Contacts of the helix formed by residues 219 - 227 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU* 5.5 1.1 - - + -
212A GLY 3.8 11.9 - - - -
213A GLY* 3.8 8.9 - - - -
215A LYS 3.1 18.6 + - - +
216A VAL* 2.9 10.3 + - - +
218A ASP* 1.3 93.6 + - - +
220A ILE* 1.3 67.0 + - - +
221A GLN 3.1 3.1 + - - -
222A LEU* 3.3 27.6 + - + -
223A ILE* 2.9 40.4 + - + +
239A MET* 3.8 22.6 - - + +
336A ASN 5.9 0.4 - - - -
399A LEU* 5.5 10.1 - - + -
419A CDP 2.8 43.1 + - - -
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Residues in contact with ILE 220 (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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216A VAL* 3.5 17.0 - - + +
217A ALA* 3.0 31.9 - - - +
218A ASP 3.6 1.0 - - - -
219A LYS* 1.3 78.7 - - - +
221A GLN* 1.3 61.4 + - - +
223A ILE* 3.9 5.4 - - - +
224A ASN* 3.0 49.5 + - - +
261A GLY* 4.4 3.4 - - - -
264A ILE* 3.7 38.1 - - + -
268A LEU* 4.3 13.8 - - + +
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Residues in contact with GLN 221 (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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218A ASP 5.2 1.3 + - - +
219A LYS* 3.1 0.6 - - - +
220A ILE* 1.3 79.6 - - - +
222A LEU* 1.3 67.0 + - - +
224A ASN* 3.4 13.9 + - - +
225A ASN* 3.0 33.8 + - + +
403A GLU* 3.6 38.2 + - + +
405A LYS* 5.3 3.6 - - + +
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Residues in contact with LEU 222 (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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211A LEU* 3.7 32.8 - - + -
218A ASP 5.6 0.2 - - - +
219A LYS* 3.3 32.8 + - + +
221A GLN* 1.3 79.1 - - - +
223A ILE* 1.3 64.5 + - - +
225A ASN* 3.1 3.2 + - - +
226A MET* 2.9 33.5 + - + +
336A ASN* 5.4 0.2 - - + -
399A LEU* 4.0 31.6 - - + +
402A LEU* 3.9 40.2 - - + -
403A GLU* 3.8 17.6 - - + +
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Residues in contact with ILE 223 (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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211A LEU* 3.8 22.4 - - + -
216A VAL* 5.3 4.7 - - + -
219A LYS* 2.9 40.5 + - + +
220A ILE 3.9 2.7 - - - +
222A LEU* 1.3 73.0 - - + +
224A ASN* 1.3 54.2 + - - +
226A MET* 3.3 6.1 + - - +
227A LEU* 2.8 51.4 + - + +
233A MET* 4.1 17.9 - - - -
235A ILE* 4.9 10.1 - - + -
239A MET* 4.7 13.2 - - + -
243A PHE* 4.7 12.8 - - + -
268A LEU* 4.3 31.0 - - + -
279A ILE* 6.4 0.2 - - + -
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Residues in contact with ASN 224 (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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220A ILE* 3.0 39.3 + - - +
221A GLN* 3.7 16.3 + - - +
223A ILE* 1.3 76.2 - - - +
225A ASN* 1.3 63.2 + - - +
227A LEU* 3.4 15.5 + - - +
228A ASP* 3.6 4.7 + - - +
267A ASP 5.5 0.7 - - - +
268A LEU* 3.6 16.7 - - - +
271A LYS* 3.5 42.7 + - - +
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Residues in contact with ASN 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLN* 3.0 24.6 + - - +
222A LEU 3.7 2.5 - - - +
224A ASN* 1.3 73.2 - - - +
226A MET* 1.3 67.0 + - - +
228A ASP* 3.2 22.8 + - - +
229A LYS* 3.7 34.0 + - - +
402A LEU 2.8 28.7 + - - +
403A GLU* 4.3 14.0 - - - +
404A GLY* 4.2 7.9 - - - +
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Residues in contact with MET 226 (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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200A LEU* 3.8 28.7 - - + -
207A PHE* 5.2 4.3 - - - -
209A ALA* 4.8 7.9 - - + -
211A LEU* 4.7 6.7 - - + -
222A LEU* 2.9 33.2 + - + +
225A ASN* 1.3 78.8 - - - +
227A LEU* 1.3 53.1 + - - +
229A LYS* 2.8 31.6 + - + +
230A VAL* 3.1 32.2 + - + +
233A MET* 3.6 22.7 - - + -
334A VAL* 5.4 5.8 - - - -
402A LEU* 3.8 42.0 - - + +
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Residues in contact with LEU 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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223A ILE* 2.8 38.3 + - + +
224A ASN* 3.5 9.2 - - - +
225A ASN 3.3 0.2 - - - -
226A MET* 1.3 72.7 - - - +
228A ASP* 1.3 58.5 + - - +
229A LYS 3.3 0.6 + - - -
230A VAL* 4.4 3.2 - - + +
233A MET* 4.1 17.9 - - + -
268A LEU* 3.5 29.6 - - - +
271A LYS* 4.0 18.6 - - + -
272A ALA* 3.7 28.5 - - + +
275A ASN* 3.5 15.3 + - - +
277A VAL* 3.7 38.4 - - + +
279A ILE* 4.3 3.1 - - + -
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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