Contacts of the helix formed by residues 226 - 241 (chain A) in PDB entry 1P39
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 LYS 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PRO* 3.0 39.5 + - + +
182A ASP* 5.0 2.5 - - - +
184A TRP* 3.4 47.2 + - + +
187A ASP* 3.7 1.6 + - - -
225A THR* 1.3 74.2 - - - +
227A SER* 1.3 58.4 + - - +
229A ALA* 3.1 6.1 + - - +
230A VAL* 2.9 35.1 + - + +
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Residues in contact with SER 227 (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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225A THR* 2.9 21.2 + - - -
226A LYS* 1.3 74.9 - - - +
228A ASP* 1.3 66.7 + - - +
230A VAL* 3.1 12.9 + - - +
231A ASN* 3.1 21.7 + - - +
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Residues in contact with ASP 228 (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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223A ARG 3.6 7.1 - - - +
224A VAL* 3.6 16.9 - - + -
225A THR* 2.9 39.6 + - - +
227A SER* 1.3 76.9 + - - +
229A ALA* 1.3 64.3 + - - +
231A ASN* 3.0 9.3 + - - +
232A TYR* 2.9 37.2 + - + -
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Residues in contact with ALA 229 (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 CYS* 3.5 12.9 - - - -
179A PRO 3.5 15.9 - - - +
181A PRO* 3.5 13.3 - - + +
184A TRP* 3.4 35.0 - - + -
225A THR 2.9 4.9 + - - -
226A LYS* 3.2 11.2 - - - +
228A ASP* 1.3 77.1 - - - +
230A VAL* 1.3 59.3 + - - +
232A TYR* 3.8 1.8 - - - +
233A GLU* 3.2 23.6 + - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO* 3.7 22.7 - - + -
226A LYS* 2.9 26.6 + - + +
227A SER* 3.1 13.4 + - - +
229A ALA* 1.3 77.3 - - - +
231A ASN* 1.3 64.0 + - - +
233A GLU* 3.6 6.9 - - - +
234A LYS* 3.2 49.2 + - + +
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Residues in contact with ASN 231 (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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13A PHE* 3.8 20.4 - - - -
19A GLU* 3.5 15.7 + - - -
227A SER 3.1 9.3 + - - +
228A ASP* 3.0 11.6 + - - +
230A VAL* 1.3 78.1 - - - +
232A TYR* 1.3 65.6 + - - +
234A LYS* 3.1 2.1 + - - +
235A LYS* 2.8 57.4 + - - +
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Residues in contact with TYR 232 (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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13A PHE* 3.5 36.9 - + - -
176A TRP* 3.2 34.6 + + - -
178A CYS* 3.5 30.3 - - + -
190A ILE* 4.7 1.4 - - - +
195A LYS* 3.3 20.4 - - - -
206A ALA* 5.6 3.6 - - + -
208A MET* 3.6 33.0 - - + -
224A VAL* 4.7 3.4 - - + -
228A ASP* 2.9 35.0 + - + +
229A ALA 3.8 5.4 - - - +
231A ASN* 1.3 75.9 + - + +
233A GLU* 1.3 57.8 + - - +
235A LYS* 4.1 0.2 - - - -
236A MET* 2.9 40.0 + - + +
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Residues in contact with GLU 233 (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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22A TYR* 3.7 22.7 + - + +
180A PHE* 5.4 2.7 - - + -
181A PRO* 3.4 30.5 - - + +
182A ASP* 5.5 0.3 - - - -
206A ALA* 5.7 3.6 - - - -
229A ALA 3.2 15.4 + - - +
230A VAL* 3.6 8.4 - - - +
232A TYR* 1.3 81.0 - - - +
234A LYS* 1.3 72.3 + - + +
236A MET* 4.0 2.9 - - - +
237A TYR* 3.0 29.8 + - - +
401A MGT 3.0 44.2 + - + +
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Residues in contact with LYS 234 (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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19A GLU* 3.3 35.4 - - + +
20A LEU 3.0 39.0 + - - +
21A ASP* 3.0 32.2 + - - +
22A TYR 5.0 0.4 - - - +
230A VAL* 3.2 36.8 + - + +
231A ASN 3.1 2.2 + - - +
