Contacts of the helix formed by residues 219 - 227 (chain B) in PDB entry 3C3C
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 LYS 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B LEU* 6.3 0.2 - - + -
212B GLY 3.6 21.1 - - - +
213B GLY* 4.1 9.6 - - - -
214B ALA 4.8 2.0 - - - +
215B LYS 3.4 24.5 + - - +
216B VAL 2.7 18.3 + - - +
217B ALA 2.8 0.2 + - - -
218B ASP* 1.3 89.8 + - - +
220B ILE* 1.3 64.1 + - - +
221B GLN 3.2 2.9 - - - -
222B LEU* 3.0 29.9 + - + +
223B ILE* 2.8 33.1 + - + +
239B MET* 3.8 24.9 - - + -
399B LEU* 5.4 16.6 - - + +
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Residues in contact with ILE 220 (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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216B VAL* 3.3 35.3 + - + +
217B ALA* 3.3 20.3 + - - +
218B ASP 3.8 0.2 - - - -
219B LYS* 1.3 77.0 - - - +
221B GLN* 1.3 56.7 + - + +
223B ILE* 3.3 3.4 + - - +
224B ASN* 2.8 40.0 + - + +
261B GLY* 4.5 6.1 - - - +
264B ILE* 3.9 47.8 - - + -
268B LEU* 4.2 16.6 - - + +
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Residues in contact with GLN 221 (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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218B ASP 5.4 0.4 + - - -
219B LYS 3.2 0.4 - - - -
220B ILE* 1.3 80.2 - - + +
222B LEU* 1.3 68.5 + - - +
224B ASN* 4.0 21.8 + - - +
225B ASN* 3.1 30.0 + - - +
403B GLU* 4.2 34.8 + - + +
405B LYS* 5.4 7.0 - - - -
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Residues in contact with LEU 222 (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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211B LEU* 4.3 30.3 - - + -
219B LYS* 3.0 33.3 + - + +
221B GLN* 1.3 79.8 - - - +
223B ILE* 1.3 64.9 + - - +
225B ASN* 3.9 1.6 - - - +
226B MET* 3.0 31.4 + - + +
336B ASN* 5.5 4.3 - - + +
399B LEU* 3.8 45.3 - - + +
402B LEU* 3.8 27.7 - - + +
403B GLU* 3.9 18.4 + - + +
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Residues in contact with ILE 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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211B LEU* 4.0 18.2 - - + -
216B VAL* 5.0 5.8 - - + -
219B LYS* 2.8 29.7 + - + +
220B ILE 3.7 4.9 - - - +
222B LEU* 1.3 71.9 - - - +
224B ASN* 1.3 63.0 + - - +
226B MET* 3.1 7.4 + - - +
227B LEU* 2.9 36.0 + - + +
233B MET* 3.8 20.9 - - - -
235B ILE* 4.6 12.8 - - + -
239B MET* 4.7 12.3 - - + -
243B PHE* 4.2 26.5 - - + -
268B LEU* 3.6 27.1 - - + -
279B ILE* 5.9 0.7 - - + -
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Residues in contact with ASN 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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220B ILE* 2.8 25.6 + - + +
221B GLN* 3.9 25.0 + - - +
223B ILE* 1.3 74.4 - - - +
225B ASN* 1.3 60.7 + - - +
227B LEU* 3.6 5.4 + - - +
268B LEU* 3.9 14.3 - - + +
271B LYS* 3.1 49.5 + - - +
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Residues in contact with ASN 225 (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 LEU* 5.5 3.2 - - - +
221B GLN* 3.1 25.9 + - - +
222B LEU 4.2 0.2 - - - +
224B ASN* 1.3 75.9 - - - +
226B MET* 1.3 67.3 + - - +
228B ASP* 3.2 21.3 + - - +
229B LYS* 3.4 35.1 + - - +
402B LEU 2.5 28.3 + - - +
403B GLU 3.6 17.8 - - - +
404B GLY* 3.6 8.4 - - - +
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Residues in contact with MET 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 LEU* 4.6 9.2 - - + -
207B PHE* 4.2 20.2 - - + -
209B ALA* 3.6 25.1 - - + -
211B LEU* 4.5 11.0 - - + -
222B LEU* 3.0 33.9 + - + +
223B ILE* 3.1 5.1 + - - +
225B ASN* 1.3 78.2 - - - +
227B LEU* 1.3 56.5 + - - +
229B LYS* 2.9 27.7 + - - +
230B VAL* 3.2 18.2 + - + +
233B MET* 3.8 15.5 - - + -
334B VAL* 4.5 15.0 - - + -
402B LEU* 4.3 32.5 - - + +
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Residues in contact with LEU 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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223B ILE* 2.9 34.7 + - + +
224B ASN* 3.8 7.9 - - - +
225B ASN 3.3 0.2 - - - -
226B MET* 1.3 76.3 - - - +
228B ASP* 1.3 60.3 + - - +
229B LYS 3.1 1.9 + - - -
230B VAL* 4.1 5.6 + - - +
233B MET* 3.5 22.4 - - + -
268B LEU* 3.7 32.3 - - + +
271B LYS* 4.0 22.2 - - + -
272B ALA* 4.2 9.9 - - + +
275B ASN* 3.5 24.4 + - - +
277B VAL* 3.9 33.8 - - + +
279B ILE* 4.3 5.6 - - + -
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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