Contacts of the helix formed by residues 221 - 239 (chain A) in PDB entry 1P4X
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A LYS* 4.6 1.6 - - - +
205A ILE* 4.1 16.0 - - + +
219A HIS* 5.7 0.4 - - - -
220A MET* 1.3 74.9 - - - +
222A ASP* 1.3 67.4 + - - +
223A ALA* 3.3 10.7 + - - +
224A GLN* 2.9 45.4 + - - +
225A GLN* 2.8 20.7 + - - +
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Residues in contact with ASP 222 (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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172A LYS* 2.7 38.6 + - - +
221A ASP* 1.3 73.1 - - + +
223A ALA* 1.3 65.8 + - - +
225A GLN* 3.2 2.9 + - - +
226A ASP* 3.0 39.3 + - - +
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Residues in contact with ALA 223 (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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221A ASP* 3.3 9.5 + - - +
222A ASP* 1.3 82.9 + - - +
224A GLN* 1.3 66.8 + - + +
226A ASP* 3.2 8.7 + - - +
227A HIS* 3.0 22.1 + - - +
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Residues in contact with GLN 224 (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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202A GLY* 3.0 30.1 + - - +
203A TYR* 3.5 15.4 - - - +
204A LEU* 3.4 22.8 + - - +
205A ILE* 3.6 13.0 - - - +
220A MET* 3.5 13.4 - - + +
221A ASP* 2.9 46.9 + - - +
223A ALA* 1.3 73.3 - - + +
225A GLN* 1.3 65.8 + - - +
227A HIS* 3.3 6.4 + - - +
228A ALA* 3.0 26.0 + - - +
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Residues in contact with GLN 225 (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 ILE 4.3 0.2 + - - -
168A THR 3.1 17.2 + - - +
171A ASN* 3.9 8.4 - - - +
172A LYS* 3.5 51.7 - - + +
220A MET* 2.8 38.5 - - + +
221A ASP 2.8 14.8 + - - +
222A ASP 3.2 8.5 + - - +
224A GLN* 1.3 72.8 - - - +
226A ASP* 1.3 66.2 + - - +
228A ALA* 3.2 2.4 + - - +
229A GLU* 2.9 58.1 + - - +
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Residues in contact with ASP 226 (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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222A ASP* 3.0 29.1 + - - +
223A ALA* 3.3 10.6 - - - +
225A GLN* 1.3 79.5 - - - +
227A HIS* 1.3 64.4 + - - +
229A GLU* 3.2 11.8 + - - +
230A GLN* 3.1 33.6 + - - +
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Residues in contact with HIS 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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203A TYR* 4.1 32.8 + + - -
223A ALA 3.0 9.9 + - - +
224A GLN* 3.8 9.0 - - - +
226A ASP* 1.3 78.3 - - - +
228A ALA* 1.3 63.3 + - - +
230A GLN* 3.2 27.4 + - + +
231A LEU* 3.0 33.0 + - + +
234A GLN* 6.0 3.1 - - - -
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Residues in contact with ALA 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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164A LEU* 4.4 16.4 - - + -
168A THR* 3.1 28.3 - - + +
203A TYR* 5.5 2.9 - - + +
220A MET* 4.0 9.6 - - - -
224A GLN 3.0 17.7 + - - +
225A GLN 3.6 3.1 - - - +
227A HIS* 1.3 77.9 - - - +
229A GLU* 1.3 56.9 + - - +
231A LEU* 3.2 8.8 + - - +
232A LEU* 2.8 35.9 + - - +
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Residues in contact with GLU 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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168A THR* 3.3 18.5 - - - +
171A ASN* 4.8 6.2 - - - +
225A GLN* 2.9 37.4 + - - +
226A ASP* 3.2 15.5 - - - +
228A ALA* 1.3 75.2 - - - +
230A GLN* 1.3 66.0 + - + +
232A LEU* 3.1 9.6 + - - +
233A ALA* 2.8 23.6 + - - +
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Residues in contact with GLN 230 (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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226A ASP* 3.1 24.4 + - - +
227A HIS* 3.4 29.3 + - + +
229A GLU* 1.3 79.7 - - + +
231A LEU* 1.3 52.8 + - - +
233A ALA* 2.9 11.3 + - - +
234A GLN* 2.7 49.6 + - + +
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Residues in contact with LEU 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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154A LEU* 4.1 24.5 - - + -
