Contacts of the helix formed by residues 227 - 243 (chain A) in PDB entry 2P3L
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 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLU* 5.8 1.2 + - - -
198A GLN* 4.9 3.4 - - - +
226A GLY* 1.3 72.3 - - - -
228A ILE* 1.3 65.5 + - - +
229A VAL* 3.4 12.8 + - - +
230A SER* 2.8 43.5 + - - +
231A SER* 3.2 22.5 + - - -
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Residues in contact with ILE 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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185A PRO 5.6 0.2 - - - +
191A ILE* 4.0 36.8 - - + +
194A MET* 3.2 46.2 - - + +
195A GLU* 3.6 12.6 - - + +
198A GLN* 3.2 35.6 - - + +
204A ALA* 6.0 0.2 - - - -
205A LEU* 4.3 26.7 - - + +
226A GLY 3.4 2.1 + - - +
227A ASN* 1.3 71.5 - - - +
229A VAL* 1.3 68.7 + - - +
231A SER* 3.0 19.0 + - - -
232A VAL* 3.1 11.8 + - - +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 3.7 23.3 - - + -
195A GLU* 3.5 23.3 + - - +
227A ASN* 3.4 11.8 + - - +
228A ILE* 1.3 77.5 - - - +
230A SER* 1.3 65.7 + - - +
232A VAL* 3.8 1.7 - - - +
233A ASN* 3.0 41.9 + - - +
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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
----------------------------------------------------------
227A ASN* 2.8 35.4 + - - +
229A VAL* 1.3 76.2 - - - +
231A SER* 1.3 57.6 + - - +
233A ASN* 3.8 6.1 - - - +
234A MET* 2.9 36.0 + - - +
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Residues in contact with SER 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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204A ALA* 6.2 0.7 - - - -
205A LEU* 3.9 32.1 + - - +
218A MET* 3.4 5.5 - - - +
226A GLY* 5.1 6.4 + - - -
227A ASN 3.2 13.4 + - - -
228A ILE* 3.0 18.9 + - - -
230A SER* 1.3 80.8 - - - +
232A VAL* 1.3 58.6 + - - +
234A MET* 3.6 7.1 + - - +
235A ILE* 3.4 25.3 + - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PRO* 3.6 22.2 - - + +
186A TYR* 3.6 37.5 - - + -
191A ILE* 4.4 10.8 - - + -
205A LEU* 3.6 23.6 - - + -
216A HIS* 3.6 7.5 - - + -
218A MET* 4.0 8.7 - - - -
228A ILE 3.1 17.3 + - - +
229A VAL 3.8 3.1 - - - +
231A SER* 1.3 74.0 + - - +
233A ASN* 1.3 68.7 + - - +
235A ILE* 3.0 7.3 + - - +
236A SER* 3.0 23.8 + - - +
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Residues in contact with ASN 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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8A THR* 5.7 2.6 - - - -
9A LEU* 4.3 28.5 + - + +
10A GLY 5.5 0.2 + - - -
229A VAL* 3.0 39.1 + - - +
230A SER* 3.8 5.9 - - - +
232A VAL* 1.3 74.6 - - - +
234A MET* 1.3 66.2 + - - +
236A SER* 3.7 7.5 + - - -
237A ARG* 3.0 24.4 + - - +
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Residues in contact with MET 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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230A SER* 2.9 23.8 + - - +
231A SER* 3.7 9.2 - - - +
232A VAL 3.3 0.2 - - - -
233A ASN* 1.3 73.7 - - - +
235A ILE* 1.3 64.0 + - + +
237A ARG* 3.4 18.2 - - + +
238A MET* 3.1 26.2 + - - +
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Residues in contact with ILE 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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207A ARG* 3.5 45.8 - - + +
216A HIS* 3.6 22.0 - - + +
218A MET* 3.6 19.3 - - + -
231A SER 3.4 15.3 - - - +
232A VAL 3.0 7.7 + - - +
234A MET* 1.3 81.5 - - + +
236A SER* 1.3 59.4 + - - +
237A ARG 3.2 0.2 - - - -
238A MET* 3.2 15.5 + - + +
239A LEU* 2.8 42.3 + - + +
