Contacts of the helix formed by residues 211 - 221 (chain A) in PDB entry 1A76
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 LEU 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A LEU 3.5 24.9 - - - +
178A LEU* 3.9 23.3 - - - +
179A TYR 5.0 0.9 - - - -
180A GLY* 4.3 11.9 - - - +
200A LEU* 4.4 14.1 - - + -
204A LEU* 3.8 16.6 - - + +
210A SER* 1.3 73.3 - - - +
212A ASP* 1.3 63.1 + - - +
214A LEU* 3.1 15.7 + - + +
215A ILE* 3.0 25.8 + - + +
265A PHE 6.0 0.2 - - - +
266A LYS* 4.0 26.7 - - + -
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Residues in contact with ASP 212 (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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210A SER* 3.2 10.3 + - - +
211A LEU* 1.3 79.4 - - - +
213A ASP* 1.3 61.5 + - - +
215A ILE* 3.4 9.8 + - - +
216A ASP* 3.1 27.9 + - - +
248A LYS* 4.5 13.9 - - - +
262A LYS* 6.1 1.6 - - - +
266A LYS* 2.8 41.4 + - - +
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Residues in contact with ASP 213 (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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208A ARG 4.9 0.7 - - - +
209A ILE* 3.6 20.7 - - + +
210A SER* 3.0 37.0 + - - +
212A ASP* 1.3 75.0 - - - +
214A LEU* 1.3 64.6 + - - +
216A ASP* 3.1 11.9 + - - +
217A ILE* 3.0 26.9 + - - +
242A VAL* 3.6 27.2 - - + +
243A ARG* 5.8 0.5 - - - -
248A LYS* 4.4 16.6 + - - -
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Residues in contact with LEU 214 (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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5A PHE* 3.5 42.5 - - + -
9A ILE* 5.0 1.8 - - + -
177A LEU* 4.5 8.5 - - + -
178A LEU* 4.0 9.4 - - + -
200A LEU* 3.9 27.4 - - + -
203A VAL* 4.4 15.3 - - + -
204A LEU* 4.2 9.0 - - + -
209A ILE* 4.0 21.3 - - + +
210A SER 3.0 12.7 + - - +
211A LEU* 3.5 14.1 - - + +
213A ASP* 1.3 77.0 - - - +
215A ILE* 1.3 58.4 + - - +
217A ILE* 3.2 11.9 + - + +
218A ALA* 2.9 26.5 + - - +
235A PHE* 4.8 4.9 - - + -
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Residues in contact with ILE 215 (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 LEU* 3.6 39.7 - - + +
211A LEU* 3.0 26.0 + - + +
212A ASP* 3.5 11.4 - - - +
214A LEU* 1.3 73.8 - - - +
216A ASP* 1.3 61.3 + - - +
218A ALA* 3.2 2.6 + - - +
219A ILE* 2.8 46.4 + - + +
262A LYS* 4.6 13.5 - - + -
265A PHE* 4.1 23.1 - - + -
266A LYS* 3.5 33.4 - - + -
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Residues in contact with ASP 216 (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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212A ASP 3.1 15.9 + - - +
213A ASP* 3.1 13.7 + - - +
215A ILE* 1.3 75.2 - - - +
217A ILE* 1.3 65.4 + - - +
219A ILE* 3.0 6.2 + - - +
220A PHE* 2.9 28.8 + - - -
242A VAL* 4.1 12.0 - - + +
247A ALA* 4.3 6.3 - - + +
248A LYS* 3.2 32.3 + - - +
251A LEU* 3.6 16.3 - - + +
258A TYR* 2.8 32.3 + - - -
262A LYS* 4.5 5.2 - - - +
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Residues in contact with ILE 217 (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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5A PHE* 3.9 2.7 - - + -
209A ILE* 3.7 30.5 - - + -
213A ASP 3.0 15.4 + - - +
214A LEU* 3.4 9.4 - - + +
216A ASP* 1.3 74.7 - - - +
218A ALA* 1.3 63.2 + - - +
220A PHE* 3.2 3.8 + - - +
221A MET* 3.0 31.7 + - - +
235A PHE* 3.5 42.0 - - + -
238A ALA* 4.2 16.2 - - + -
239A TYR* 4.0 30.7 - - + +
242A VAL* 4.0 15.5 - - + -
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Residues in contact with ALA 218 (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 VAL* 4.1 15.4 - - + +
5A PHE* 4.0 8.0 - - + -
178A LEU* 3.5 33.7 - - + -
214A LEU 2.9 12.9 + - - +
215A ILE* 3.3 9.6 - - + +
217A ILE* 1.3 77.1 - - - +
219A ILE* 1.3 51.7 + - - +
221A MET* 3.2 1.9 + - - +
222A GLY 2.7 38.6 + - - +
223A THR* 3.8 8.3 - - + -
265A PHE* 6.1 0.2 - - + -
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Residues in contact with ILE 219 (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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215A ILE* 2.8 38.1 + - + +
216A ASP* 3.0 9.8 + - - +
218A ALA* 1.3 73.0 - - - +
220A PHE* 1.3 63.3 + - - +
222A GLY 3.1 4.3 + - - -
223A THR* 4.0 11.4 - - + -
226A ASN* 2.9 30.6 - - - +
229A GLY* 3.7 1.7 - - - -
230A VAL* 4.2 1.2 - - - +
251A LEU* 4.0 18.8 - - + -
255A VAL* 4.0 23.3 - - + -
258A TYR* 3.6 29.4 - - + -
261A ILE* 4.1 27.1 - - + -
262A LYS* 4.1 5.4 - - + -
265A PHE* 5.4 0.2 - - + -
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Residues in contact with PHE 220 (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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216A ASP 2.9 25.0 + - - -
217A ILE* 3.4 7.6 - - - +
219A ILE* 1.3 75.8 - - - +
221A MET* 1.3 60.6 + - - +
229A GLY* 3.3 0.2 - - - -
230A VAL* 2.8 45.4 + - + +
233A ILE* 3.7 28.1 - - + +
238A ALA* 3.5 30.3 - - + -
241A LEU* 3.6 29.4 - - + -
242A VAL* 4.9 0.2 - - + -
247A ALA* 3.9 25.6 - - + -
250A VAL* 3.6 25.6 - - + -
251A LEU* 3.3 31.2 - - + -
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Residues in contact with MET 221 (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 VAL* 4.0 13.0 - - + -
4A GLN* 3.4 41.1 - - + +
5A PHE* 3.9 8.3 - - - -
8A PHE* 5.1 2.0 - - + -
217A ILE* 3.0 24.4 + - + +
218A ALA 3.7 3.6 - - - +
220A PHE* 1.3 78.7 - - + +
222A GLY* 1.3 60.5 + - - +
228A GLY* 4.2 4.5 + - - +
229A GLY* 3.8 7.2 + - - -
233A ILE 3.9 6.5 - - - +
234A GLY* 4.1 8.3 - - - +
235A PHE* 3.6 52.3 - - + +
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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