Contacts of the strand formed by residues 353 - 361 (chain A) in PDB entry 3CRK
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 GLY 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A ASP* 3.3 13.9 - - - -
292A GLY 4.0 1.3 - - - -
293A GLY 3.8 3.6 - - - -
294A GLY* 3.4 15.7 - - - +
348A SER* 3.4 0.7 + - - -
349A MET* 2.8 35.2 + - - +
352A PHE* 1.3 85.5 - - - +
354A THR* 1.3 59.6 + - - -
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Residues in contact with THR 354 (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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288A MET 3.6 1.2 - - - +
289A SER* 3.4 2.1 - - - -
290A ASP* 2.9 50.8 + - - +
294A GLY* 3.7 8.0 - - - -
295A VAL* 4.4 5.1 + - + +
300A ILE* 5.5 2.0 - - + -
346A LEU* 4.5 19.3 - - + -
347A PHE 3.8 10.8 - - - +
348A SER* 2.8 25.7 + - - +
353A GLY* 1.3 73.4 - - - -
355A ASP* 1.3 77.5 + - - +
356A ALA* 4.1 1.6 - - + +
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Residues in contact with ASP 355 (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 LYS* 3.5 19.5 + - + +
288A MET 3.3 2.5 - - - -
289A SER* 2.8 32.1 + - - -
290A ASP 5.3 0.2 - - - +
346A LEU* 3.6 2.3 - - - -
347A PHE* 2.9 78.6 + - + +
354A THR* 1.3 77.8 - - - +
356A ALA* 1.3 60.5 + - - +
357A VAL 4.2 0.2 - - - -
287B LYS* 4.0 19.7 + - - -
355B ASP* 4.3 1.6 - - - +
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Residues in contact with ALA 356 (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 LEU* 4.0 28.9 - - + +
286A ILE 3.5 1.4 - - - +
287A LYS* 3.3 2.8 - - - -
288A MET* 2.7 49.5 + - + +
344A LEU* 5.1 0.2 - - + -
345A GLN 3.5 4.7 - - - -
346A LEU* 3.5 21.8 - - + -
354A THR* 4.1 1.3 - - + -
355A ASP* 1.3 73.2 - - - +
357A VAL* 1.3 61.4 - - - +
358A ILE 4.2 0.2 - - - -
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Residues in contact with VAL 357 (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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285A SER* 4.5 4.3 - - - -
286A ILE 3.2 14.6 - - - +
287A LYS* 4.3 11.4 - - + -
343A ASP 3.9 0.2 - - - +
344A LEU* 3.3 5.7 - - - +
345A GLN* 2.8 52.0 + - + +
347A PHE* 3.8 24.7 - - + -
356A ALA* 1.3 74.5 - - - +
358A ILE* 1.3 69.4 + - - +
359A TYR* 3.5 48.8 + - + +
347B PHE* 4.5 1.3 - - + -
349B MET* 4.8 5.2 - - + -
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Residues in contact with ILE 358 (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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245A LEU* 4.5 5.4 - - + -
248A MET* 3.9 38.8 - - + -
249A LEU* 3.9 25.4 - - + -
252A LEU* 3.8 31.0 - - + -
285A SER* 3.4 5.0 - - - -
286A ILE* 2.9 42.6 + - + +
337A ALA* 4.4 1.8 - - + -
343A ASP 3.6 7.9 - - - +
344A LEU* 4.1 10.8 - - + +
356A ALA 5.7 0.2 - - - +
357A VAL* 1.3 74.9 - - - +
359A TYR* 1.3 63.4 + - - +
360A LEU* 3.4 27.6 - - + +
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Residues in contact with TYR 359 (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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283A ASP* 4.5 8.7 - - - +
284A LEU 3.8 1.3 - - - -
285A SER* 3.5 20.9 - - - -
337A ALA* 4.5 2.4 - - - +
342A GLY* 3.0 7.3 - - - -
343A ASP* 2.8 39.5 + - + +
345A GLN* 3.7 25.1 + - - -
357A VAL* 3.5 42.4 - - + +
358A ILE* 1.3 75.0 - - - +
360A LEU* 1.3 63.5 + - - +
297B LEU* 3.8 47.2 - - + +
347B PHE* 3.8 9.7 - - - +
348B SER 2.8 39.7 + - - -
349B MET* 5.1 0.2 - - - +
350B GLU 5.8 0.2 - - - -
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Residues in contact with LEU 360 (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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238A MET* 3.5 39.9 - - + -
240A TYR* 4.2 24.2 - - + +
245A LEU* 4.1 20.9 - - + -
248A MET* 5.1 0.9 - - + -
283A ASP* 3.5 8.8 - - - +
284A LEU* 2.8 49.0 + - + +
286A ILE* 3.8 16.2 - - + -
337A ALA* 6.4 0.4 - - - -
342A GLY* 4.6 3.8 - - - -
358A ILE* 3.4 31.4 - - + +
359A TYR* 1.3 75.5 - - - +
361A LYS* 1.3 61.5 + - - +
362A ALA 3.5 0.2 + - - -
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Residues in contact with LYS 361 (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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238A MET* 3.5 19.6 - - - +
240A TYR* 5.9 1.2 - - - -
282A GLU* 3.8 29.2 + - + +
283A ASP* 4.8 7.9 + - - +
340A PHE 3.7 15.4 + - - +
341A GLN* 3.5 29.6 + - - +
342A GLY* 5.0 1.0 - - - -
360A LEU* 1.3 74.3 - - - +
362A ALA* 1.3 63.4 + - - +
363A LEU 3.5 7.8 + - - +
366A ASP* 3.7 33.8 - - + +
367A SER* 3.4 24.1 + - - +
297B LEU* 6.3 0.8 - - - +
298B ARG* 4.7 12.9 - - - +
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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