Contacts of the strand formed by residues 414 - 431 (chain A) in PDB entry 5KFU
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 GLU 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A ALA* 3.6 12.3 - - - +
333A THR* 4.4 9.9 - - - +
334A ARG 4.6 0.2 - - - -
407A ASN* 2.8 21.7 + - - -
409A SER* 3.4 17.3 + - - +
411A ILE* 3.4 33.3 + - + +
412A GLN 3.3 1.1 - - - +
413A THR* 1.3 99.3 - - - +
415A TRP* 1.3 61.0 + - - +
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Residues in contact with TRP 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU 4.0 4.9 - - - +
332A ALA* 2.7 38.6 + - - +
333A THR 4.1 4.7 - - - +
334A ARG* 4.3 12.1 - - + -
337A VAL* 3.8 18.6 - - + -
370A ILE* 5.2 0.4 - - + -
372A VAL* 5.5 0.6 - - - +
400A PHE* 3.5 28.5 - + - -
403A ILE* 3.9 29.8 - - + -
404A LYS* 3.8 23.8 - - + -
406A CYS* 4.8 4.8 + - + +
407A ASN* 3.3 37.3 - - + +
409A SER* 4.4 0.4 - - - -
414A GLU* 1.3 75.0 - - - +
416A SER* 1.3 64.2 + - - +
417A PRO 3.3 18.0 + - - -
418A PRO* 3.7 9.7 - - - +
419A LEU* 3.3 38.2 - - + +
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Residues in contact with SER 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A CYS 3.7 0.5 - - - +
407A ASN* 2.9 10.5 + - - +
408A THR* 2.7 39.2 + - - -
409A SER* 3.0 32.9 + - - -
415A TRP* 1.3 76.1 - - - +
417A PRO* 1.3 68.1 - - - +
418A PRO* 4.8 2.0 - - - -
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Residues in contact with PRO 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A VAL* 3.6 31.2 - - + -
373A GLN* 4.1 17.3 - - + +
406A CYS 4.6 3.6 - - - +
408A THR* 3.8 17.7 - - + +
415A TRP* 3.3 13.0 + - - -
416A SER* 1.3 88.6 - - - +
418A PRO* 1.3 78.4 - - + +
419A LEU* 4.0 3.5 - - - +
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Residues in contact with PRO 418 (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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330A ALA* 3.5 25.4 - - + +
331A LEU 3.3 17.0 - - - +
332A ALA* 4.3 15.0 - - + -
372A VAL* 3.7 1.2 - - - -
373A GLN* 3.0 48.2 + - + +
415A TRP 3.7 7.6 - - - +
416A SER* 4.4 2.7 - - - -
417A PRO* 1.3 88.1 - - + +
419A LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 3.7 5.8 - - - +
330A ALA* 3.3 4.9 - - - -
331A LEU* 3.0 41.4 + - + +
337A VAL* 3.9 18.2 - - + -
370A ILE* 4.0 19.1 - - + -
371A ARG 3.4 13.7 - - - +
372A VAL* 3.8 19.1 - - + -
403A ILE* 4.4 1.1 - - + -
415A TRP* 3.3 45.1 - - + +
417A PRO 4.0 0.4 - - - +
418A PRO* 1.3 71.4 - - - +
420A THR* 1.3 59.3 + - - +
421A MET 3.5 7.2 - - - +
422A LEU* 3.8 23.8 - - + -
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Residues in contact with THR 420 (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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324A ASN* 3.4 7.4 - - - +
325A PHE* 2.8 43.6 + - - +
326A PRO* 5.1 4.7 - - + +
327A GLY 5.2 0.9 - - - +
330A ALA* 3.9 12.6 - - + -
371A ARG* 2.9 38.8 + - - +
372A VAL 3.8 4.0 + - - -
373A GLN* 3.9 31.0 - - + +
418A PRO 3.7 0.2 + - - -
419A LEU* 1.3 75.5 - - - +
421A MET* 1.3 60.1 + - - +
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Residues in contact with MET 421 (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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322A SER* 5.2 3.6 - - - -
323A LYS 3.3 10.8 - - - +
324A ASN* 3.5 20.0 - - - +
325A PHE* 4.1 2.1 - - - -
369A SER* 3.8 17.5 - - - +
370A ILE* 3.2 31.1 - - - +
371A ARG* 3.1 33.2 + - + +
378A LEU* 3.5 29.8 - - + +
379A SER* 4.2 2.9 - - - -
419A LEU* 3.5 3.0 - - - +
420A THR* 1.3 81.4 - - - +
422A LEU* 1.3 87.6 + - - +
423A PHE* 3.5 15.7 - - + -
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Residues in contact with LEU 422 (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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322A SER* 3.3 2.1 - - - -
323A LYS 2.9 31.9 + - - -
325A PHE* 3.8 11.2 - - + -
331A LEU* 3.8 12.6 - - + -
337A VAL* 4.1 2.7 - - + +
340A TRP* 3.6 32.3 - - + -
341A LEU* 3.9 34.1 - - + +
344A LEU* 3.6 14.8 - - + +
369A SER 3.6 2.5 - - - -
370A ILE* 3.7 19.1 - - + -
403A ILE* 4.8 2.5 - - + -
419A LEU* 3.8 21.1 - - + -
421A MET* 1.3 86.0 - - - +
