Contacts of the helix formed by residues 227 - 238 (chain A) in PDB entry 1A8H
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 TRP 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 3.7 33.9 - - + +
202A SER 3.5 24.2 + - - -
203A ILE* 5.0 1.8 - - + -
225A TYR* 3.0 11.4 + + - +
226A VAL* 1.3 92.9 - - + +
228A PHE* 1.3 63.4 + - + +
229A ASP 2.9 9.9 + - - -
230A ALA* 6.4 0.4 - - + -
231A LEU* 3.1 53.3 + - + +
264A PRO* 3.4 37.7 - - + -
268A PHE* 3.7 22.0 - + - -
272A MET* 3.8 3.7 - - - +
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Residues in contact with PHE 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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104A VAL* 3.4 23.2 - - - +
107A VAL* 4.1 27.6 - - + -
108A LEU* 3.7 26.9 - - + -
111A VAL* 4.4 15.5 - - + -
117A ILE* 5.5 1.8 - - + -
161A PHE* 4.0 30.5 - + + -
201A LEU* 4.9 0.7 - - + -
203A ILE* 3.3 39.2 - - + +
224A THR* 3.8 19.1 - - + +
225A TYR 4.7 0.8 + - - -
226A VAL 3.7 0.4 - - - -
227A TRP* 1.3 78.8 - - + +
229A ASP* 1.3 57.1 + - - +
232A LEU* 3.5 15.0 - - + +
272A MET* 4.0 42.0 - - + -
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 4.7 4.6 - - - +
52A HIS* 3.0 36.0 - - - +
95A THR* 3.7 8.3 - - - +
100A HIS* 2.8 48.7 + - - -
104A VAL* 4.2 4.0 - - - -
214A ILE* 3.5 12.7 - - + +
224A THR* 3.8 23.6 - - + +
226A VAL* 2.8 18.2 + - - +
227A TRP 2.9 0.4 - - - -
228A PHE* 1.3 80.5 - - - +
230A ALA* 1.3 64.5 + - - +
231A LEU 3.4 0.4 + - - -
232A LEU 3.6 3.3 + - - -
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Residues in contact with ALA 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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11A ILE* 3.8 14.6 - - + +
50A ASP* 3.3 36.1 - - - +
95A THR* 4.4 4.7 - - - -
226A VAL* 2.7 23.3 + - + +
227A TRP* 6.4 0.2 - - + -
229A ASP* 1.3 75.3 - - + +
231A LEU* 1.3 58.7 + - + +
233A ASN* 2.6 35.9 + - - +
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Residues in contact with LEU 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 TRP* 3.1 44.1 + - + +
230A ALA* 1.3 83.6 - - + +
232A LEU* 1.3 56.6 + - - +
233A ASN* 3.1 6.7 + - - -
234A TYR* 3.1 27.7 - - + +
264A PRO* 4.0 18.4 - - + +
265A HIS* 4.0 32.1 - - + +
268A PHE* 4.6 1.6 - - + -
269A TRP* 3.5 33.1 - - + +
272A MET* 3.7 26.2 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A HIS* 3.9 2.2 - - + -
103A VAL* 4.1 2.5 - - + +
104A VAL* 3.6 31.2 - - + +
107A VAL* 3.7 39.9 - - + -
227A TRP 4.3 0.2 + - - -
228A PHE* 3.5 32.3 - - + +
229A ASP 3.6 6.3 + - - +
230A ALA 3.3 1.4 - - - -
231A LEU* 1.3 74.1 - - - +
233A ASN* 1.3 59.2 + - - +
234A TYR 3.2 0.9 - - - -
235A VAL* 3.0 14.3 + - + +
236A SER* 2.7 28.9 + - - +
269A TRP* 3.6 28.3 - - + -
272A MET* 4.8 4.5 - - + -
278A ILE* 5.2 4.9 - - + -
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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 0.2 - - - -
9A THR 5.1 2.2 + - - -
11A ILE* 3.8 32.6 - - + +
46A LEU* 3.8 7.7 - - - +
