Contacts of the strand formed by residues 368 - 383 (chain A) in PDB entry 2CW9
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 ARG 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A GLU* 5.5 2.9 - - - +
332A ILE* 4.0 6.1 - - - -
366A HIS 3.8 9.8 + - - +
367A SER* 1.3 81.2 - - - +
369A ILE* 1.3 66.8 + - - +
370A LEU 3.9 0.3 + - - -
397A LEU* 3.7 2.4 - - - +
398A VAL* 3.0 41.3 + - + +
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Residues in contact with ILE 369 (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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325A PRO* 4.5 4.7 - - + +
328A LEU* 3.8 31.2 - - + -
329A GLU* 3.9 31.5 + - + +
332A ILE* 3.7 9.2 - - + -
368A ARG* 1.3 76.0 - - - +
370A LEU* 1.3 64.7 + - - +
371A ASP* 3.8 13.2 - - - +
372A ILE* 4.0 26.9 - - + -
395A ALA* 5.4 0.2 - - + -
396A GLN 4.0 4.5 - - - +
397A LEU* 3.3 22.7 - - + -
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Residues in contact with LEU 370 (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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368A ARG 3.9 1.6 + - - -
369A ILE* 1.3 74.3 - - - +
371A ASP* 1.3 66.6 + - + +
396A GLN* 2.8 48.1 + - + +
397A LEU* 4.8 1.1 - - - +
398A VAL* 5.3 9.0 - - + -
416A VAL* 4.2 18.2 - - + -
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Residues in contact with ASP 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 3.7 2.9 - - - +
370A LEU* 1.3 85.4 - - + +
372A ILE* 1.3 88.2 + - - +
373A ASP* 4.0 17.5 - - - +
395A ALA* 3.3 4.5 - - - +
396A GLN* 3.0 45.9 + - + +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU* 4.2 21.2 - - + +
324A ILE* 3.7 34.3 - - + -
325A PRO* 4.2 23.8 - - + -
328A LEU* 4.3 6.7 - - + -
369A ILE* 4.0 20.2 - - + -
371A ASP* 1.3 89.1 + - - +
373A ASP* 1.3 69.8 + - - +
375A VAL* 4.6 13.7 - - + -
393A PHE* 4.3 11.2 - - + -
394A GLN 3.6 3.6 - - - -
395A ALA* 4.3 10.1 - - + -
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Residues in contact with ASP 373 (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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273A ILE* 5.8 3.6 - - - +
276A SER* 5.0 2.9 + - - -
320A GLU* 5.0 4.5 - - - +
371A ASP* 4.0 14.0 - - - +
372A ILE* 1.3 78.7 - - - +
374A ASN* 1.3 83.1 + - - +
375A VAL* 3.3 8.2 + - - +
393A PHE* 3.7 3.1 - - - +
394A GLN* 2.8 48.5 + - - +
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Residues in contact with ASN 374 (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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273A ILE* 5.1 1.2 + - - +
276A SER* 3.6 12.0 + - - -
277A ARG* 3.6 42.8 - - - +
280A THR* 3.5 27.7 + - - +
320A GLU* 6.0 0.2 - - - -
373A ASP* 1.3 102.9 - - - +
375A VAL* 1.3 63.2 + - - +
376A ASP* 3.5 1.8 + - - -
392A THR 3.5 8.8 - - - +
393A PHE* 3.5 4.2 - - - -
394A GLN* 3.5 23.0 + - + +
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 4.0 41.0 - - + +
319A CYS* 4.4 4.3 - - + -
320A GLU* 3.8 39.2 + - + +
324A ILE* 4.1 20.0 - - + -
372A ILE* 4.6 3.8 - - + -
373A ASP 4.3 5.8 - - - +
374A ASN* 1.3 76.4 - - - +
376A ASP* 1.3 64.7 + - - +
391A ILE* 4.9 3.8 - - + -
392A THR 3.4 9.0 - - - +
393A PHE* 4.0 14.1 - - + -
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Residues in contact with ASP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 4.0 24.3 - - + +
281A ASP* 4.9 6.9 - - - +
284A THR* 3.2 24.8 + - - +
