Contacts of the strand formed by residues 353 - 361 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B ASP* 3.3 17.0 - - - -
293B GLY 3.9 0.9 - - - -
294B GLY* 3.4 15.8 - - - +
348B SER* 3.3 0.9 - - - -
349B MET* 2.7 35.8 + - - +
352B PHE* 1.3 87.6 - - - +
354B THR* 1.3 64.0 + - - -
355B ASP* 5.1 1.9 - - - +
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Residues in contact with THR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B MET 3.6 1.7 - - - +
289B SER* 3.5 1.0 - - - -
290B ASP* 2.9 53.6 + - - +
292B GLY 5.9 0.2 - - - -
294B GLY* 3.9 13.5 - - - +
295B VAL* 4.7 8.1 - - + +
300B ILE* 5.8 1.6 - - + -
346B LEU* 4.7 11.1 - - - +
347B PHE 3.8 1.4 + - - -
348B SER* 3.1 28.7 - - - +
353B GLY* 1.3 75.9 - - - -
355B ASP* 1.3 73.3 + - - +
356B ALA* 5.1 1.6 - - - +
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Residues in contact with ASP 355 (chain B).
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* 4.1 21.8 + - - -
347A PHE* 4.2 19.7 - - + -
355A ASP* 4.3 2.9 - - - +
287B LYS* 3.3 24.4 + - + +
288B MET 3.2 4.3 - - - +
289B SER* 2.9 28.6 + - - -
290B ASP 4.8 1.4 + - - +
345B GLN 4.1 0.2 - - - +
346B LEU* 3.5 2.6 - - - -
347B PHE* 2.9 39.7 + - - +
349B MET* 5.8 0.5 - - - +
352B PHE* 5.7 3.6 - - - -
353B GLY 5.1 1.2 - - - +
354B THR* 1.3 83.6 + - - +
356B ALA* 1.3 60.0 + - - +
357B VAL* 4.9 1.1 - - + -
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LEU* 3.9 28.9 - - + +
286B ILE 3.5 1.4 - - - +
287B LYS* 3.2 2.3 - - - -
288B MET* 2.7 48.4 + - + +
344B LEU* 4.8 0.4 - - + -
345B GLN 3.5 4.9 - - - -
346B LEU* 3.5 21.5 - - + -
354B THR* 5.1 2.2 - - - +
355B ASP* 1.3 73.4 - - - +
357B VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A PHE* 4.0 28.3 - - + -
349A MET* 4.7 5.8 - - + -
285B SER* 4.5 4.0 - - - -
286B ILE 3.3 15.0 - - - +
287B LYS* 4.0 19.1 - - + +
343B ASP 3.8 0.3 - - - +
344B LEU* 3.2 6.7 - - - +
345B GLN 2.8 38.9 + - - +
347B PHE* 4.5 5.2 - - + -
356B ALA* 1.3 80.5 - - - +
358B ILE* 1.3 69.4 + - - +
359B TYR* 3.5 40.0 + - + +
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Residues in contact with ILE 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B LEU* 4.7 3.8 - - + -
248B MET* 3.8 36.3 - - + -
249B LEU* 3.9 24.7 - - + -
252B LEU* 3.8 25.4 - - + -
284B LEU 3.7 0.9 - - - +
285B SER* 3.4 4.5 - - - -
286B ILE* 2.8 46.0 + - + +
337B ALA* 4.6 0.2 - - + -
343B ASP 3.5 6.3 - - - +
344B LEU* 4.3 13.0 - - + -
356B ALA 4.2 0.2 - - - -
357B VAL* 1.3 76.3 - - - +
359B TYR* 1.3 62.5 + - - +
360B LEU* 3.6 33.4 - - + -
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Residues in contact with TYR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A LEU* 3.9 39.6 - - + +
347A PHE* 3.4 24.9 - - - +
348A SER 2.9 31.0 + - - -
283B ASP* 4.4 16.6 - - - +
284B LEU 3.8 1.6 - - - -
285B SER* 3.4 22.0 - - - -
342B GLY* 3.1 6.2 - - - -
343B ASP* 2.8 41.7 + - + +
345B GLN* 3.7 24.8 + - + -
357B VAL* 3.5 32.0 - - + +
358B ILE* 1.3 73.2 - - - +
360B LEU* 1.3 68.3 - - - +
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B MET* 3.6 39.5 - - + -
240B TYR* 3.5 31.6 - - + +
245B LEU* 4.0 23.6 - - + -
248B MET* 4.2 6.3 - - + -
283B ASP* 3.4 8.9 - - - +
284B LEU* 2.8 38.3 + - + +
286B ILE* 4.5 8.1 - - + -
337B ALA* 4.7 8.3 - - - +
342B GLY* 4.5 4.3 - - - -
358B ILE* 3.6 20.4 - - + -
359B TYR* 1.3 84.1 - - - +
361B LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ARG* 4.9 11.5 - - - +
238B MET* 3.5 19.4 - - - +
239B VAL 5.4 0.2 - - - +
240B TYR* 5.5 1.7 - - - -
282B GLU* 3.7 31.4 + - + +
283B ASP* 5.1 5.9 + - - +
284B LEU 4.5 0.4 - - - -
340B PHE 3.7 21.8 + - - +
341B GLN* 3.6 29.2 - - - +
342B GLY* 5.0 0.8 - - - -
360B LEU* 1.3 74.6 - - - +
362B ALA* 1.3 63.4 + - - +
363B LEU 3.6 8.2 + - - +
366B ASP* 3.8 27.9 - - + +
367B SER* 3.6 22.8 + - - +
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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