Contacts of the helix formed by residues 228 - 235 (chain A) in PDB entry 2X1L
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 TYR 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A TYR* 3.4 26.0 - - - -
131A GLU 2.7 22.9 + - - -
132A ARG* 3.8 6.6 - - - +
133A PHE* 3.7 29.8 - + + -
206A LEU* 4.5 16.8 - - + +
207A SER 3.6 14.6 - - - +
208A ILE* 2.9 31.1 + - - +
209A SER* 4.2 2.2 - - - +
210A ARG* 5.1 11.0 - - + -
213A PHE* 6.4 0.4 - - - -
226A VAL 3.6 2.0 + - - -
227A MET* 1.3 70.4 - - - +
229A VAL* 1.3 76.1 + - + +
230A TRP* 2.8 35.9 + + + -
231A VAL* 2.9 28.8 + - + +
232A ASP* 3.3 7.1 + - - +
269A PHE* 3.6 12.9 - + - -
273A TYR* 5.3 1.4 - + - -
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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
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13A TYR* 3.9 9.2 - - + +
50A ASP* 3.6 22.4 - - - +
52A HIS* 3.4 33.9 - - + +
53A GLY* 4.0 11.7 - - - +
131A GLU* 3.7 39.9 - - + +
213A PHE* 6.1 2.8 - - + -
227A MET 3.2 6.5 + - - -
228A TYR* 1.3 77.0 - - + +
230A TRP* 1.3 57.7 + - + +
232A ASP* 3.5 8.0 + - - +
233A ALA* 2.7 35.6 + - - +
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Residues in contact with TRP 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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13A TYR* 3.4 21.3 + + - -
130A ASP 4.0 4.2 + - - -
131A GLU* 3.3 29.2 + - - +
228A TYR* 2.8 30.3 + + + -
229A VAL* 1.3 82.3 - - + +
231A VAL* 1.3 59.5 + - - +
233A ALA* 3.7 4.2 - - + +
234A LEU* 2.8 62.4 + - + +
266A ILE* 3.6 28.9 - - + -
269A PHE* 3.4 54.6 - + + -
270A HIS* 4.0 2.7 - + - -
273A TYR* 5.8 1.1 - - + -
277A PHE* 6.1 0.7 - - + -
600A MET* 3.5 38.6 - - + -
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Residues in contact with VAL 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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107A ILE* 5.2 5.2 - - + -
108A TRP* 4.4 16.4 - - + -
111A MET* 4.3 23.3 - - + -
208A ILE* 3.7 35.0 - - + +
227A MET* 4.8 8.1 - - + -
228A TYR* 2.9 21.1 + - + +
230A TRP* 1.3 76.2 - - - +
232A ASP* 1.3 57.3 + - - +
234A LEU* 4.1 2.8 - - - +
235A THR* 2.7 34.3 + - - +
274A TRP* 5.7 0.2 - - - -
277A PHE* 3.8 26.1 - - + -
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Residues in contact with ASP 232 (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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50A ASP* 4.6 2.3 - - - +
52A HIS* 2.9 32.4 + - - +
95A THR* 3.6 7.9 + - - -
100A HIS* 2.6 65.8 + - - -
104A SER* 3.9 10.0 + - - +
216A GLY* 5.3 0.2 - - - -
217A VAL* 3.8 20.6 + - + +
227A MET* 4.5 12.6 - - + +
228A TYR 3.3 7.0 + - - +
229A VAL* 3.5 11.9 - - - +
230A TRP 3.3 0.2 - - - -
231A VAL* 1.3 79.6 - - - +
233A ALA* 1.3 61.7 + - - +
235A THR* 3.4 5.7 + - - -
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Residues in contact with ALA 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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11A ILE* 3.6 7.7 - - + +
50A ASP* 3.2 34.8 - - - +
95A THR* 4.4 1.1 - - - -
229A VAL 2.7 18.4 + - - +
230A TRP* 3.3 10.5 + - + +
232A ASP* 1.3 75.3 - - - +
234A LEU* 1.3 54.7 + - - +
236A ASN* 2.7 38.5 + - - +
600A MET* 3.8 16.4 - - + -
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Residues in contact with LEU 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 TRP* 2.8 45.3 + - + +
231A VAL* 4.1 4.0 - - - +
233A ALA* 1.3 73.2 - - - +
235A THR* 1.3 60.9 + - - +
236A ASN* 3.1 1.9 + - - +
237A TYR* 3.3 22.9 + - + -
269A PHE* 3.6 22.2 - - + +
270A HIS* 3.9 18.6 - - + +
273A TYR* 4.7 2.2 - - + -
274A TRP* 3.3 40.6 - - + -
277A PHE* 3.9 26.2 - - + -
600A MET* 3.7 21.8 - - + -
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Residues in contact with THR 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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100A HIS* 3.7 4.3 - - - -
103A ALA* 3.9 28.5 - - + +
104A SER* 4.0 7.0 - - - +
107A ILE* 3.4 35.9 - - + +
231A VAL* 2.7 19.9 + - - +
232A ASP* 3.4 10.4 + - - -
233A ALA 3.2 0.8 - - - -
234A LEU* 1.3 72.3 - - - +
236A ASN* 1.3 59.4 + - - +
237A TYR 3.1 2.5 - - - -
238A LEU* 2.9 30.9 + - + -
239A THR* 3.0 9.0 + - - +
243A PHE* 4.7 0.4 - - + -
274A TRP* 4.3 8.5 - - - -
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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