Contacts of the helix formed by residues 229 - 250 (chain A) in PDB entry 1P22
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 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A THR 3.9 1.4 + - - +
184A SER* 3.0 38.2 + - - +
187A MET* 3.5 42.3 - - + +
188A LEU 3.9 1.4 - - - +
189A TRP* 3.8 25.4 - - - +
227A PRO 3.7 1.0 - - - -
228A PRO* 1.3 84.9 - - - +
230A SER* 1.3 62.8 + - - +
231A PHE 3.4 0.9 - - - -
232A TYR* 3.3 16.8 - - - +
233A ARG* 3.2 27.2 + - - +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 3.4 10.0 - - - -
229A ASN* 1.3 74.6 + - - +
231A PHE* 1.3 69.2 + - - +
232A TYR 2.9 2.1 + - - -
233A ARG* 3.0 28.9 + - - +
234A ALA* 2.7 30.1 + - - +
135B GLU* 4.6 7.8 + - - +
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Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TRP* 5.4 1.6 - - + -
215A TYR* 3.8 42.0 - + - -
227A PRO 5.6 2.5 - - - -
228A PRO* 3.5 29.6 - - + +
230A SER* 1.3 77.4 - - - +
232A TYR* 1.3 71.7 + + + +
234A ALA* 3.9 5.7 - - - +
235A LEU* 3.1 47.6 + - + +
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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
----------------------------------------------------------
187A MET* 5.3 2.9 - - - -
189A TRP* 3.5 18.6 - - + -
190A LYS* 2.9 66.2 + - + +
193A ILE* 3.8 15.6 - - + +
215A TYR* 3.3 22.7 + - + +
216A LEU* 3.9 17.7 - - + -
227A PRO* 4.2 28.5 - - + +
228A PRO* 4.3 3.6 - - + -
229A ASN* 3.3 25.8 - - - +
230A SER 2.9 1.0 + - - -
231A PHE* 1.3 81.9 - + + +
233A ARG* 1.3 66.4 + - - +
234A ALA 3.1 0.7 - - - -
235A LEU* 2.9 21.1 + - + +
236A TYR* 3.2 10.4 + - - +
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Residues in contact with ARG 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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170A CYS* 6.5 0.2 - - - -
173A GLU* 2.5 41.6 + - - +
180A TYR* 3.2 30.8 + - - -
183A THR* 5.6 0.4 + - - -
184A SER* 4.6 4.0 + - - -
189A TRP* 3.5 39.6 - - + +
229A ASN* 3.2 18.4 + - - +
230A SER* 3.0 35.1 + - - +
232A TYR* 1.3 76.2 - - - +
234A ALA* 1.3 62.2 + - + +
236A TYR* 3.6 3.8 + - - +
237A PRO* 3.2 17.0 - - - +
132B VAL* 5.6 0.2 - - - +
135B GLU* 3.6 47.9 + - + +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A SER* 2.7 27.1 + - - +
231A PHE* 3.9 6.1 - - - +
233A ARG* 1.3 75.4 - - + +
235A LEU* 1.3 58.9 + - - +
236A TYR 3.5 0.2 - - - -
237A PRO* 3.2 20.1 - - - +
238A LYS* 4.1 18.6 + - - +
135B GLU* 6.3 1.3 - - + -
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Residues in contact with LEU 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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193A ILE* 4.8 7.4 - - + -
212A TRP* 4.1 38.4 - - + +
215A TYR* 5.6 0.7 - - + -
231A PHE* 3.1 42.6 + - + +
232A TYR* 2.9 10.1 + - + +
234A ALA* 1.3 78.8 - - - +
236A TYR* 1.3 66.4 + - - +
237A PRO 3.3 0.7 - - - -
238A LYS* 2.8 34.9 + - + +
239A ILE* 3.1 34.6 + - + +
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Residues in contact with TYR 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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166A ALA* 3.5 28.3 + - + +
167A LYS* 6.4 0.2 - - + -
189A TRP* 3.7 24.5 - + + -
192A LEU* 3.6 22.0 - - + +
193A ILE* 3.8 27.1 - - + +
196A MET* 3.7 23.2 - - + +
203A TRP* 3.8 21.4 - + - -
232A TYR 3.2 8.0 + - - +
233A ARG 3.8 7.0 - - - +
235A LEU* 1.3 75.5 - - - +
237A PRO* 1.3 64.1 - - + +
239A ILE* 3.2 8.3 + - - +
240A ILE* 2.9 48.3 + - + +
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Residues in contact with PRO 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 ARG 3.2 16.6 - - - +
234A ALA* 3.2 19.3 - - - +
236A TYR* 1.3 94.8 - - + +
238A LYS* 1.3 58.8 + - + +
240A ILE* 3.3 9.2 + - + +
241A GLN* 2.8 32.5 + - + +
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Residues in contact with LYS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 4.1 21.8 + - - +
235A LEU* 2.8 24.4 + - + +
237A PRO* 1.3 76.1 - - + +
239A ILE* 1.3 61.4 + - - +
241A GLN* 3.3 7.6 + - - +
242A ASP* 2.8 30.8 + - - +
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 4.3 13.2 - - + -
203A TRP* 3.3 47.1 - - + -
206A LEU* 4.6 6.3 - - + -
212A TRP* 3.5 44.2 - - + +
235A LEU* 3.1 35.5 + - + +
236A TYR* 3.6 5.6 - - - +
238A LYS* 1.3 72.3 - - - +
240A ILE* 1.3 66.6 + - - +
242A ASP* 3.4 6.2 - - - +
243A ILE* 3.2 25.5 + - + +
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Residues in contact with ILE 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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167A LYS* 6.4 2.9 - - - -
203A TRP* 3.9 21.5 - - + +
236A TYR* 2.9 40.5 + - + +
237A PRO* 3.5 10.8 - - + +
