Contacts of the strand formed by residues 283 - 290 (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 ASP 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ALA 4.0 0.5 - - - +
279A LEU* 3.8 1.9 - - - +
280A GLY* 3.0 27.9 + - - +
282A GLU* 1.3 90.2 - - - +
284A LEU* 1.3 59.9 + - - +
285A SER* 4.0 12.4 + - - +
359A TYR* 4.5 10.2 - - + -
360A LEU 3.5 7.8 - - - +
361A LYS* 4.8 8.5 + - - +
362A ALA* 4.0 3.6 - - - -
295B VAL 4.3 0.9 - - - +
296B PRO* 3.3 5.1 - - - +
297B LEU* 2.7 42.6 + - - +
298B ARG 5.2 0.9 + - - -
350B GLU* 2.8 29.0 + - + +
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Residues in contact with LEU 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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197A VAL* 3.9 18.8 - - + -
236A ILE* 3.6 23.1 - - + -
237A HIS 4.2 0.7 - - - +
238A MET* 3.8 34.8 - - + -
277A VAL* 3.9 16.6 - - + -
278A ALA 3.4 9.2 - - - +
279A LEU* 3.8 16.2 - - + -
283A ASP* 1.3 72.1 - - - +
285A SER* 1.3 62.0 + - - +
286A ILE* 4.1 12.8 - - + -
359A TYR* 3.7 0.5 - - - -
360A LEU* 2.8 59.6 + - + +
362A ALA* 4.1 6.6 - - - +
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Residues in contact with SER 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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276A MET 3.6 0.5 - - - +
277A VAL* 3.4 4.2 - - - +
278A ALA* 2.8 38.2 + - - +
283A ASP* 4.0 11.1 + - - +
284A LEU* 1.3 73.2 - - - +
286A ILE* 1.3 63.7 + - - +
287A LYS 4.1 0.4 - - - -
357A VAL* 4.5 1.6 - - - -
358A ILE 3.4 4.3 - - - -
359A TYR* 3.5 26.7 - - - -
349B MET* 3.9 37.6 - - - -
350B GLU 4.1 2.3 + - - -
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Residues in contact with ILE 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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197A VAL* 3.8 22.0 - - + -
201A VAL* 4.5 2.7 - - + -
245A LEU* 3.6 31.4 - - + -
249A LEU* 4.0 23.6 - - + -
275A ILE* 4.2 22.2 - - + -
276A MET 3.3 7.0 - - - +
277A VAL* 4.3 4.9 - - + -
284A LEU* 4.1 11.7 - - + -
285A SER* 1.3 78.1 - - - +
287A LYS* 1.3 61.7 + - - +
288A MET* 5.2 0.7 - - + +
356A ALA 3.5 1.7 - - - +
357A VAL* 3.2 4.9 - - - +
358A ILE* 2.9 44.4 + - + +
360A LEU* 3.8 15.3 - - + -
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Residues in contact with LYS 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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274A LYS 3.4 1.6 - - - +
275A ILE* 3.2 9.3 - - - +
276A MET* 2.8 43.0 + - + +
285A SER 4.1 0.6 - - - -
286A ILE* 1.3 73.7 - - - +
288A MET* 1.3 60.8 + - - +
289A SER* 3.8 20.9 - - - +
347A PHE* 4.4 9.2 - - + -
355A ASP* 3.5 29.6 + - + +
356A ALA 3.3 7.6 - - - +
357A VAL* 4.3 7.4 - - + +
349B MET* 3.2 42.1 - - + +
352B PHE* 4.9 6.3 - - - -
355B ASP* 4.1 21.4 + - - -
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Residues in contact with MET 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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249A LEU* 3.8 13.5 - - + +
252A LEU* 3.5 48.5 - - + +
253A PHE* 3.6 44.9 - - + +
256A ALA* 4.0 11.0 - - + -
273A ILE* 3.5 21.3 - - + -
274A LYS 3.4 3.1 - - - -
275A ILE* 3.7 12.1 - - + -
286A ILE* 4.0 1.4 + - + -
287A LYS* 1.3 73.2 - - - +
289A SER* 1.3 58.4 + - - +
290A ASP* 5.3 0.9 - - - +
354A THR 3.6 1.9 - - - +
355A ASP* 3.3 2.4 - - - -
356A ALA* 2.7 49.9 + - + +
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Residues in contact with SER 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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272A PRO 4.2 1.6 - - - +
273A ILE* 3.5 6.9 - - - +
274A LYS* 2.8 51.5 + - - +
287A LYS* 3.8 16.3 + - - +
288A MET* 1.3 74.1 - - - +
290A ASP* 1.3 61.2 + - - +
291A ARG* 5.2 1.6 + - - -
354A THR 3.4 4.0 - - - -
355A ASP* 2.8 26.1 + - - -
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Residues in contact with ASP 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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256A ALA* 3.4 38.3 - - + +
259A ALA* 4.6 4.4 - - - +
260A THR* 3.8 13.0 - - - +
272A PRO 4.9 4.3 - - - -
273A ILE* 4.5 4.7 - - + -
288A MET* 5.3 1.2 - - - +
289A SER* 1.3 76.4 - - - +
291A ARG* 1.3 64.1 + - - +
292A GLY* 3.0 18.6 + - - -
294A GLY 5.1 0.2 + - - -
352A PHE* 5.1 2.6 - - - -
353A GLY* 3.3 2.9 - - - -
354A THR* 2.9 51.6 + - - +
355A ASP* 5.3 0.2 - - - +
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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