Contacts of the helix formed by residues 282 - 292 (chain A) in PDB entry 4CCN
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 LEU 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A LEU* 4.5 1.3 - - - -
280A ARG* 3.2 50.9 + - + +
281A ALA* 1.3 74.5 - - - +
283A PRO* 1.3 75.7 - - + +
284A ALA* 3.2 10.1 - - + +
285A ALA* 3.0 13.9 + - + +
286A ALA* 2.9 20.9 + - - +
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Residues in contact with PRO 283 (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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248A ASP* 4.4 3.1 - - - +
251A LEU* 3.9 17.9 - - + +
252A ARG* 3.4 69.1 - - + +
282A LEU* 1.3 89.0 - - + +
284A ALA* 1.3 57.1 + - - +
286A ALA* 4.4 5.2 - - + -
287A TRP* 2.8 55.3 + - + +
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Residues in contact with ALA 284 (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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252A ARG* 5.0 3.4 - - - +
282A LEU* 3.2 9.1 - - + +
283A PRO* 1.3 80.7 - - - +
285A ALA* 1.3 54.5 + - - +
287A TRP* 4.9 1.9 - - - +
288A SER* 2.7 31.7 + - - -
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Residues in contact with ALA 285 (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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258A PHE* 4.3 17.3 - - + -
277A PRO* 5.3 7.2 - - + -
280A ARG 5.3 1.6 - - - +
282A LEU* 3.0 16.7 + - + +
284A ALA* 1.3 78.4 - - - +
286A ALA* 1.3 66.5 + - - +
287A TRP 3.3 0.2 - - - -
288A SER* 3.1 13.9 + - - -
289A LEU* 3.1 23.0 + - + +
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Residues in contact with ALA 286 (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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251A LEU* 3.6 32.3 - - + -
258A PHE* 4.6 3.7 - - + -
262A LEU* 4.1 17.3 - - + -
281A ALA* 5.4 0.4 - - + -
282A LEU 2.9 13.5 + - - +
283A PRO 3.9 1.6 - - - +
285A ALA* 1.3 77.3 - - - +
287A TRP* 1.3 61.0 + - + +
289A LEU* 3.3 14.2 + - - +
290A TYR* 3.2 20.6 + - - +
296A LEU* 3.7 14.9 - - + +
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Residues in contact with TRP 287 (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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244A THR* 3.6 27.6 - - + -
247A LEU* 4.3 6.1 - - + -
248A ASP* 3.2 47.6 + - + +
251A LEU* 4.7 10.0 - - + +
252A ARG* 5.5 1.3 - - - -
283A PRO* 2.8 44.6 + - + +
284A ALA* 4.9 1.6 - - - +
286A ALA* 1.3 71.0 - - + +
288A SER* 1.3 59.5 + - - +
290A TYR* 3.7 27.8 - + + +
291A GLN* 3.0 28.4 + - - +
296A LEU* 4.6 4.5 - - + -
329A LEU* 3.6 25.6 - - + -
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Residues in contact with SER 288 (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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284A ALA 2.7 23.2 + - - -
285A ALA* 3.1 9.3 + - - -
287A TRP* 1.3 75.7 - - - +
289A LEU* 1.3 65.6 + - - +
291A GLN* 3.6 5.7 + - - +
292A ALA* 3.2 21.3 + - - +
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Residues in contact with LEU 289 (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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258A PHE* 3.6 34.8 - - + -
264A ALA* 3.8 14.6 - - + -
266A ARG* 5.4 1.1 - - - +
275A LEU* 3.9 35.0 - - + +
277A PRO* 4.2 9.6 - - + -
285A ALA 3.1 16.3 + - - +
286A ALA* 3.6 7.0 - - - +
287A TRP 3.3 0.2 - - - -
288A SER* 1.3 78.0 - - - +
290A TYR* 1.3 59.6 + - - +
292A ALA* 2.9 22.4 + - + +
294A CYS* 2.9 32.1 + - + +
296A LEU* 4.8 2.5 - - + -
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Residues in contact with TYR 290 (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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286A ALA 3.2 11.1 + - - +
287A TRP* 3.7 28.3 - + + +
289A LEU* 1.3 80.8 - - - +
291A GLN* 1.3 61.7 + - + +
293A GLY* 2.9 19.9 + - - -
294A CYS 3.5 11.0 - - - +
296A LEU* 4.5 7.1 - - + +
329A LEU* 3.6 38.1 - - + -
331A PRO* 3.4 46.3 - - + +
332A PRO* 3.7 6.4 - - + +
414A HIS* 3.1 33.4 - - - +
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Residues in contact with GLN 291 (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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287A TRP 3.0 17.9 + - - +
288A SER* 4.0 6.5 - - - +
290A TYR* 1.3 82.9 - - + +
292A ALA* 1.3 56.9 + - - +
293A GLY 3.0 4.6 + - - -
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Residues in contact with ALA 292 (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 ARG* 3.0 33.2 + - - +
288A SER 3.2 15.5 + - - +
289A LEU* 2.9 14.4 + - + +
291A GLN* 1.3 76.5 - - - +
293A GLY* 1.3 58.8 + - - +
294A CYS 3.3 1.3 - - - -
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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