Contacts of the helix formed by residues 236 - 250 (chain A) in PDB entry 1A9Z
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 VAL 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.6 23.6 - - + +
12A ILE* 4.2 25.8 - - + -
15A HIS* 3.8 36.9 - - + +
180A PRO* 5.0 0.4 - - + -
181A VAL 2.6 15.6 + - - +
182A GLY 3.7 26.5 - - - +
183A ALA* 3.8 6.1 - - - +
234A ILE 3.4 1.3 + - - -
235A HIS* 1.3 72.0 + - - +
237A MET* 1.3 59.8 + - - +
239A LEU* 3.4 8.5 - - + +
240A ALA* 2.9 26.3 + - - +
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Residues in contact with MET 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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15A HIS* 3.8 31.2 - - + +
19A GLN* 3.8 37.0 - - - +
183A ALA 4.2 7.4 - - - +
184A HIS* 3.9 24.0 - - + +
185A PRO* 4.1 14.4 - - + -
235A HIS* 2.9 26.5 + - + +
236A VAL* 1.3 75.1 - - - +
238A ASP* 1.3 61.0 + - - +
240A ALA* 3.3 2.9 + - - +
241A ASP* 2.9 32.9 + - - +
316A ARG* 3.5 27.1 - - - +
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Residues in contact with ASP 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 ILE* 4.2 2.7 - - + -
235A HIS* 3.0 14.1 + - - +
237A MET* 1.3 73.5 - - - +
239A LEU* 1.3 67.1 + - - +
241A ASP* 3.2 3.3 + - - +
242A GLY 2.9 19.4 + - - -
312A TRP* 3.2 15.2 + - + +
313A ARG 4.3 1.7 - - - +
314A VAL* 3.3 28.9 - - + +
315A THR* 2.9 24.9 + - - +
316A ARG* 2.8 59.8 + - - +
321A MET* 5.6 0.2 - - - +
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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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12A ILE* 3.8 26.9 - - + -
177A TYR* 4.1 15.5 - - + -
180A PRO* 3.6 38.6 - - + -
234A ILE* 3.9 17.2 - - + +
235A HIS 3.0 10.5 + - - +
236A VAL* 3.4 12.8 - - + +
238A ASP* 1.3 78.0 - - - +
240A ALA* 1.3 63.3 + - - +
242A GLY* 3.2 9.7 + - - -
243A HIS* 2.9 24.3 + - + -
261A LEU* 3.7 40.9 - - + +
312A TRP* 4.8 1.3 - - - -
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Residues in contact with ALA 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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12A ILE* 5.5 0.8 - - + +
15A HIS* 3.6 31.0 - - + +
16A THR* 3.6 22.5 + - - +
19A GLN* 3.7 9.0 - - + -
236A VAL 2.9 17.1 + - - +
237A MET* 3.6 6.5 - - - +
238A ASP 3.3 0.2 - - - -
239A LEU* 1.3 76.6 - - - +
241A ASP* 1.3 63.4 + - - +
243A HIS* 3.1 13.8 + - - +
244A VAL* 3.2 16.8 + - - +
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Residues in contact with ASP 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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19A GLN* 2.7 33.3 + - - +
237A MET 2.9 15.5 + - - +
238A ASP* 3.2 5.8 + - - +
240A ALA* 1.3 76.4 - - - +
242A GLY* 1.3 62.5 + - - +
244A VAL* 2.9 18.5 + - - +
245A VAL* 3.0 17.3 + - + +
312A TRP* 4.1 9.2 - - + +
316A ARG* 2.9 30.0 + - - -
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Residues in contact with GLY 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 ASP 2.9 12.1 + - - -
239A LEU 3.2 4.0 + - - -
241A ASP* 1.3 75.0 - - - +
243A HIS* 1.3 57.0 + - - +
245A VAL* 3.9 1.4 - - - +
246A ALA* 2.8 32.4 + - - +
261A LEU* 5.0 11.1 - - - +
310A LEU* 5.2 2.4 - - - +
312A TRP* 3.2 33.8 - - - +
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Residues in contact with HIS 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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12A ILE* 4.6 0.9 - - + -
16A THR* 3.9 16.5 + - + -
78A ILE* 3.9 20.2 - - + +
80A PHE* 3.3 25.9 - + - -
120A ILE* 4.0 6.9 - - + +