423A PHE* 1.3 62.8 + - - +
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Residues in contact with PHE 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLY* 4.0 9.0 - - - -
321A CYS 3.0 26.7 - - - -
322A SER* 3.5 15.0 - - - -
341A LEU* 5.8 0.6 - - - +
344A LEU* 4.1 0.8 - - - +
367A VAL 3.6 0.8 - - - +
368A VAL* 3.5 6.4 - - - +
369A SER* 2.9 44.8 + - - +
378A LEU* 5.6 7.0 - - + -
382A ARG* 3.8 30.1 - - - -
421A MET* 3.5 13.7 - - + -
422A LEU* 1.3 77.2 - - - +
424A LEU* 1.3 84.1 + - - +
425A CYS* 4.1 16.6 - - + -
6T T 4.8 25.8 - + + -
7T G 5.5 10.3 - + - -
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE 4.2 0.2 - - - +
320A GLY* 3.3 1.6 - - - -
321A CYS* 2.8 40.2 + - + +
341A LEU* 3.9 18.2 - - + +
344A LEU* 4.0 14.3 - - + +
345A ALA* 3.8 37.0 - - + +
348A LEU* 4.0 19.7 - - + +
366A LEU* 4.4 8.7 - - + -
367A VAL 3.4 1.1 - - - +
368A VAL* 3.8 17.3 - - + -
395A MET* 5.2 4.0 - - + +
396A SER* 5.3 0.4 - - - -
399A ALA* 3.7 30.1 - - + -
423A PHE* 1.3 84.0 - - - +
425A CYS* 1.3 61.0 + - - +
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Residues in contact with CYS 425 (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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318A THR* 3.6 31.6 - - - -
319A ILE 3.5 10.5 - - - -
320A GLY* 4.2 3.4 - - - -
348A LEU* 4.7 0.2 - - - -
365A GLN 3.7 0.5 - - - +
366A LEU* 3.5 7.9 - - - +
367A VAL* 2.7 53.2 + - + +
382A ARG* 4.8 10.8 - - - +
423A PHE* 4.1 19.5 - - + -
424A LEU* 1.3 76.0 - - - +
426A ALA* 1.3 62.4 - - - +
427A THR* 3.7 10.0 + - - -
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Residues in contact with ALA 426 (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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318A THR* 3.4 3.6 - - - -
319A ILE* 2.8 34.3 + - + +
348A LEU* 4.4 4.8 - - + +
352A LEU* 3.7 33.9 - - + -
363A ALA* 3.7 13.2 - - + -
365A GLN 3.4 4.7 - - - -
387A LEU* 3.8 13.7 - - + -
425A CYS* 1.3 69.7 - - - +
427A THR* 1.3 66.8 + - - +
429A PHE* 4.2 2.0 - - + -
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Residues in contact with THR 427 (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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317A LYS 4.4 2.9 - - - -
318A THR* 3.5 25.8 - - + -
363A ALA* 3.7 3.7 - - - +
364A THR 3.1 18.2 + - - -
365A GLN* 2.9 43.9 + - - +
367A VAL* 4.1 10.8 - - + +
382A ARG* 6.1 0.9 - - - +
425A CYS* 3.7 18.2 - - - +
426A ALA* 1.3 81.0 - - - +
428A LYS* 1.3 70.0 + - - +
429A PHE* 3.6 3.6 - - - -
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Residues in contact with LYS 428 (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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317A LYS 4.7 2.0 + - - -
364A THR* 2.9 35.9 + - - +
365A GLN* 3.3 38.9 + - + +
427A THR* 1.3 82.9 - - - +
429A PHE* 1.3 67.3 + - - +
430A SER* 4.2 1.2 + - - -
1P A 4.6 10.7 - - - -
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Residues in contact with PHE 429 (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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317A LYS* 3.4 32.5 - - - -
318A THR* 4.1 7.4 - - - -
319A ILE* 4.1 22.9 - - + -
352A LEU* 4.5 3.1 - - + -
355A ASP* 3.5 20.0 - - - -
361A ARG* 3.6 42.4 - - + +
362A VAL 3.2 9.0 - - - -
363A ALA* 3.4 35.2 - - + -
390A TYR* 4.4 4.5 - - - -
426A ALA 4.2 7.2 - - - -
427A THR* 4.5 0.4 - - - -
428A LYS* 1.3 79.9 - - - +
430A SER* 1.3 61.7 + - - +
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Residues in contact with SER 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 3.2 4.6 - - - -
362A VAL* 2.8 39.1 + - - +
364A THR* 3.9 17.3 - - - +
428A LYS 4.2 0.9 + - - -
429A PHE* 1.3 76.1 + - - +
431A ALA* 1.3 69.4 + - - +
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Residues in contact with ALA 431 (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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360A ASP 3.6 9.4 - - - +
361A ARG* 4.3 1.8 - - - +
362A VAL* 4.7 1.7 - - - +
430A SER* 1.3 80.3 - - - +
432A SER* 1.3 60.4 + - - +
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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