233A GLU* 1.3 87.0 + - + +
235A LYS* 1.3 65.2 - - - +
238A TYR 3.0 10.6 + - - -
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Residues in contact with LYS 235 (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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13A PHE* 3.5 31.2 - - + +
16A ILE* 3.4 36.1 + - + +
17A ASP* 4.4 2.8 - - - +
18A ASN* 3.2 28.9 + - - +
19A GLU* 4.1 13.3 + - + -
231A ASN* 2.8 47.0 + - - +
234A LYS* 1.3 71.9 - - - +
236A MET* 1.3 57.8 + - - +
238A TYR* 3.2 4.5 + - - +
239A LEU* 2.9 28.1 + - - +
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Residues in contact with MET 236 (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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13A PHE* 4.0 25.1 - - + -
16A ILE* 4.2 2.0 - - - -
197A LEU* 4.4 9.6 - - + -
205A SER 3.6 19.5 - - - +
206A ALA* 3.6 38.8 - - + +
207A GLU 4.2 10.5 - - - +
208A MET* 4.2 10.3 - - + -
232A TYR* 2.9 27.9 + - + +
233A GLU* 4.3 1.6 - - - +
235A LYS* 1.3 75.9 - - - +
237A TYR* 1.3 57.1 + - - +
239A LEU* 3.6 28.3 - - + +
240A ASN* 3.0 40.3 + - - +
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Residues in contact with TYR 237 (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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20A LEU* 3.5 32.8 - - + +
21A ASP 3.2 22.0 - - - -
22A TYR* 3.4 26.5 - + + -
23A GLU* 2.9 47.2 + - - +
26A SER* 3.7 26.1 - - - -
29A GLU* 5.3 1.4 + - - -
204A TYR* 3.8 21.1 - + + -
233A GLU 3.0 22.6 + - - +
235A LYS 3.2 0.2 - - - -
236A MET* 1.3 77.2 - - - +
238A TYR* 1.3 58.1 + - - +
240A ASN* 4.6 2.7 - - - +
241A LYS* 2.9 52.4 + - + +
401A MGT 6.0 0.7 - - - -
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Residues in contact with TYR 238 (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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10A PHE* 4.5 3.8 - + - -
16A ILE* 3.7 12.3 - - + -
17A ASP* 3.9 12.1 + - - -
18A ASN* 3.1 58.8 + - + +
19A GLU* 3.4 17.7 - - - -
20A LEU* 3.9 12.5 - - + +
234A LYS 3.0 18.9 + - - +
235A LYS 3.2 2.7 + - - +
237A TYR* 1.3 76.5 - - - +
239A LEU* 1.3 59.4 + - - +
242A ILE* 2.9 65.8 + - + +
243A VAL* 3.5 22.6 + - + +
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Residues in contact with LEU 239 (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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10A PHE* 3.6 33.2 - - + +
16A ILE* 3.8 22.9 - - + -
197A LEU* 3.9 19.1 - - + -
235A LYS 2.9 16.3 + - - +
236A MET* 3.6 23.3 - - + +
238A TYR* 1.3 77.3 - - - +
240A ASN* 1.3 59.3 + - - +
243A VAL* 3.2 21.3 + - + +
244A ARG* 2.8 50.0 + - + +
258A TYR* 4.3 8.7 - - + +
262A HIS* 6.4 0.9 - - + -
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Residues in contact with ASN 240 (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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203A SER 3.2 21.4 - - - +
204A TYR* 3.2 30.0 + - + +
205A SER 2.7 28.3 + - - +
236A MET* 3.0 26.6 + - - +
237A TYR* 4.1 2.5 - - - +
239A LEU* 1.3 80.6 - - - +
241A LYS* 1.3 66.4 + - - +
244A ARG* 3.0 39.4 + - - +
245A ASN* 3.1 14.4 + - - -
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Residues in contact with LYS 241 (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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20A LEU* 3.7 19.9 - - + +
23A GLU* 2.9 31.3 + - - -
29A GLU* 5.5 4.0 - - - +
204A TYR* 3.8 19.9 - - + +
237A TYR* 2.9 36.7 + - + +
240A ASN* 1.3 74.1 - - - +
242A ILE* 1.3 71.0 + - + +
245A ASN* 2.7 25.4 + - - +
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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