Contacts of the helix formed by residues 226 - 235 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS* 4.4 10.3 - - + +
224B ARG 3.5 4.4 + - - -
225B ASN* 1.3 75.8 + - - +
227B SER* 1.3 57.9 + - - +
229B PRO* 3.0 4.6 - - - +
230B LEU* 2.9 46.5 + - + +
602B HEM 3.4 39.2 - - + +
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ARG* 3.4 10.5 - - - +
126B MET* 3.8 22.2 - - - -
129B ASP* 2.9 35.6 + - - +
225B ASN* 2.8 17.5 + - - -
226B ALA* 1.3 79.3 - - - +
228B ASN* 1.3 56.8 + - - +
230B LEU* 4.0 8.0 - - - +
231B ALA* 2.9 30.3 + - - +
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 3.3 39.0 - - + +
126B MET* 4.4 7.4 - - - +
222B GLN* 3.1 27.1 + - - +
225B ASN 3.2 7.4 + - - +
226B ALA 3.1 1.0 - - - -
227B SER* 1.3 75.2 - - - +
229B PRO* 1.3 72.3 - - + +
231B ALA* 3.0 13.5 + - - +
232B HIS* 3.0 16.5 + - - -
257B THR* 3.2 21.9 + - - -
259B GLY* 3.3 19.9 - - - -
314B VAL* 3.8 7.5 - - - +
601B PLP 4.8 0.7 + - - -
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Residues in contact with PRO 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ASN 3.2 13.0 - - - +
226B ALA 3.0 19.3 - - - +
228B ASN* 1.3 89.6 - - + +
230B LEU* 1.3 54.4 + - - +
232B HIS 3.2 0.9 + - - -
233B TYR* 2.9 28.1 + - - +
259B GLY* 3.5 26.9 - - - +
262B THR* 4.2 7.0 - - + -
263B GLY* 3.3 7.9 - - - +
314B VAL* 3.7 21.8 - - + +
602B HEM 3.8 33.0 - - + -
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS* 3.6 29.8 - - + -
66B HIS 4.4 4.5 - - - +
67B HIS* 4.1 25.8 - - + +
125B ARG* 4.1 22.0 - - - +
129B ASP* 5.4 1.8 - - - +
226B ALA* 2.9 35.3 + - + +
227B SER* 3.8 8.1 - - - +
229B PRO* 1.3 79.8 - - - +
231B ALA* 1.3 56.8 + - - +
233B TYR* 3.0 7.3 + - + +
234B ASP* 2.9 34.8 + - - +
602B HEM 4.0 29.2 - - + -
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 4.7 6.5 - - + -
122B ILE* 4.1 16.6 - - + +
125B ARG* 3.7 33.4 - - + +
227B SER 2.9 20.3 + - - +
228B ASN 3.4 5.2 - - - +
230B LEU* 1.3 77.9 - - - +
232B HIS* 1.3 62.5 + - - +
233B TYR 3.4 0.3 + - - -
235B THR* 2.8 32.9 + - + +
236B THR* 4.0 0.8 + - - -
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Residues in contact with HIS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL* 3.2 26.1 - - + +
119B LYS* 6.1 2.2 - - + -
121B ARG* 4.6 3.2 - - - -
122B ILE* 3.4 23.9 - - + +
228B ASN* 3.0 25.6 + - - -
229B PRO 3.7 1.6 - - - +
230B LEU 3.2 0.2 - - - -
231B ALA* 1.3 79.1 - - - +
233B TYR* 1.3 55.7 + - - +
236B THR* 3.4 26.6 + - + -
237B ALA* 3.2 29.6 + - - +
259B GLY 3.6 15.5 - - - +
260B THR* 2.7 57.6 + - + +
263B GLY* 4.2 2.9 - - - -
264B ILE* 3.9 4.2 - - + +
601B PLP 4.3 2.5 - - - -
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Residues in contact with TYR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ALA* 4.7 9.7 - - - +
67B HIS* 3.7 27.5 - + - -
229B PRO 2.9 13.9 + - - +
230B LEU* 3.3 13.9 - - + +
232B HIS* 1.3 77.5 - - - +
234B ASP* 1.3 80.9 + - - +
235B THR 3.6 0.5 + - - -
237B ALA* 3.6 5.2 - - - +
263B GLY* 3.4 24.2 - - - -
266B ARG* 4.1 6.3 - - + -
267B LYS* 3.1 69.8 - - + +
270B GLU* 2.8 30.8 + - - -
602B HEM 3.9 27.0 - - + +
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS* 2.9 33.3 + - - +
68B THR 3.5 24.9 + - - +
69B ALA* 5.2 0.9 - - - -
70B PRO* 3.4 9.2 - - + +
125B ARG* 3.0 34.3 + - - +
230B LEU* 2.9 14.7 + - - +
233B TYR* 1.3 84.4 - - - +
235B THR* 1.3 64.8 + - + +
238B ASP* 3.1 27.1 - - - +
267B LYS* 4.3 6.8 + - - +
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Residues in contact with THR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B THR 4.8 5.2 - - - +
70B PRO* 3.9 19.0 - - + +
121B ARG* 2.7 23.3 + - - +
125B ARG* 5.2 3.8 - - - +
231B ALA* 2.8 22.1 + - + +
233B TYR 3.4 0.2 - - - -
234B ASP* 1.3 87.6 - - + +
236B THR* 1.3 81.9 + - - +
237B ALA 3.3 2.0 - - - -
238B ASP* 3.0 4.2 + - - +
239B GLU* 2.8 32.4 + - - +
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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
------------------------------------------------------------
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