Contacts of the helix formed by residues 232 - 239 (chain A) in PDB entry 3CKI
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A VAL 4.0 1.2 + - - -
231A ALA* 1.3 77.3 - - - +
233A HIS* 1.3 63.8 + - - +
234A ARG* 3.7 15.0 + - - -
235A PHE* 2.9 21.1 + - - +
236A TYR* 3.1 15.6 + - - +
285A LEU* 3.6 12.5 - - + +
298A TYR* 4.7 10.4 - - + +
299A ASN* 3.5 16.8 - - + +
317A LEU* 5.6 0.9 - - - +
337A LEU* 4.1 16.4 - - + +
338A PHE 3.2 9.7 + - - +
339A THR* 2.5 35.4 + - - -
341A GLN* 4.0 2.6 + - - -
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Residues in contact with HIS 233 (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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232A ASP* 1.3 73.7 - - - +
234A ARG* 1.3 87.2 + - + +
236A TYR* 3.9 2.0 - - - -
237A ARG* 3.1 46.3 + - - +
238A TYR* 5.8 1.7 + + - -
285A LEU 3.1 19.1 + - - +
286A LYS 4.0 2.5 - - - +
287A SER* 3.5 21.1 - - - -
288A PRO* 3.3 25.9 - - + +
298A TYR 5.8 0.2 - - - -
299A ASN* 2.9 36.8 + - - +
300A MET 3.3 28.3 - - - -
301A ALA* 3.9 9.2 + - - +
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Residues in contact with ARG 234 (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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232A ASP* 3.1 10.2 + - - +
233A HIS* 1.3 96.6 - - + +
235A PHE* 1.3 60.2 + - - +
238A TYR* 2.9 61.8 + - + +
298A TYR 5.5 2.8 + - - -
300A MET 4.0 3.6 + - - -
301A ALA 3.4 24.0 + - - -
302A LYS 3.5 20.0 + - - -
303A SER* 3.7 10.9 - - - +
310A ASP* 2.8 30.5 + - - -
312A TRP* 4.0 7.5 - - - +
339A THR* 3.9 3.6 - - - -
340A TYR* 3.7 17.3 + - - +
341A GLN* 3.4 31.5 - - - +
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Residues in contact with PHE 235 (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 ALA* 4.0 7.4 - - + -
232A ASP* 2.9 22.2 + - - +
234A ARG* 1.3 75.1 - - - +
236A TYR* 1.3 61.1 + - - +
239A MET* 2.8 46.9 + - + +
240A GLY 3.0 7.1 + - - -
247A THR* 3.9 24.5 - - + -
250A TYR* 3.7 30.3 - + - -
251A LEU* 3.7 26.9 - - + -
338A PHE* 3.6 24.9 - + + +
339A THR* 3.4 21.5 - - - -
340A TYR* 4.1 5.7 - - - +
387A THR* 3.5 26.0 - - + -
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Residues in contact with TYR 236 (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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232A ASP 3.1 10.5 + - - +
233A HIS 3.7 6.3 - - - +
235A PHE* 1.3 79.8 - - - +
237A ARG* 1.3 67.2 + - + +
240A GLY* 3.2 5.7 - - - -
241A ARG 3.2 8.3 + - - -
242A GLY* 2.8 49.3 + - - -
243A GLU 3.6 3.4 - - - -
244A GLU* 3.6 27.7 + - - -
247A THR* 3.5 22.4 - - - +
284A ILE* 3.7 17.5 - - + -
285A LEU 3.9 7.9 - - - +
286A LYS* 3.3 64.0 + - + +
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Residues in contact with ARG 237 (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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233A HIS* 3.1 40.2 + - - +
234A ARG 4.1 1.6 - - - +
236A TYR* 1.3 89.8 - - + +
238A TYR* 1.3 85.4 + - + +
241A ARG* 2.9 27.5 - - - +
242A GLY* 3.3 9.5 + - - +
286A LYS 4.4 7.4 + - - +
287A SER* 4.7 4.2 - - - +
288A PRO* 3.4 26.9 - - - +
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Residues in contact with TYR 238 (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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233A HIS* 5.8 1.5 + + - -
234A ARG* 2.9 54.8 + - + +
237A ARG* 1.3 98.5 + - + +
239A MET* 1.3 58.7 + - - +
241A ARG* 4.2 14.3 + - - +
310A ASP* 6.0 1.6 - - - -
340A TYR* 3.3 41.9 - + + -
393A THR* 5.4 1.0 + - - -
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Residues in contact with MET 239 (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 PHE* 2.8 39.5 + - + +
238A TYR* 1.3 73.1 - - - +
240A GLY* 1.3 59.0 + - - +
241A ARG* 3.1 16.4 + - - -
246A THR* 4.3 6.6 - - - +
250A TYR* 3.6 46.7 - - + +
340A TYR* 3.4 26.0 - - + -
387A THR* 3.0 32.3 - - - +
393A THR* 3.7 22.2 - - + -
394A ILE 5.2 1.1 - - - +
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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