47A THR 5.7 1.2 - - - -
93A ILE* 3.6 24.4 - - + +
100A HIS* 3.6 19.6 - - + -
230A ALA 2.6 24.5 + - - +
231A LEU 3.1 2.8 + - - +
232A LEU* 1.3 78.5 - - - +
234A TYR* 1.3 97.1 + - - +
236A SER* 3.9 0.9 - - - -
237A ALA* 3.0 27.2 + - - +
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Residues in contact with TYR 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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6A TYR* 2.5 30.8 + - - +
8A THR* 3.2 31.4 + - - -
9A THR 3.7 13.7 - - - -
10A PRO* 3.9 15.1 - - + +
11A ILE* 4.6 2.3 + - + +
46A LEU* 4.1 1.2 - - + +
231A LEU* 3.1 27.9 - - + +
232A LEU 3.2 0.2 - - - -
233A ASN* 1.3 100.5 - - - +
235A VAL* 1.3 60.2 + - - +
238A LEU* 3.7 10.0 - - - +
250A TRP* 4.2 9.9 - - + -
255A HIS* 3.3 28.7 - + + +
256A LEU 5.3 0.5 + - - -
257A ILE* 4.7 2.1 - - - +
265A HIS* 2.4 41.9 + + - -
269A TRP* 3.8 16.8 - + + -
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Residues in contact with VAL 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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103A VAL* 3.8 13.5 - - + -
107A VAL* 5.5 0.2 - - + -
232A LEU* 3.0 16.8 + - + +
234A TYR* 1.3 79.7 - - - +
236A SER* 1.3 64.4 - - - +
237A ALA 3.3 1.8 - - - -
238A LEU* 3.2 14.4 + - - +
240A TYR* 3.1 43.1 + - + +
246A TYR* 4.2 17.3 - - + -
250A TRP* 4.2 26.9 - - + -
269A TRP* 4.9 6.3 - - + -
278A ILE* 4.3 21.1 - - + -
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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
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93A ILE* 4.5 4.3 - - - -
99A ARG* 4.5 10.4 - - - +
100A HIS* 3.0 44.5 + - - -
103A VAL* 3.1 36.0 - - - +
232A LEU* 2.7 17.8 + - - +
233A ASN* 3.8 3.8 - - - -
235A VAL* 1.3 70.2 - - - +
237A ALA* 1.3 61.0 + - - +
238A LEU 3.0 4.9 - - - -
239A ASP* 3.1 17.8 + - - +
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Residues in contact with ALA 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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44A PHE* 4.4 9.0 - - + -
46A LEU* 3.4 45.8 - - + -
91A ASP* 3.9 8.7 - - - +
93A ILE* 4.0 11.4 - - + +
99A ARG* 3.8 18.8 + - - +
233A ASN 3.0 7.5 + - - +
234A TYR 4.8 1.1 - - - +
235A VAL 3.3 0.2 - - - -
236A SER* 1.3 77.0 - - - +
238A LEU* 1.3 62.9 + - + +
239A ASP* 3.4 7.6 + - - +
245A ALA* 5.2 1.0 - - - +
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Residues in contact with LEU 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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6A TYR* 3.7 27.6 - - + +
44A PHE* 3.7 35.7 - - + -
234A TYR 3.7 14.1 - - - +
235A VAL* 3.2 7.8 + - - +
236A SER 3.0 1.2 - - - -
237A ALA* 1.3 78.8 - - - +
239A ASP* 1.3 74.5 + - - +
240A TYR 3.0 0.4 + - - -
243A GLY* 3.9 2.3 - - - -
245A ALA* 3.8 26.6 - - + +
246A TYR* 3.2 34.1 + - + +
249A PHE* 4.1 4.5 - - + -
250A TRP* 3.9 28.9 - - + +
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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