Contacts of the helix formed by residues 222 - 233 (chain B) in PDB entry 3C6M
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 ASP 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B SER* 2.3 32.3 + - - -
146B PRO* 4.6 1.9 - - - +
147B TYR* 3.5 17.2 - - + -
148B GLN* 3.2 30.3 + - - +
150B ILE* 3.9 0.9 - - - +
220B GLU* 3.0 24.2 + - - +
221B ILE* 1.3 78.3 - - + +
223B GLN* 1.3 63.2 + - - +
224B MET* 3.0 20.8 + - - +
225B VAL* 3.0 24.4 + - + +
226B ILE* 3.6 3.3 + - - +
253B ILE* 5.0 0.4 - - - -
401B MTA 3.6 1.6 - - - +
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Residues in contact with GLN 223 (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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147B TYR* 5.6 0.2 - - - -
221B ILE 3.8 4.2 + - - -
222B ASP* 1.3 73.6 + - - +
224B MET* 1.3 59.0 + - + +
225B VAL 3.3 0.2 + - - -
226B ILE* 3.3 14.2 + - - +
227B ASP* 2.8 55.5 + - - +
230B LYS* 5.1 1.7 + - - -
244B LEU* 4.5 14.3 - - - +
253B ILE* 3.6 45.5 - - + +
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Residues in contact with MET 224 (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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141B TYR* 3.8 26.6 + - - +
143B GLU* 3.8 18.2 - - + +
144B ASP 3.5 23.8 - - - +
145B SER* 3.7 19.5 - - - -
146B PRO* 4.2 8.7 - - - -
150B ILE* 3.7 13.9 - - + +
222B ASP* 3.0 13.0 + - - +
223B GLN* 1.3 77.0 - - + +
225B VAL* 1.3 59.5 + - - +
227B ASP* 3.7 15.7 - - - +
228B GLY* 3.1 21.3 + - - -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLN* 3.5 28.7 - - - +
150B ILE* 3.7 19.5 - - + -
162B LEU* 4.0 25.7 - - + +
164B LEU* 4.1 9.2 - - + -
200B GLY 3.9 18.2 - - - -
201B ASP 4.4 0.2 - - - +
220B GLU* 4.4 1.3 - - - +
222B ASP* 3.0 14.1 + - + +
224B MET* 1.3 74.2 - - - +
226B ILE* 1.3 68.1 + - - +
228B GLY* 3.2 2.3 + - - -
229B CYS* 2.9 29.6 + - - -
401B MTA 3.4 22.7 - - + +
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Residues in contact with ILE 226 (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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200B GLY* 3.7 20.9 - - - +
218B MET* 4.2 6.5 - - + -
220B GLU* 3.9 21.1 - - + -
222B ASP 3.6 0.6 + - - +
223B GLN* 3.3 17.7 + - - +
225B VAL* 1.3 77.9 - - - +
227B ASP* 1.3 64.4 + - - +
229B CYS* 3.1 0.4 + - - -
230B LYS* 2.9 30.5 + - + +
241B LEU* 4.0 30.9 - - + +
244B LEU* 4.7 8.5 - - + -
251B VAL* 3.7 19.3 - - + -
253B ILE* 3.7 29.4 - - + -
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Residues in contact with ASP 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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141B TYR* 5.4 3.4 - - + +
223B GLN* 2.8 48.2 + - - +
224B MET* 3.7 20.4 - - + +
226B ILE* 1.3 77.4 - - - +
228B GLY* 1.3 64.3 + - - +
229B CYS 3.3 0.2 + - - -
230B LYS* 3.7 23.9 + - - +
231B LYS* 3.4 24.1 + - - +
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Residues in contact with GLY 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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141B TYR* 4.8 14.5 - - - -
150B ILE* 6.0 0.4 - - - -
152B ILE* 3.6 18.2 - - - -
224B MET 3.1 12.0 + - - -
225B VAL 3.2 3.5 + - - -
227B ASP* 1.3 78.4 - - - +
229B CYS* 1.3 55.6 + - - +
231B LYS* 6.1 0.2 - - - -
232B TYR* 3.0 43.7 + - - +
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Residues in contact with CYS 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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152B ILE* 4.6 0.4 - - - -
162B LEU* 3.9 28.0 - - - -
200B GLY 3.9 12.6 - - - +
201B ASP* 3.8 28.5 - - - +
225B VAL* 2.9 20.9 + - - +
226B ILE 3.9 1.1 - - - +
228B GLY* 1.3 74.8 - - - +
230B LYS* 1.3 62.8 + - - +
231B LYS 3.1 1.3 - - - -
233B MET* 2.8 47.8 + - + -
237B CYS* 3.5 12.4 - - - -
241B LEU* 4.2 2.2 - - + -
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Residues in contact with LYS 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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223B GLN* 5.1 2.0 + - - -
226B ILE* 2.9 18.7 + - + +
227B ASP* 3.7 28.9 + - - +
229B CYS* 1.3 74.7 - - - +
231B LYS* 1.3 61.6 + - - +
234B ARG* 3.0 32.6 + - - +
237B CYS* 4.2 10.2 - - - -
238B GLY 5.8 0.2 - - - -
241B LEU* 2.8 36.2 - - + +
242B ASP* 3.2 31.0 + - - +
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Residues in contact with LYS 231 (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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227B ASP 3.4 15.9 + - - +
228B GLY 3.8 3.4 - - - +
229B CYS 3.1 0.4 - - - -
230B LYS* 1.3 82.8 - - + +
232B TYR* 1.3 97.7 + - + +
233B MET 4.0 0.2 - - - -
234B ARG* 4.5 9.3 - - - +
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Residues in contact with TYR 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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140B VAL* 3.4 38.2 + - + -
141B TYR* 4.0 29.2 - + + -
152B ILE* 4.1 10.3 - - + -
160B ASN* 2.6 36.9 - - - +
172B GLU* 3.4 5.1 - - - +
228B GLY* 3.0 25.4 + - - +
231B LYS* 1.3 113.6 + - + +
233B MET* 1.3 61.5 + - - +
234B ARG 3.6 3.4 - - - -
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Residues in contact with MET 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 4.1 10.5 - - + -
160B ASN* 3.7 36.6 - - - +
162B LEU* 4.0 15.0 - - + +
170B LEU* 3.3 30.3 - - + +
172B GLU* 3.3 9.6 - - - +
201B ASP* 4.8 5.2 - - + +
229B CYS* 2.8 45.0 + - + +
232B TYR* 1.3 72.1 - - - +
234B ARG* 1.3 59.3 + - - +
235B LYS 3.1 3.6 - - - -
236B THR* 2.8 44.7 + - + +
237B CYS* 2.9 12.3 + - - -
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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