Contacts of the helix formed by residues 222 - 243 (chain A) in PDB entry 4P9U
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 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TYR 3.9 2.2 - - - +
220A PHE 3.1 0.8 - - - -
221A SER* 1.3 80.7 - - - +
223A PRO* 1.3 71.1 - - - +
224A GLN* 3.0 32.4 + - - +
225A ALA* 2.9 18.0 + - + +
226A ARG* 3.3 14.2 + - - +
262A ILE* 4.5 3.8 - - - +
265A GLN* 3.4 28.9 + - - +
266A MET* 3.6 34.1 - - + +
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Residues in contact with PRO 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 6.0 0.7 - - + -
174A GLU* 6.0 0.7 - - - +
221A SER 3.7 7.6 - - - +
222A ASN* 1.3 90.7 - - - +
224A GLN* 1.3 59.8 + - - +
226A ARG* 3.1 34.9 + - + +
227A GLU* 3.0 30.9 + - - +
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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
----------------------------------------------------------
222A ASN* 3.0 21.3 + - - +
223A PRO* 1.3 78.3 - - - +
225A ALA* 1.3 58.3 + - - +
227A GLU* 4.1 3.5 + - - +
228A LEU* 3.6 27.9 + - - +
262A ILE* 3.8 13.6 - - + +
265A GLN* 4.1 16.8 + - - +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TYR* 3.4 51.7 + - + +
220A PHE* 4.4 3.3 - - + -
222A ASN* 2.9 13.2 + - + +
224A GLN* 1.3 78.7 - - - +
226A ARG* 1.3 59.5 + - - +
227A GLU 3.3 0.4 - - - -
228A LEU* 3.3 3.8 + - - +
229A ALA* 2.9 29.4 + - - +
262A ILE* 3.8 16.8 - - + +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.9 24.7 - - + +
174A GLU* 4.7 12.9 + - - -
177A ILE* 3.7 30.6 - - - +
178A ALA 4.7 0.4 - - - +
181A PHE* 3.2 45.6 - - + -
220A PHE* 2.7 51.7 + - + +
221A SER* 3.8 14.8 + - - +
222A ASN 3.6 8.7 - - - +
223A PRO* 3.1 38.0 + - - +
225A ALA* 1.3 77.0 - - - +
227A GLU* 1.3 56.3 + - - +
229A ALA 3.3 0.2 + - - -
230A MET* 3.0 26.0 + - - +
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.5 17.2 - - - +
139A VAL* 5.7 4.0 - - - +
223A PRO* 3.0 17.5 + - - +
224A GLN* 4.5 4.9 - - - +
226A ARG* 1.3 74.9 - - - +
228A LEU* 1.3 65.7 + - + +
230A MET* 3.2 27.9 + - + +
231A GLU* 3.0 27.5 + - - +
234A ARG* 4.7 4.2 + - - +
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Residues in contact with LEU 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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219A TYR* 5.6 1.1 - - - +
224A GLN 3.6 14.7 + - - +
225A ALA* 3.3 9.0 + - - +
227A GLU* 1.3 79.1 - - + +
229A ALA* 1.3 60.7 + - - +
231A GLU* 3.4 8.6 + - + +
232A PHE* 2.9 29.3 + - - +
255A TYR* 3.8 13.2 - - + -
258A ALA* 3.6 31.9 - - + -
259A SER* 4.7 1.6 - - - +
262A ILE* 3.9 20.2 - - + -
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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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181A PHE* 3.4 28.9 - - + -
220A PHE* 3.9 6.1 - - + -
225A ALA 2.9 15.9 + - - +
226A ARG 3.5 0.7 - - - +
227A GLU 3.2 0.4 - - - -
228A LEU* 1.3 77.8 - - - +
230A MET* 1.3 57.5 + - - +
232A PHE* 3.2 2.6 + - - +
233A TYR* 2.9 44.2 + - - +
255A TYR* 3.8 24.1 - - - +
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Residues in contact with MET 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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132A ILE* 4.7 5.1 - - + +
135A CYS* 3.3 34.1 - - + +
136A GLU* 3.6 17.0 - - - +
138A LEU* 3.7 17.7 - - + -
139A VAL* 6.1 2.2 - - + -
181A PHE* 3.6 14.4 - - + -
226A ARG 3.0 16.3 + - - +
227A GLU* 3.2 31.4 - - - +
228A LEU 3.3 0.2 - - - -
229A ALA* 1.3 76.4 - - - +
231A GLU* 1.3 62.0 + - - +
233A TYR* 3.1 12.9 + - + +
234A ARG* 2.9 56.3 + - + +
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Residues in contact with GLU 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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227A GLU 3.0 17.7 + - - +
228A LEU* 3.6 10.1 - - + +
230A MET* 1.3 75.7 - - - +
232A PHE* 1.3 58.2 + - - +
234A ARG* 3.3 21.5 + - - +
235A GLN* 3.0 61.9 + - - +
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Residues in contact with PHE 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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113A MET* 5.1 0.9 - - + -
189A PHE* 3.7 29.2 - + - -
228A LEU 2.9 14.3 + - - +
229A ALA 3.3 7.4 - - - +
231A GLU* 1.3 76.8 - - - +
233A TYR* 1.3 70.0 + + - +
235A GLN* 3.2 9.7 + - - +
236A LEU* 2.9 58.0 + - + +
251A VAL* 3.5 31.6 - - + -
252A ILE* 4.0 17.3 - - + -
255A TYR* 3.4 53.8 - + + -
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Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 3.5 6.2 - - - +
131A VAL* 4.1 20.2 - - + -
132A ILE* 3.6 23.1 - - + +
135A CYS* 4.3 5.6 - - - -
