Contacts of the helix formed by residues 194 - 205 (chain A) in PDB entry 1PJR
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A LYS* 2.7 34.7 + - - +
181A GLN* 3.5 15.2 + - - -
184A LEU* 3.7 11.8 - - - +
189A SER 4.9 0.3 - - - +
190A LEU* 3.8 17.2 - - + +
191A ASP* 2.9 32.1 + - - +
192A PHE 3.2 0.6 - - - -
193A ASP* 1.3 76.1 - - - +
195A LEU* 1.3 59.0 + - - +
197A MET* 3.9 12.9 - - - +
198A THR* 2.7 45.3 + - - +
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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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93A HIS* 4.0 28.3 - - + +
96A CYS* 3.6 11.1 - - + +
97A VAL* 3.8 31.6 - - + -
100A LEU* 4.1 14.2 - - + +
113A PHE* 4.3 7.6 - - + -
115A ILE* 4.3 12.3 - - + -
190A LEU* 4.0 19.1 - - + -
191A ASP 3.9 7.4 - - - +
192A PHE* 3.4 31.4 - - + +
193A ASP 3.3 0.6 - - - -
194A ASP* 1.3 77.6 - - - +
196A ILE* 1.3 59.1 + - + +
199A THR* 2.8 29.5 + - - +
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Residues in contact with ILE 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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92A PHE* 4.2 17.7 - - + -
93A HIS* 4.7 19.7 - - + +
96A CYS* 4.2 15.5 - - - -
153A ASN* 5.8 3.4 - - - +
192A PHE 5.4 0.2 - - - +
193A ASP* 3.7 8.2 + - - +
194A ASP 3.2 0.2 - - - -
195A LEU* 1.3 76.3 - - + +
197A MET* 1.3 66.4 + - - +
199A THR* 3.3 3.6 + - - +
200A ILE* 3.1 26.7 + - + +
229A ASN* 5.9 0.2 - - - +
231A ALA* 3.7 38.6 - - + +
232A GLN* 3.6 31.9 - - + +
235A LEU* 4.1 15.7 - - + -
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Residues in contact with MET 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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152A LYS* 4.3 33.0 - - + +
155A LEU* 4.1 31.6 - - + +
157A PRO* 4.7 22.2 - - + -
158A PRO* 5.6 1.3 - - + -
177A TYR* 4.6 6.1 - - - +
181A GLN* 4.6 10.5 - - - +
193A ASP 3.7 11.6 + - - +
194A ASP* 3.2 24.3 + - - +
196A ILE* 1.3 79.6 - - - +
198A THR* 1.3 58.7 + - - +
200A ILE* 3.3 5.5 + - - +
201A GLN* 3.0 49.6 + - + +
231A ALA* 5.5 0.4 - - - +
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Residues in contact with THR 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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100A LEU* 4.2 6.3 - - + -
104A ILE* 3.7 30.1 - - + -
107A ILE* 4.0 16.6 - - + -
109A ILE* 4.5 8.3 - - + -
190A LEU* 4.3 12.4 - - + +
194A ASP* 2.7 34.9 + - - +
197A MET* 1.3 71.6 - - - +
199A THR* 1.4 59.7 + - - -
201A GLN* 3.1 18.0 + - - +
202A LEU* 2.9 26.2 + - - +
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Residues in contact with THR 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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96A CYS* 3.4 28.4 - - + +
99A ILE* 4.3 14.2 - - - +
100A LEU* 3.8 21.3 - - + +
195A LEU 2.8 22.2 - - - +
196A ILE 3.3 2.3 + - - +
198A THR* 1.4 75.2 - - - +
200A ILE* 1.3 62.3 + - - +
202A LEU* 3.5 7.8 - - - +
203A PHE* 3.0 34.7 + - - -
235A LEU* 3.7 21.0 - - - +
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Residues in contact with ILE 200 (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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155A LEU* 3.8 34.3 - - + -
196A ILE* 3.1 21.5 + - + +
197A MET* 3.3 8.0 + - + +
199A THR* 1.3 75.6 - - - +
201A GLN* 1.3 60.3 + - - +
203A PHE* 3.4 7.4 + - - +
204A ASP* 3.0 37.5 + - - +
231A ALA 3.8 23.1 - - - +
234A THR* 4.5 3.4 - - + -
235A LEU* 4.2 24.7 - - + +
238A LYS* 4.0 17.7 - - + -
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Residues in contact with GLN 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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107A ILE* 4.8 5.2 - - + +
109A ILE* 6.1 0.8 - - - +
157A PRO* 5.1 8.0 - - - +
197A MET* 3.0 39.9 + - + +
198A THR* 3.1 26.1 + - - +
200A ILE* 1.3 72.2 - - + +
202A LEU* 1.3 61.7 + - - +
204A ASP* 3.8 4.2 - - - +
205A ARG* 2.9 73.8 + - - +
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Residues in contact with LEU 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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99A ILE* 4.1 21.3 - - + +
100A LEU* 4.0 22.7 - - + -
103A ASP* 3.5 31.9 - - + +
104A ILE* 4.6 0.7 - - - +
106A ARG* 4.6 0.4 - - + -
107A ILE* 4.3 24.6 - - + +
198A THR 2.9 16.6 + - - +
199A THR* 3.5 5.6 - - - +
201A GLN* 1.3 74.8 - - - +
203A PHE* 1.3 58.6 + - + +
206A VAL* 2.9 59.2 + - + +
209A VAL* 4.2 23.1 - - + -
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Residues in contact with PHE 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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99A ILE* 4.1 26.7 - - + -
199A THR* 3.0 37.4 + - - +
200A ILE* 3.4 7.8 + - - +
202A LEU* 1.3 75.5 - - + +
204A ASP* 1.3 66.2 + - - +
206A VAL 4.4 3.6 - - - -
207A PRO* 3.6 23.2 - - - +
209A VAL* 4.1 11.0 - - + -
210A LEU* 3.7 58.0 - - + +
213A TYR* 4.1 17.5 - + + -
235A LEU* 3.8 20.2 - - + -
238A LYS* 4.6 10.8 - - + -
239A LEU* 4.2 18.8 - - + -
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Residues in contact with ASP 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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200A ILE* 3.0 25.9 + - - +
201A GLN* 4.1 4.7 - - - +
203A PHE* 1.3 78.9 - - - +
205A ARG* 1.3 63.4 + - + +
207A PRO* 4.1 10.5 - - - +
210A LEU* 5.4 1.6 - - - +
238A LYS* 2.6 38.1 + - - -
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Residues in contact with ARG 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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107A ILE* 4.2 29.7 + - + +
201A GLN* 2.9 57.2 + - - +
202A LEU 4.0 1.1 - - - +
204A ASP* 1.3 81.4 - - + +
206A VAL* 1.3 59.0 + - - +
207A PRO* 3.6 5.5 - - - +
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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
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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