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.8 26.9 - - - +
10A GLY* 3.6 18.0 + - - -
13A TRP* 4.6 1.9 - - - +
186A TYR* 4.6 0.5 - - - +
216A HIS* 2.9 25.5 + - - -
232A VAL* 3.0 17.8 + - - +
233A ASN* 3.4 9.1 + - - -
235A ILE* 1.3 76.6 - - - +
237A ARG* 1.3 57.2 + - - +
239A LEU* 3.3 3.4 + - - +
240A ILE* 2.9 36.2 + - - +
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Residues in contact with ARG 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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9A LEU* 4.6 12.0 - - + +
233A ASN 3.0 13.9 + - - +
234A MET* 3.4 23.4 - - + +
236A SER* 1.3 75.6 - - - +
238A MET* 1.3 56.5 + - - +
240A ILE* 3.2 9.8 + - - +
241A ASN* 2.8 71.0 + - - +
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Residues in contact with MET 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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207A ARG* 4.0 23.6 - - + +
234A MET 3.1 12.2 + - - +
235A ILE* 3.5 21.3 - - + +
237A ARG* 1.3 78.1 - - - +
239A LEU* 1.3 91.6 + - + +
241A ASN* 3.3 12.9 + - + +
242A ARG* 3.1 67.0 + - + +
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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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13A TRP* 3.5 27.4 - - + +
28A TYR* 2.6 24.4 + - - +
207A ARG* 3.6 22.4 - - - +
213A ASN* 3.8 31.4 - - - +
215A THR 4.0 11.0 - - - +
216A HIS* 3.6 36.1 - - + -
235A ILE* 2.8 26.5 + - + +
236A SER 3.8 2.7 - - - +
238A MET* 1.3 84.9 - - + +
240A ILE* 1.3 62.1 + - - +
242A ARG* 3.4 9.4 + - - -
243A PHE* 3.6 3.3 + - - -
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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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9A LEU* 3.4 45.5 - - + +
12A LYS* 4.6 12.8 - - + -
13A TRP* 3.8 24.0 - - + +
16A ARG* 4.0 20.8 + - - +
236A SER 2.9 23.2 + - - +
237A ARG* 3.7 7.9 - - - +
239A LEU* 1.3 72.4 - - - +
241A ASN* 1.3 70.6 + - - +
242A ARG 3.1 1.1 - - - -
243A PHE* 3.0 29.3 + - + +
244A THR* 4.2 5.0 + - + +
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Residues in contact with ASN 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 ARG* 2.8 65.7 + - - +
238A MET* 3.4 12.7 - - + +
240A ILE* 1.3 75.1 - - - +
242A ARG* 1.3 59.9 + - + +
244A THR* 2.6 33.7 + - - -
245A MET* 4.0 3.1 + - - +
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Residues in contact with ARG 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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28A TYR* 3.6 17.9 - - + -
31A SER* 3.8 11.1 + - - -
32A GLY* 3.7 19.0 + - - -
33A ILE* 3.8 17.0 - - - +
207A ARG* 5.4 0.8 - - - +
209A PRO* 5.6 6.3 + - - +
211A SER 5.3 1.8 + - - -
213A ASN* 2.9 28.7 + - - +
238A MET* 3.1 58.3 + - + +
239A LEU* 3.7 9.0 - - - +
240A ILE 3.1 1.2 - - - -
241A ASN* 1.3 73.6 - - + +
243A PHE* 1.3 64.8 + - - +
244A THR 3.0 3.1 + - - -
245A MET* 3.3 42.8 + - + +
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Residues in contact with PHE 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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13A TRP* 3.5 35.4 - + - -
16A ARG* 3.7 50.5 - - + +
17A LEU* 3.7 23.3 - - - -
20A LEU* 3.9 24.9 - - + -
28A TYR* 3.5 38.3 - + + -
239A LEU 3.6 1.3 + - - -
240A ILE* 3.0 30.2 + - + +
242A ARG* 1.3 76.7 - - - +
244A THR* 1.3 57.2 + - + +
245A MET 3.6 1.4 + - - +
246A ARG* 2.9 24.7 + - - -
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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