316A LEU* 3.9 16.3 - - - +
374A ASN 4.3 0.4 - - - +
375A VAL* 1.3 77.5 - - - +
377A LEU* 1.3 76.9 + - - +
378A ALA 3.9 0.2 - - - -
391A ILE* 3.2 7.4 - - - +
392A THR* 2.9 35.3 + - - +
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Residues in contact with LEU 377 (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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284A THR* 4.3 5.4 - - - +
296A MSE 3.7 30.9 - - + +
300A LEU* 6.3 0.2 - - + -
312A LYS* 4.1 35.4 - - + -
315A PHE* 5.0 5.6 - - + -
316A LEU* 4.0 18.1 - - + +
376A ASP* 1.3 89.0 + - - +
378A ALA* 1.3 60.1 + - - +
379A MSE 4.1 1.8 - - - +
389A LEU* 3.8 30.1 - - + -
390A ILE 3.6 16.6 - - - +
391A ILE* 4.2 10.1 - - + -
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Residues in contact with ALA 378 (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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284A THR* 4.2 27.6 - - - +
287A LEU* 3.6 36.4 - - + +
288A GLY* 5.3 1.9 + - - -
292A SER* 5.9 0.9 - - - -
296A MSE 4.6 2.7 - - - +
376A ASP 3.8 1.4 + - - -
377A LEU* 1.3 73.9 - - - +
379A MSE 1.3 62.2 + - - +
390A ILE* 2.8 20.2 + - + +
392A THR* 4.0 14.8 - - + -
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Residues in contact with MSE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.5 39.3 - - + +
292A SER* 5.4 10.3 - - - +
295A GLU* 5.0 7.6 - - - +
296A MSE 3.4 18.9 - - - +
377A LEU* 3.9 1.4 - - - +
378A ALA* 1.3 81.4 - - - +
380A GLY* 1.3 74.8 + - - +
381A LYS* 4.2 16.6 - - + -
389A LEU* 3.8 1.9 - - - -
390A ILE* 2.9 60.3 + - + +
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Residues in contact with GLY 380 (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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292A SER 5.6 1.2 + - - +
295A GLU* 3.9 20.8 - - - +
296A MSE 3.7 20.5 - - - +
299A VAL* 3.8 11.9 - - - -
379A MSE 1.3 86.5 - - - +
381A LYS* 1.3 64.5 + - - +
388A VAL 3.3 10.5 - - - -
389A LEU* 4.6 1.1 - - - -
390A ILE* 4.8 0.9 - - - -
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Residues in contact with LYS 381 (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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295A GLU* 5.2 5.6 - - - +
299A VAL* 3.4 13.2 - - - +
379A MSE 4.2 19.5 - - + -
380A GLY* 1.3 76.0 - - - +
382A MSE 1.3 57.5 + - - +
383A VAL* 4.0 19.8 - - + +
388A VAL* 2.7 69.6 + - + +
390A ILE* 4.3 13.2 - - + +
424A ALA* 5.1 6.0 - - - +
441A LEU* 5.2 4.5 - - - +
442A ASP* 5.8 3.0 + - - +
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Residues in contact with MSE 382 (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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298A GLU* 4.7 6.7 - - + +
299A VAL* 4.1 19.3 - - + +
302A GLU* 3.9 35.7 - - + +
381A LYS* 1.3 75.3 - - - +
383A VAL* 1.3 72.9 + - - +
386A GLY* 3.8 22.9 - - - -
387A PRO* 3.8 20.6 - - + -
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Residues in contact with VAL 383 (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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381A LYS* 4.0 20.2 - - + +
382A MSE 1.3 86.1 - - - +
384A GLU* 1.3 66.6 + - - +
385A GLN* 3.7 14.4 - - - +
386A GLY* 3.0 40.8 + - - +
388A VAL* 3.6 24.0 - - + -
426A CYS* 3.9 6.7 - - - -
441A LEU* 4.2 10.8 - - + -
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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