Contacts of the strand formed by residues 224 - 231 (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 THR 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LYS 3.7 1.4 - - - -
223A ASN* 1.3 97.6 + - - +
225A CYS* 1.3 65.0 + - - +
226A LYS* 3.6 10.2 + - + +
274A GLY 5.5 0.2 + - - -
276A GLY 3.4 10.8 - - - +
277A ILE 4.1 1.6 - - - -
278A GLN* 3.6 40.6 - - + +
470A PHE* 3.4 8.1 - - - -
471A GLN* 2.8 38.4 + - - +
472A GLU 4.3 2.0 - - - -
473A ARG* 3.1 24.1 + - - +
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Residues in contact with CYS 225 (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 THR* 1.3 71.6 - - - +
226A LYS* 1.3 63.8 + - - +
227A LEU* 3.7 1.2 + - - -
276A GLY 2.8 14.6 + - - +
277A ILE* 3.4 9.1 - - + +
278A GLN 3.2 19.6 + - - -
333A CYS* 2.0 50.0 - - - -
334A LEU* 3.6 30.1 - - - -
364A VAL* 4.0 3.1 - - - -
411A PHE* 3.9 11.9 - - + -
470A PHE* 3.8 16.0 - - + -
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Residues in contact with LYS 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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224A THR* 3.6 7.2 + - + +
225A CYS* 1.3 72.3 - - - +
227A LEU* 1.3 59.8 + - - +
278A GLN* 3.2 50.7 + - + +
279A ILE 5.1 1.9 + - - +
280A GLU* 3.5 35.4 - - + +
332A VAL* 3.9 2.1 - - - +
333A CYS* 3.3 32.6 + - + +
334A LEU 3.4 2.1 + - - +
469A CYS 5.6 0.8 + - - -
471A GLN* 3.0 42.8 - - + +
472A GLU 3.7 15.6 + - - -
474A SER 3.4 14.9 + - - -
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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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225A CYS* 4.8 1.8 - - - +
226A LYS* 1.3 76.7 - - - +
228A LEU* 1.3 61.4 + - - +
229A VAL* 3.6 25.8 + - + -
255A ILE* 3.8 17.7 - - + -
277A ILE* 3.0 31.4 - - + -
278A GLN 2.8 43.4 + - - +
279A ILE* 3.6 9.3 - - + +
280A GLU* 2.9 25.5 + - - -
281A GLN 3.7 1.7 + - - -
332A VAL* 4.9 0.7 - - - -
334A LEU* 3.1 21.5 - - + +
335A ALA* 5.2 0.2 - - - -
336A HIS* 4.7 13.5 - - + -
407A LEU* 4.6 13.7 - - + -
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Residues in contact with LEU 228 (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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226A LYS 4.3 0.2 + - - -
227A LEU* 1.3 72.4 - - - +
229A VAL* 1.3 60.0 + - - +
230A VAL* 3.9 10.7 - - + +
280A GLU* 5.3 0.4 - - - -
281A GLN* 3.7 28.3 - - + +
283A ARG* 3.6 27.8 - - + -
325A ILE* 3.6 36.3 - - + -
328A GLU* 4.0 21.8 - - + +
332A VAL* 4.0 22.4 - - + +
334A LEU 2.8 9.0 + - - +
335A ALA* 3.2 10.2 - - + -
336A HIS* 2.8 27.0 + - - +
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Residues in contact with VAL 229 (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* 3.6 30.9 + - + +
228A LEU* 1.3 71.7 - - - +
230A VAL* 1.3 64.6 + - - +
251A LEU* 3.9 27.4 - - + -
255A ILE* 4.3 6.5 - - + -
279A ILE* 4.0 17.3 - - + -
281A GLN 3.0 11.6 + - - +
282A ILE* 3.3 13.2 - - + -
283A ARG* 2.8 27.0 + - - +
336A HIS* 3.7 3.8 - - + +
338A PHE* 3.6 32.1 - - + -
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Residues in contact with VAL 230 (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 LEU* 3.9 25.6 - - + -
229A VAL* 1.3 82.9 - - - +
231A ALA* 1.3 64.5 + - - +
283A ARG* 3.3 19.1 - - + +
285A LEU* 4.2 7.0 - - + -
298A TYR* 3.6 24.2 - - + +
321A PHE* 4.1 20.4 - - + -
325A ILE* 4.3 6.3 - - + -
336A HIS 2.9 13.6 + - - +
337A LEU* 3.5 12.9 - - + +
338A PHE* 2.7 34.3 + - - +
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Residues in contact with ALA 231 (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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230A VAL* 1.3 75.8 - - - +
232A ASP* 1.3 63.9 + - - +
235A PHE* 4.0 17.5 - - + -
236A TYR 5.1 0.2 - - - +
247A THR* 4.0 10.8 - - + -
251A LEU* 3.9 25.3 - - + +
283A ARG 2.8 12.8 + - - +
284A ILE* 4.3 7.1 - - + +
285A LEU* 2.8 30.7 + - - +
338A PHE* 3.6 6.3 - - + -
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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