156A LEU* 5.5 3.4 - - + -
161A PHE* 3.3 32.3 - - + -
164A LEU* 4.7 10.8 - - + -
203A TYR* 5.3 11.0 - - + +
227A HIS* 3.0 25.5 + - + +
228A ALA* 3.3 13.5 - - - +
230A GLN* 1.3 74.8 - - - +
232A LEU* 1.3 67.3 + - + +
234A GLN* 3.1 31.2 + - + +
235A VAL* 3.1 17.7 + - + +
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Residues in contact with LEU 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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3A TYR* 3.9 21.8 - - + +
5A ASN* 5.1 3.6 - - - +
7A ASP* 5.5 0.2 - - - +
9A ILE* 3.6 12.9 - - + +
161A PHE* 3.7 28.7 - - + -
164A LEU* 4.9 6.5 - - + -
165A ALA* 4.0 24.7 - - + +
168A THR* 3.5 31.2 - - + +
228A ALA 2.8 22.9 + - - +
229A GLU* 3.7 7.0 - - - +
231A LEU* 1.3 74.9 - - + +
233A ALA* 1.3 57.5 + - - +
235A VAL 3.5 0.2 + - - -
236A ASN* 3.0 34.5 + - - +
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Residues in contact with ALA 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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229A GLU 2.8 12.9 + - - +
230A GLN* 3.0 17.0 - - - +
232A LEU* 1.3 75.7 - - - +
234A GLN* 1.3 63.0 + - + +
236A ASN* 3.3 8.0 + - - +
237A GLN* 3.1 32.6 + - - +
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Residues in contact with GLN 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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154A LEU* 5.5 5.3 - - + +
227A HIS* 6.0 3.4 - - - -
230A GLN* 2.7 36.1 + - + +
231A LEU* 3.6 24.1 - - + +
233A ALA* 1.3 70.9 - - - +
235A VAL* 1.3 66.5 + - + +
237A GLN* 2.9 18.1 + - - +
238A LEU* 2.9 30.2 + - + +
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Residues in contact with VAL 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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9A ILE* 4.2 6.1 - - + -
146A PHE* 4.4 5.6 - - + -
149A ILE* 5.3 4.5 - - + -
150A ILE* 4.6 8.1 - - + -
154A LEU* 4.2 16.4 - - + -
161A PHE* 3.5 41.3 - - + -
231A LEU* 3.1 16.2 + - + +
232A LEU 3.8 6.3 - - - +
234A GLN* 1.3 77.4 - - + +
236A ASN* 1.3 63.2 + - - +
238A LEU* 3.0 24.4 + - + +
239A LEU* 3.1 33.8 + - + +
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Residues in contact with ASN 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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7A ASP* 2.8 28.5 - - - +
8A LYS* 3.6 30.5 - - - +
9A ILE* 3.3 25.5 - - - +
232A LEU* 3.0 22.0 + - - +
233A ALA* 3.7 7.8 - - - +
235A VAL* 1.3 77.1 - - - +
237A GLN* 1.3 61.5 + - - +
239A LEU* 3.4 6.2 + - - +
240A ALA* 3.3 18.4 + - - +
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Residues in contact with GLN 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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233A ALA* 3.1 23.5 + - - +
234A GLN* 2.9 16.2 + - - +
236A ASN* 1.3 74.8 - - - +
238A LEU* 1.3 60.0 + - + +
240A ALA* 2.7 36.8 + - + +
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Residues in contact with LEU 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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145A TYR* 4.1 5.5 + - - -
149A ILE* 4.1 28.4 - - + +
153A HIS* 3.7 52.0 - - + +
154A LEU* 5.8 1.3 - - + -
234A GLN* 2.9 22.6 + - + +
235A VAL* 3.4 21.1 - - + +
237A GLN* 1.3 79.1 - - + +
239A LEU* 1.3 58.1 + - - +
240A ALA 3.3 2.3 + - - +
242A LYS* 5.7 0.3 - - - +
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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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8A LYS* 2.8 50.4 + - + +
9A ILE 4.7 0.2 - - - +
142A TYR* 3.8 14.6 - - + +
145A TYR* 4.1 18.2 - - + -
146A PHE* 3.7 38.6 - - + -
149A ILE* 3.4 36.8 - - + -
235A VAL* 3.1 25.2 + - + +
236A ASN* 3.4 10.1 + - - +
237A GLN 3.1 0.8 - - - -
238A LEU* 1.3 75.9 - - - +
240A ALA* 1.3 55.0 + - - +
242A LYS* 4.0 8.9 - - - +
244A HIS* 4.8 2.4 - - + +
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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