Contacts of the helix formed by residues 226 - 235 (chain F) in PDB entry 1M54
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65F HIS* 4.6 4.9 - - + -
224F ARG 3.3 5.5 + - - -
225F ASN* 1.3 71.4 + - - +
227F SER* 1.3 69.5 + - - +
228F ASN 2.5 2.1 + - - -
229F PRO* 2.7 15.2 - - - -
230F LEU* 2.8 29.6 + - + +
1620F HEM 3.2 46.5 - - + +
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Residues in contact with SER 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ARG* 2.7 40.7 + - - +
126F MET* 3.8 7.2 - - - -
129F ASP* 2.3 39.0 + - - +
225F ASN* 2.6 25.9 + - - -
226F ALA* 1.3 74.5 - - - +
228F ASN* 1.3 54.9 + - - -
230F LEU* 3.9 7.7 - - - +
231F ALA* 2.9 25.8 + - - +
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Residues in contact with ASN 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F LYS* 5.5 1.6 - - - +
122F ILE* 3.2 58.5 - - + +
126F MET* 4.8 4.3 - - + +
222F GLN* 3.9 22.6 + - - +
225F ASN* 3.0 10.0 + - + +
226F ALA 2.5 9.5 + - - -
227F SER* 1.3 68.0 - - - +
229F PRO* 1.3 91.5 - - + +
230F LEU 3.0 1.5 + - - -
231F ALA 3.4 5.4 + - - -
232F HIS* 3.5 7.2 + - - -
257F THR* 3.8 20.8 - - - +
259F GLY* 3.0 17.2 - - - -
314F VAL* 5.1 0.2 - - - -
1610F PLP 4.9 0.6 + - - -
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Residues in contact with PRO 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F ASN 3.7 3.4 - - - +
226F ALA 2.7 7.3 - - - +
228F ASN* 1.3 99.2 - - + +
230F LEU* 1.3 69.6 - - - +
231F ALA 3.3 0.3 + - - -
232F HIS 3.3 2.8 + - - -
233F TYR 3.3 15.1 + - - -
258F GLY 5.1 0.4 - - - +
259F GLY* 3.6 15.5 - - - +
262F THR* 4.9 5.2 - - + -
263F GLY* 3.4 17.1 - - - +
314F VAL* 3.1 42.0 - - + -
315F LEU 5.1 0.4 - - - +
1620F HEM 3.3 27.9 - - + +
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Residues in contact with LEU 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F HIS* 4.1 22.9 - - + +
66F HIS* 5.1 4.5 - - + +
67F HIS* 3.9 31.6 - - + +
125F ARG* 3.7 14.8 - - - +
129F ASP* 4.7 5.4 - - - +
226F ALA* 2.8 39.9 + - + +
227F SER* 3.4 10.1 - - - +
229F PRO* 1.3 85.5 - - - +
231F ALA* 1.3 55.2 + - - +
233F TYR* 2.9 22.9 - - + +
234F ASP* 3.0 20.0 + - - +
1620F HEM 3.1 22.2 - - + -
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Residues in contact with ALA 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F ARG* 4.7 5.8 - - + +
122F ILE* 4.4 14.1 - - + +
125F ARG* 3.3 29.4 - - + +
227F SER 2.9 18.3 + - - +
228F ASN 3.8 5.4 - - - +
229F PRO 3.2 0.2 - - - -
230F LEU* 1.3 71.2 - - - +
232F HIS* 1.3 60.8 + - - +
233F TYR 2.7 10.4 + - - -
234F ASP* 3.1 0.6 + - - -
235F THR* 2.8 35.5 + - + +
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Residues in contact with HIS 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F VAL* 3.3 35.1 + - + +
119F LYS* 6.2 0.2 - - - +
121F ARG* 3.8 8.0 - - + +
122F ILE* 2.9 28.0 - - + +
228F ASN* 3.5 12.7 + - - -
229F PRO 3.3 6.5 + - - +
231F ALA* 1.3 75.9 - - - +
233F TYR* 1.3 53.9 + - - +
236F THR* 3.1 26.1 + - + -
237F ALA* 2.7 32.9 + - - +
259F GLY 3.4 7.2 - - - +
260F THR* 3.0 55.3 + - + +
263F GLY* 4.3 2.5 - - - -
264F ILE* 3.7 4.5 - - - +
1610F PLP 4.4 2.0 + - - -
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Residues in contact with TYR 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F TRP* 4.3 1.9 + - - -
60F ALA* 5.4 7.0 - - + +
67F HIS* 4.2 17.5 - + - -
229F PRO 3.3 11.2 + - - +
230F LEU* 2.9 14.8 - - + +
231F ALA 2.7 1.8 + - - -
232F HIS* 1.3 78.8 - - - +
234F ASP* 1.3 82.5 + - - +
237F ALA* 3.0 18.9 - - - +
238F ASP* 3.9 0.9 - - - +
263F GLY* 3.0 26.5 - - - +
266F ARG* 4.0 1.6 - - + -
267F LYS* 3.1 62.4 + - + -
270F GLU* 2.5 30.0 + - - -
1620F HEM 3.7 37.8 - - + +
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Residues in contact with ASP 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F HIS* 3.1 17.4 + - - +
68F THR 2.7 31.2 + - - +
70F PRO* 3.3 9.2 - - - +
125F ARG* 2.7 35.6 + - - +
230F LEU* 3.0 12.0 + - - +
231F ALA 4.1 0.4 - - - +
233F TYR* 1.3 100.6 - - - +
235F THR* 1.3 62.4 + - + +
238F ASP* 2.7 28.6 - - - +
267F LYS* 4.9 1.9 + - - +
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Residues in contact with THR 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F THR* 4.6 7.0 - - + +
69F ALA 3.9 8.3 - - - +
70F PRO* 3.9 26.5 - - + -
71F ALA 5.3 0.2 - - - +
85F GLY* 6.2 0.4 - - - -
121F ARG* 3.7 16.3 + - - +
125F ARG* 6.0 0.9 - - - +
231F ALA* 2.8 19.1 + - + +
234F ASP* 1.3 83.6 - - + +
236F THR* 1.3 74.5 + - - -
237F ALA 3.0 1.3 - - - -
238F ASP* 2.8 2.3 + - - +
239F GLU* 2.7 34.2 + - - +
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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