 - - + +
97A GLU* 3.3 21.7 + - - +
104A LEU* 3.8 26.0 - - + +
200A ASN* 3.1 38.9 + - - +
201A TYR* 5.6 1.2 - - - -
203A ILE* 1.3 83.9 - - + +
205A LEU* 1.3 65.9 + - + +
207A ASP 5.5 0.4 + - - -
208A ARG* 4.6 3.8 - - - +
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Residues in contact with LEU 205 (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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89A VAL* 3.9 26.5 - - + -
92A LEU* 4.3 15.5 - - + -
93A MET* 3.7 25.8 - - + -
96A ILE* 3.5 28.5 - - + -
104A LEU* 4.0 11.4 - - + -
109A LEU* 4.3 16.4 - - + -
160A LEU* 6.0 2.5 - - + -
163A LEU* 5.5 3.1 - - + -
201A TYR* 2.8 23.2 + - + +
204A LYS* 1.3 79.9 - - + +
206A ARG* 1.3 57.8 + - - +
207A ASP 3.3 2.7 - - - -
208A ARG* 2.7 26.6 + - + +
209A ILE* 3.3 18.0 + - + +
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Residues in contact with ARG 206 (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 5.0 0.2 - - - +
164A LYS* 3.0 36.5 + - + +
202A HIS* 2.9 59.4 + - + +
203A ILE* 3.4 27.1 + - - +
205A LEU* 1.3 75.8 - - - +
207A ASP* 1.3 87.0 + - - +
208A ARG 3.2 0.9 + - - -
209A ILE* 3.2 20.4 + - - +
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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