181A PHE* 3.8 23.2 - + - -
185A ASP* 2.3 48.5 + - - +
188A LEU* 3.6 32.5 - - + -
189A PHE* 4.7 1.3 - + - -
229A ALA* 2.9 35.0 + - + +
230A MET* 3.3 16.4 - - + +
232A PHE* 1.3 95.3 - + - +
234A ARG* 1.3 57.4 + - - +
236A LEU* 3.3 9.1 + - + +
237A LEU* 2.9 24.6 + - - +
255A TYR* 5.4 0.4 - - - -
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Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.0 29.2 - - + +
136A GLU* 4.7 7.7 + - - -
227A GLU* 4.7 4.8 + - - +
230A MET* 2.9 53.3 + - - +
231A GLU* 3.6 39.6 + - - +
232A PHE 3.3 0.2 - - - -
233A TYR* 1.3 72.8 - - - +
235A GLN* 1.3 62.1 + - - +
237A LEU* 3.3 5.6 + - + +
238A ALA* 2.9 27.4 + - - +
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Residues in contact with GLN 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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231A GLU* 3.0 51.4 + - - +
232A PHE* 3.2 9.7 + - - +
234A ARG* 1.3 74.6 - - + +
236A LEU* 1.3 59.7 + - - +
238A ALA* 3.1 9.0 + - - +
239A VAL* 2.9 33.5 + - - +
251A VAL* 3.6 33.3 - - + +
254A GLN* 5.3 4.7 + - - +
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Residues in contact with LEU 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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113A MET* 4.0 26.7 - - + -
117A PHE* 3.9 6.7 - - + -
128A MET* 3.4 18.4 - - + -
188A LEU* 4.3 13.5 - - + -
192A LEU* 5.0 1.6 - - + -
232A PHE* 2.9 60.0 + - + +
233A TYR* 3.3 6.0 + - - +
235A GLN* 1.3 75.6 - - - +
237A LEU* 1.3 58.2 + - - +
239A VAL* 3.1 8.1 + - - +
240A CYS* 2.9 28.9 + - - +
248A LEU* 3.6 28.7 - - + -
251A VAL* 4.1 5.8 - - + -
252A ILE* 4.4 1.8 - - + -
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Residues in contact with LEU 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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125A GLU* 4.0 27.4 - - + +
128A MET* 3.2 16.3 - - + +
129A ILE* 3.6 33.0 - - + -
132A ILE* 4.0 15.9 - - + -
233A TYR 2.9 14.6 + - - +
234A ARG* 3.5 11.2 - - + +
236A LEU* 1.3 76.0 - - - +
238A ALA* 1.3 58.9 + - - +
240A CYS* 3.3 1.6 + - + -
241A GLN* 2.9 61.0 + - + +
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Residues in contact with ALA 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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234A ARG 2.9 14.1 + - - +
235A GLN* 3.1 12.1 + - - +
237A LEU* 1.3 76.5 - - - +
239A VAL* 1.3 57.1 + - + +
241A GLN* 3.9 11.4 - - - +
242A SER* 2.9 32.4 + - - -
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Residues in contact with VAL 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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117A PHE* 4.0 10.8 - - + -
235A GLN 2.9 22.1 + - - +
236A LEU* 3.1 10.5 + - - +
238A ALA* 1.3 77.1 - - + +
240A CYS* 1.3 57.9 + - - +
242A SER* 3.3 3.0 + - - -
243A GLY* 2.9 28.6 + - - -
244A GLU 3.5 23.5 + - - +
245A ARG* 4.3 4.9 - - + +
247A HIS* 4.7 3.4 - - + +
248A LEU* 4.0 34.3 - - + +
251A VAL* 4.2 20.0 - - + -
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Residues in contact with CYS 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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117A PHE* 3.6 50.1 - - + +
121A LYS* 3.3 46.5 - - - +
124A ALA* 4.1 2.5 - - - -
125A GLU* 3.6 15.3 - - + -
128A MET* 4.6 4.7 - - - -
236A LEU 2.9 14.1 + - - +
237A LEU* 3.9 4.3 - - + +
239A VAL* 1.3 78.9 - - - +
241A GLN* 1.3 63.2 + - - +
243A GLY* 3.6 8.6 + - - -
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Residues in contact with GLN 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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121A LYS* 4.1 16.7 + - - +
125A GLU* 3.1 26.7 + - - +
129A ILE* 4.6 8.9 - - - +
237A LEU* 2.9 46.5 + - + +
238A ALA* 3.9 10.9 - - - +
240A CYS* 1.3 75.8 - - - +
242A SER* 1.3 65.5 + - - +
243A GLY* 3.5 0.3 + - - -
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Residues in contact with SER 242 (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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238A ALA 2.9 19.5 + - - -
239A VAL* 3.8 4.3 - - - -
241A GLN* 1.3 78.6 - - - +
243A GLY* 1.3 60.3 + - - +
244A GLU* 3.1 27.1 + - - +
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Residues in contact with GLY 243 (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 6.1 0.7 - - - -
121A LYS* 6.0 1.3 - - - -
239A VAL 2.9 10.9 + - - -
240A CYS* 3.6 8.0 + - - -
241A GLN 3.3 3.0 - - - -
242A SER* 1.3 77.4 - - - +
244A GLU* 1.3 61.1 + - - +
245A ARG* 3.4 23.4 + - - +
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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