239A ILE* 1.3 76.1 - - - +
241A GLN* 1.3 65.1 + - + +
242A ASP 3.1 0.5 + - - -
243A ILE* 3.1 14.1 + - + +
244A GLU* 3.0 45.9 + - + +
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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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237A PRO 2.8 21.7 + - - +
238A LYS* 3.3 8.5 + - - +
240A ILE* 1.3 75.2 - - + +
242A ASP* 1.3 51.1 + - - +
244A GLU* 3.3 18.3 + - - +
245A THR* 2.8 52.2 + - - +
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Residues in contact with ASP 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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206A LEU* 3.0 26.3 - - + +
210A ARG* 2.6 37.3 + - - -
238A LYS 2.8 18.3 + - - +
239A ILE* 3.4 10.8 - - - +
241A GLN* 1.3 71.4 - - - +
243A ILE* 1.3 55.5 + - - +
244A GLU 2.7 3.7 + - - -
245A THR* 2.7 36.2 + - - -
246A ILE* 2.8 16.7 + - - +
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Residues in contact with ILE 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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202A LEU* 3.4 29.8 - - + +
203A TRP* 3.2 45.3 - - + +
206A LEU* 3.7 18.3 - - + +
239A ILE* 3.3 19.1 - - + +
240A ILE* 3.1 15.6 + - + +
242A ASP* 1.3 78.9 - - - +
244A GLU* 1.3 57.5 + - + +
246A ILE* 4.1 7.8 - - - +
247A GLU* 3.1 31.5 + - + +
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Residues in contact with GLU 244 (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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240A ILE* 3.0 38.5 + - + +
241A GLN* 3.5 24.0 + - - +
242A ASP 2.7 5.7 + - - -
243A ILE* 1.3 76.5 - - + +
245A THR* 1.3 57.7 + - + +
247A GLU* 4.0 2.7 - - - +
248A SER* 2.9 26.4 + - - -
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Residues in contact with THR 245 (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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241A GLN* 2.8 29.2 + - - +
242A ASP* 2.7 33.6 + - - -
244A GLU* 1.3 71.2 - - + +
246A ILE* 1.3 55.9 + - - +
248A SER* 3.3 5.3 - - - -
249A ASN* 2.8 43.2 + - - +
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Residues in contact with ILE 246 (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 LEU* 4.5 14.1 - - + -
206A LEU* 3.8 31.0 - - + -
242A ASP* 2.8 22.8 + - - +
243A ILE* 4.1 4.5 - - - +
245A THR* 1.3 72.6 + - - +
247A GLU* 1.3 59.0 + - + +
248A SER 2.5 15.5 + - - -
249A ASN* 3.6 7.2 - - - +
250A TRP* 2.8 37.8 + - + +
254A ARG* 4.1 25.8 - - - +
482A ARG* 5.7 0.2 - - - +
529A GLU 4.3 17.5 - - - +
530A PHE* 4.1 19.3 - - + -
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Residues in contact with GLU 247 (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 LEU* 5.9 2.9 - - + -
243A ILE* 3.1 21.4 + - + +
244A GLU* 4.0 2.9 - - - +
246A ILE* 1.3 82.2 - - + +
248A SER* 1.3 55.7 + - - +
250A TRP* 4.3 3.6 - - - -
251A ARG* 2.9 73.2 + - - +
481A LYS* 4.6 17.5 - - - +
482A ARG* 2.4 34.9 + - - -
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Residues in contact with SER 248 (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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244A GLU 2.9 22.1 + - - -
245A THR* 3.3 9.0 - - - -
246A ILE 2.5 5.3 + - - -
247A GLU* 1.3 70.9 - - - +
249A ASN* 1.3 56.9 + - - -
250A TRP 2.5 3.3 + - - -
251A ARG* 2.4 36.7 + - - +
252A CYS* 3.6 12.7 - - - -
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Residues in contact with ASN 249 (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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245A THR* 2.8 29.3 + - - +
246A ILE* 3.0 5.7 + - - +
248A SER* 1.3 72.9 + - - +
250A TRP* 1.3 58.1 + - - +
251A ARG 3.2 2.0 - - - -
252A CYS* 4.2 9.0 - - - -
253A GLY 2.7 49.1 + - - +
254A ARG* 3.1 36.6 + - - +
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Residues in contact with TRP 250 (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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246A ILE* 2.8 27.8 - - + +
247A GLU* 4.3 2.0 - - - -
248A SER 2.5 5.5 + - - -
249A ASN* 1.3 80.3 - - - +
251A ARG* 1.3 58.2 + - - +
252A CYS 3.5 0.9 - - - -
253A GLY 4.8 0.4 - - - -
254A ARG* 3.8 17.7 - - + -
482A ARG* 2.9 51.5 + - - +
484A VAL* 5.8 2.0 - - + -
494A VAL* 5.3 14.9 - - + +
512A LEU* 6.0 0.2 - - - +
515A LEU* 4.8 11.0 - - + -
527A PHE* 5.6 2.9 - + - -
528A ASP 4.7 4.2 + - - -
529A GLU 3.9 15.1 + - - -
530A PHE* 4.9 0.4 - - - -
531A GLN 4.4 12.6 - - - -
532A ILE* 3.2 45.3 - - + -
544A TRP* 4.9 3.4 - + + -
545A ASP 3.6 34.8 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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