Contacts of the helix formed by residues 264 - 276 (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 ILE 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A VAL* 4.9 1.3 - - + -
220A ILE* 3.7 34.5 - - + -
260A GLU 4.7 2.5 - - - +
261A GLY* 3.2 21.7 - - - +
263A LYS* 1.3 82.0 - - + +
265A VAL* 1.3 60.5 + - + +
266A LYS 3.2 2.7 - - - -
267A ASP* 2.8 41.6 + - + +
268A LEU* 3.1 38.7 + - + +
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 5.2 0.4 - - + -
242A THR* 4.0 17.5 - - + +
243A PHE* 3.9 38.5 - - + -
246A VAL* 4.1 15.9 - - + -
247A LEU* 4.0 24.5 - - + -
261A GLY 3.4 16.4 - - - +
262A ALA* 3.5 17.6 + - - +
263A LYS 3.7 0.2 - - - -
264A ILE* 1.3 81.2 - - + +
266A LYS* 1.3 63.9 + - - +
267A ASP 3.2 0.3 + - - -
268A LEU* 3.3 7.8 + - - +
269A MET* 3.0 23.2 + - + +
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Residues in contact with LYS 266 (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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246A VAL* 5.3 5.0 - - + +
247A LEU* 5.6 3.6 - - - -
262A ALA 4.9 0.8 + - - +
263A LYS 5.1 5.8 - - - +
264A ILE 4.7 1.3 - - - -
265A VAL* 1.3 82.9 - - - +
267A ASP* 1.3 70.7 + - - +
269A MET* 3.5 6.1 + - - +
270A SER* 3.0 32.4 + - - -
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Residues in contact with ASP 267 (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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224A ASN* 5.7 0.7 - - - -
263A LYS 4.1 3.7 - - - +
264A ILE* 2.8 39.7 + - + +
266A LYS* 1.3 87.9 + - - +
268A LEU* 1.3 64.7 + - + +
270A SER* 3.3 8.2 + - - -
271A LYS* 2.9 30.2 + - - +
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Residues in contact with LEU 268 (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* 5.2 2.0 - - + -
220A ILE* 4.3 13.0 - - + +
223A ILE* 4.3 33.4 - - + -
224A ASN* 3.6 32.1 - - - +
227A LEU* 3.5 12.0 - - + +
235A ILE* 6.5 0.2 - - + -
243A PHE* 4.0 29.4 - - + -
264A ILE* 3.1 35.1 + - + +
265A VAL* 3.5 5.2 - - - +
267A ASP* 1.3 78.9 - - + +
269A MET* 1.3 64.7 + - + +
271A LYS* 3.2 2.5 + - - -
272A ALA* 3.0 21.5 + - - +
279A ILE* 6.3 0.4 - - - -
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Residues in contact with MET 269 (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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235A ILE* 5.8 1.1 - - - -
243A PHE* 4.6 13.0 - - + -
247A LEU* 3.8 42.6 - - + -
265A VAL* 3.0 23.4 + - + +
266A LYS* 3.8 6.1 - - - +
268A LEU* 1.3 76.3 - - - +
270A SER* 1.3 57.1 + - - +
272A ALA* 3.4 4.8 + - - +
273A GLU* 2.9 34.2 + - - +
279A ILE* 4.0 40.2 - - + -
281A LEU* 5.3 2.0 - - + -
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Residues in contact with SER 270 (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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266A LYS* 3.0 23.1 + - - -
267A ASP* 3.4 9.9 - - - -
269A MET* 1.3 75.1 - - - +
271A LYS* 1.3 60.0 + - - +
273A GLU* 3.5 8.6 + - - +
274A LYS* 3.1 28.4 + - - +
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Residues in contact with LYS 271 (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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224A ASN* 3.5 37.7 + - - +
227A LEU* 4.0 20.0 - - + -
228A ASP* 3.4 37.8 + - - -
267A ASP 2.9 16.6 + - - +
268A LEU 3.2 3.1 + - - +
270A SER* 1.3 72.6 - - - +
272A ALA* 1.3 65.7 + - - +
274A LYS* 3.4 16.8 + - - +
275A ASN* 3.0 32.9 + - - +
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Residues in contact with ALA 272 (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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227A LEU* 3.7 19.2 - - + +
268A LEU 3.0 13.0 + - - +
269A MET* 3.5 8.5 - - - +
271A LYS* 1.3 74.8 - - - +
273A GLU* 1.3 53.4 + - - +
275A ASN* 3.0 3.0 + - - -
276A GLY 2.8 31.4 + - - -
277A VAL* 3.1 19.6 + - - +
279A ILE* 3.8 35.2 - - + -
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Residues in contact with GLU 273 (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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269A MET* 2.9 20.8 + - - +
270A SER* 3.6 9.3 - - - +
271A LYS 3.3 0.2 - - - -
272A ALA* 1.3 78.8 - - - +
274A LYS* 1.3 60.9 + - - +
275A ASN 3.4 0.2 + - - -
276A GLY* 3.5 9.3 + - - +
277A VAL 5.0 3.1 - - - -
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Residues in contact with LYS 274 (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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228A ASP* 5.3 1.8 + - - -
270A SER 3.1 15.3 + - - +
271A LYS* 3.7 21.1 - - - +
272A ALA 3.3 0.2 - - - -
273A GLU* 1.3 77.7 - - - +
275A ASN* 1.3 79.2 + - - +
276A GLY 3.8 0.2 + - - -
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Residues in contact with ASN 275 (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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227A LEU 3.5 22.6 + - - +
228A ASP* 3.4 28.8 + - - +
230A VAL 5.4 1.0 - - - +
271A LYS* 3.0 21.0 + - - +
272A ALA 3.0 4.7 + - - +
274A LYS* 1.3 105.9 + - - +
276A GLY* 1.3 60.4 + - - +
277A VAL* 3.3 7.6 + - + +
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Residues in contact with GLY 276 (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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231A ASN* 3.9 7.7 - - - +
272A ALA 2.8 5.7 + - - -
273A GLU* 3.5 7.5 + - - -
274A LYS 3.4 3.4 - - - -
275A ASN* 1.3 79.3 - - - +
277A VAL* 1.3 61.4 + - - +
278A LYS* 3.7 2.4 + - - +
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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
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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