122A SER* 4.6 1.0 + - - -
175A LEU* 3.9 15.2 - - + +
177A TYR* 2.6 47.4 + + - -
239A LEU* 2.9 33.9 + - + -
240A ALA 3.1 8.6 + - - +
241A ASP 3.1 1.2 - - - -
242A GLY* 1.3 74.6 - - - +
244A VAL* 1.3 59.9 + - - +
246A ALA* 4.5 3.6 - - - -
247A MET* 3.0 29.6 + - - +
261A LEU* 4.0 11.2 - - + +
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Residues in contact with VAL 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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16A THR 4.5 1.6 - - - +
19A GLN* 3.7 25.4 - - + -
20A LEU* 4.0 34.8 - - + +
23A ASN* 4.0 21.3 - - + +
25A HIS* 4.3 1.1 - - - +
240A ALA 3.2 13.0 + - - +
241A ASP* 2.9 8.6 + - - +
243A HIS* 1.3 76.6 - - + +
245A VAL* 1.3 59.9 + - + +
247A MET* 3.3 3.0 + - - +
248A GLU* 2.8 50.5 + - - +
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Residues in contact with VAL 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 ASP* 3.0 16.3 + - + +
242A GLY* 3.9 7.2 - - - +
244A VAL* 1.3 72.9 - - + +
246A ALA* 1.3 63.1 + - - +
248A GLU* 3.2 8.8 + - - +
249A LYS* 2.7 49.2 + - + +
310A LEU* 3.7 33.0 - - + +
311A ASN 5.8 1.1 - - - +
312A TRP* 4.5 13.9 - - + -
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Residues in contact with ALA 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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120A ILE* 4.1 11.6 - - + +
173A ALA* 5.1 0.4 - - + -
175A LEU* 4.2 20.6 - - + -
242A GLY 2.8 23.1 + - - +
243A HIS 4.0 3.1 - - - +
245A VAL* 1.3 72.9 - - - +
247A MET* 1.3 63.5 + - - +
250A LEU* 2.9 45.1 + - + +
310A LEU* 4.2 19.3 - - + +
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Residues in contact with MET 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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1A MET* 4.1 11.4 - - + +
3A VAL* 3.9 20.2 - - + -
20A LEU* 3.5 16.6 - - + -
25A HIS* 3.4 41.5 - - + +
76A THR* 3.6 38.6 - - + +
78A ILE* 4.0 8.3 - - + -
120A ILE* 3.4 18.5 - - + +
243A HIS 3.0 17.5 + - - +
244A VAL 3.6 2.0 - - - +
246A ALA* 1.3 83.0 - - - +
248A GLU* 1.3 68.3 + - + +
250A LEU* 5.3 0.4 - - - -
251A ALA* 3.3 23.1 + - - +
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Residues in contact with GLU 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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1A MET* 4.9 6.8 - - + +
23A ASN* 3.2 24.6 + - - +
25A HIS* 2.6 40.9 + - + +
244A VAL* 2.8 28.4 + - - +
245A VAL* 3.9 7.1 - - - +
247A MET* 1.3 77.9 - - + +
249A LYS* 1.3 65.4 + - + +
250A LEU 3.6 0.2 + - - -
251A ALA* 4.1 8.1 + - - +
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Residues in contact with LYS 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 VAL* 2.7 37.0 + - + +
248A GLU* 1.3 79.1 - - + +
250A LEU* 1.3 65.3 + - - +
251A ALA 4.6 2.5 - - - +
253A LYS* 4.5 6.2 - - - +
309A GLU 4.9 3.4 + - - +
310A LEU* 2.9 49.5 + - + +
311A ASN* 3.9 10.9 - - - +
410A PGE 4.2 23.4 - - - +
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Residues in contact with LEU 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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120A ILE* 6.2 0.9 - - + -
171A SER* 2.8 21.5 + - - +
173A ALA* 4.0 17.0 - - + -
246A ALA* 2.9 29.1 + - + +
247A MET* 5.3 0.2 - - - -
249A LYS* 1.3 76.2 - - - +
251A ALA* 1.3 68.4 + - - +
253A LYS* 2.8 20.9 + - + +
257A HIS* 3.7 39.7 - - + +
259A TYR* 3.9 15.7 - - + +
310A LEU* 4.3 7.2 - - + -
410A PGE 3.5 39.5 - - - -
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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