Contacts of the helix formed by residues 226 - 235 (chain A) in PDB entry 4L0D
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 ALA 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A HIS* 4.3 9.9 - - + +
224A ARG 3.6 3.8 + - - -
225A ASN* 1.3 76.4 + - - +
227A SER* 1.3 63.4 + - - +
229A PRO* 3.1 4.5 - - - +
230A LEU* 2.9 43.2 + - + +
602A HEM 3.5 36.7 - - + +
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Residues in contact with SER 227 (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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125A ARG* 3.3 6.6 - - - +
126A MET* 3.6 27.4 + - - -
129A ASP* 2.9 36.6 + - - +
225A ASN* 2.8 20.2 + - - -
226A ALA* 1.3 79.5 - - - +
228A ASN* 1.3 56.0 + - - +
230A LEU* 4.1 6.1 - - - -
231A ALA* 2.9 30.4 + - - +
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Residues in contact with ASN 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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122A ILE* 3.1 37.4 - - + +
126A MET* 4.2 12.1 - - - +
222A GLN* 3.1 27.2 + - - +
225A ASN 3.3 6.9 + - - +
226A ALA 3.2 0.8 - - - -
227A SER* 1.3 74.7 - - - +
229A PRO* 1.3 74.2 - - + +
230A LEU 3.1 0.7 - - - -
231A ALA* 3.0 4.7 + - - +
232A HIS* 3.0 26.0 + - - -
257A THR* 3.3 22.3 + - - -
259A GLY* 3.5 18.0 - - - -
314A VAL* 4.1 3.2 - - - +
601A PLP 4.9 0.7 + - - -
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Residues in contact with PRO 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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225A ASN 3.2 13.5 - - - +
226A ALA 3.1 17.3 - - - +
228A ASN* 1.3 87.1 - - + +
230A LEU* 1.3 56.9 + - - +
232A HIS 3.2 1.3 + - - +
233A TYR* 2.9 23.4 + - - +
259A GLY* 3.6 26.2 - - - +
262A THR* 4.0 13.9 - - + -
263A GLY* 3.4 10.7 - - - -
314A VAL* 3.8 21.1 - - + +
602A HEM 3.9 29.2 - - + -
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Residues in contact with LEU 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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65A HIS* 3.5 31.4 - - + -
66A HIS 4.5 3.8 - - - +
67A HIS* 4.4 21.3 - - + +
125A ARG* 4.0 22.2 - - - +
129A ASP* 5.4 1.8 - - - +
226A ALA* 2.9 35.6 + - + +
227A SER* 3.9 5.6 - - - +
229A PRO* 1.3 76.1 - - - +
231A ALA* 1.3 59.5 + - - +
233A TYR* 2.9 7.8 + - + +
234A ASP* 2.9 34.6 + - - +
602A HEM 4.0 32.3 - - + -
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.8 6.7 - - + +
122A ILE* 4.2 15.7 - - + +
125A ARG* 3.5 34.3 - - + +
227A SER 2.9 21.3 + - - +
228A ASN 3.0 5.1 + - - +
230A LEU* 1.3 75.8 - - - +
232A HIS* 1.3 62.4 + - - +
235A THR* 2.9 34.9 + - + +
236A THR* 5.0 0.2 - - - -
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Residues in contact with HIS 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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118A VAL* 3.3 25.0 - - + +
119A LYS* 6.3 1.6 - - + -
121A ARG* 4.4 4.1 - - - -
122A ILE* 3.3 24.6 - - + +
228A ASN* 3.0 29.1 + - - -
229A PRO 3.6 2.7 - - - +
230A LEU 3.1 0.2 - - - -
231A ALA* 1.3 79.0 - - - +
233A TYR* 1.3 59.5 + - - +
236A THR* 3.5 28.0 + - + -
237A ALA* 3.3 25.3 + - - +
259A GLY 3.6 15.0 - - - +
260A THR* 2.9 52.7 + - + +
263A GLY* 4.2 2.7 - - - -
264A ILE* 4.2 4.2 + - + +
601A PLP 4.5 1.6 - - - -
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Residues in contact with TYR 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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60A ALA* 5.0 8.1 - - - +
67A HIS* 3.6 28.0 - + - -
229A PRO 2.9 14.3 + - - +
230A LEU* 2.9 13.6 + - + +
232A HIS* 1.3 79.0 - - - +
234A ASP* 1.3 76.1 + - - +
237A ALA* 3.7 4.0 - - - +
263A GLY* 3.5 20.9 - - - -
266A ARG* 4.1 2.5 - - + -
267A LYS* 3.1 70.3 - - + +
270A GLU* 2.9 33.2 + - - -
602A HEM 3.9 33.8 - - + +
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Residues in contact with ASP 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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67A HIS* 3.0 31.5 + - - +
68A THR 3.4 28.7 + - - +
69A ALA* 5.2 0.9 - - - -
70A PRO* 3.4 11.8 - - + +
125A ARG* 2.9 39.1 + - - +
230A LEU* 2.9 13.7 + - - +
233A TYR* 1.3 84.0 - - - +
235A THR* 1.3 64.0 + - + +
238A ASP* 3.3 24.0 - - - +
267A LYS* 4.4 6.4 + - - +
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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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68A THR 4.9 3.4 - - - +
70A PRO* 3.9 19.7 - - + -
121A ARG* 2.7 24.6 + - - +
125A ARG* 5.1 3.4 - - - +
231A ALA* 2.9 21.7 + - + +
233A TYR 3.4 0.2 - - - -
234A ASP* 1.3 86.9 - - + +
236A THR* 1.3 78.2 + - - +
237A ALA 3.3 1.3 - - - -
238A ASP* 3.0 5.8 + - - +
239A GLU* 2.9 31.8 + - - +
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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