Contacts of the strand formed by residues 431 - 453 (chain A) in PDB entry 1QFG
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 SER 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A TYR* 3.3 12.8 + - - -
390A TRP* 2.1 41.9 + - - -
391A PHE 3.3 10.5 - - - -
392A GLY* 4.1 2.9 - - - -
393A TYR* 3.3 10.7 - - - -
426A LYS* 4.1 0.9 - - - +
427A ASP 3.0 14.1 + - - +
428A PRO* 3.6 17.0 - - - +
429A ALA 3.6 1.2 - - - -
430A ASN* 1.3 95.4 - - - +
432A GLY* 1.3 57.8 + - - +
433A PRO* 4.6 0.2 - - - +
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Residues in contact with GLY 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A TRP* 3.0 13.6 - - - -
391A PHE 2.8 34.0 + - - -
393A TYR* 3.0 17.9 + - - -
431A SER* 1.3 79.4 + - - +
433A PRO* 1.3 72.9 - - - +
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Residues in contact with PRO 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASN* 6.0 0.2 - - - +
389A ALA 3.5 7.6 - - - +
390A TRP* 3.1 34.5 - - + -
391A PHE* 5.6 0.2 - - - -
393A TYR* 4.9 2.8 + - - +
431A SER 4.6 0.2 - - - +
432A GLY* 1.3 86.8 - - - +
434A TYR* 1.3 61.7 - - - +
435A ARG* 4.9 7.2 - - + +
475A VAL* 4.0 30.9 - - + +
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Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 3.4 37.0 - + - -
387A ILE* 4.1 12.7 - - + +
388A ASN* 3.6 0.5 + - - -
389A ALA 2.7 41.0 + - - +
391A PHE* 3.6 37.9 - + + -
433A PRO* 1.3 74.1 - - - +
435A ARG* 1.3 59.8 + - - +
436A ILE* 3.4 39.6 - - + +
473A ASN* 5.8 1.3 - - - -
475A VAL* 4.5 0.7 - - - -
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Residues in contact with ARG 435 (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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387A ILE 3.3 7.2 - - - +
388A ASN* 3.0 36.6 - - - +
389A ALA 4.6 0.4 - - - +
433A PRO* 4.9 5.3 - - + +
434A TYR* 1.3 76.9 - - - +
436A ILE* 1.3 68.6 + - - +
473A ASN* 3.5 5.9 + - - +
474A ARG* 2.8 93.4 + - + +
475A VAL* 3.8 23.2 - - + +
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Residues in contact with ILE 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASN 4.0 0.4 - - - +
386A ASP* 3.6 1.6 - - - +
387A ILE* 2.6 47.5 + - + +
434A TYR* 3.4 49.1 - - + +
435A ARG* 1.3 84.2 - - - +
437A LEU* 1.3 61.2 + - - +
438A ASN* 3.5 31.9 - - - +
471A SER* 3.6 12.6 - - - +
472A LEU 3.3 6.5 - - - +
473A ASN* 3.8 27.8 - - + +
474A ARG* 5.0 2.9 - - - -
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 4.2 14.6 - - + +
385A ASN 3.4 6.3 - - - +
386A ASP* 3.0 35.4 - - + +
436A ILE* 1.3 74.2 - - - +
438A ASN* 1.3 65.1 + - - +
439A LYS* 4.0 25.0 - - + +
470A GLU 4.1 1.0 - - - +
471A SER* 3.8 1.4 - - - -
472A LEU* 2.9 57.4 + - + +
474A ARG* 4.3 9.2 - - - +
3B KDO 3.5 11.0 - - - +
4B GMH 4.4 18.6 - - - +
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Residues in contact with ASN 438 (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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114A ASN* 3.0 39.7 + - - +
115A PHE* 5.4 1.4 - - - +
383A MET* 4.5 5.6 - - + +
384A ARG* 3.4 4.7 - - - +
385A ASN* 2.8 34.5 + - + +
387A ILE* 3.6 16.4 - - - +
436A ILE* 3.5 10.8 - - - +
437A LEU* 1.3 74.5 - - - +
439A LYS* 1.3 64.5 + - - +
440A GLN* 5.9 0.9 - - + +
470A GLU 3.9 1.8 - - - +
471A SER* 2.9 29.8 + - - -
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A MET 3.2 8.3 - - - +
384A ARG* 3.2 36.0 - - + +
437A LEU* 4.0 21.1 - - + +
438A ASN* 1.3 79.3 - - - +
440A GLN* 1.3 67.7 + - - +
469A GLN* 3.5 5.7 - - - +
470A GLU* 3.0 58.9 + - + +
2000A DPO 3.1 31.8 + - - +
4B GMH 5.1 4.4 + - - -
9B KDO 4.9 2.2 + - - -
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Residues in contact with GLN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 5.7 0.2 + - - -
112A GLN* 3.4 16.3 + - - +
114A ASN* 4.4 3.2 - - - +
142A LYS* 2.4 36.9 + - - +
381A MET* 4.6 4.8 - - - +
382A ARG* 3.2 5.5 - - - +
383A MET* 2.9 54.2 + - + +
438A ASN* 5.9 1.3 - - + +
439A LYS* 1.3 78.3 - - - +
441A LYS* 1.3 62.3 + - - +
468A ASP 3.5 8.1 - - - +
469A GLN* 4.5 9.8 + - + +
1110A GOL 3.1 31.3 + - - -
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Residues in contact with LYS 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 5.3 2.3 - - - -
380A PHE* 3.9 17.7 - - + -
381A MET* 3.3 10.8 - - - +
382A ARG* 4.1 10.1 - - + -
440A GLN* 1.3 73.1 - - - +
442A GLN* 1.3 62.9 + - - +
443A THR* 5.6 0.2 - - - +
466A TRP 4.0 1.1 - - - +
467A ALA* 3.4 2.9 - - - +
468A ASP* 2.9 45.6 + - + +
1009A FTT 3.7 19.0 + - - +
1100A DDQ 4.1 26.3 - - - -
2000A DPO 2.4 46.7 + - - +
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Residues in contact with GLN 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR 3.9 9.3 + - - -
141A GLY* 3.4 1.0 - - - -
142A LYS* 2.5 54.1 + - - +
379A ASP* 4.4 3.0 + - - -
380A PHE* 3.4 6.4 - - - -
381A MET* 3.0 47.6 + - + +
441A LYS* 1.3 77.0 - - - +
443A THR* 1.3 64.0 + - - +
444A GLY 4.1 0.2 - - - -
463A ARG* 3.9 13.1 - - - +
465A ASP* 3.6 18.4 - - - +
466A TRP 2.9 10.5 - - - +
467A ALA* 4.2 9.4 - - + -
511A PHE* 3.6 6.2 - - - -
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Residues in contact with THR 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL* 5.9 3.4 - - + -
379A ASP 3.3 9.4 - - - +
380A PHE* 3.2 19.3 - - + -
441A LYS* 5.6 0.3 - - - +
442A GLN* 1.3 73.6 - - - +
444A GLY* 1.3 65.7 - - - +
445A VAL* 5.5 2.5 - - + -
465A ASP* 3.6 2.6 - - - -
466A TRP* 2.8 44.6 + - + +
1100A DDQ 3.1 38.9 - - + -
1103A GOL 4.1 21.3 + - - +
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Residues in contact with GLY 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL* 3.4 4.7 - - - +
379A ASP 2.8 33.6 + - - +
443A THR* 1.3 76.1 - - - +
445A VAL* 1.3 64.8 + - - +
446A TYR* 4.7 0.7 - - - -
463A ARG* 3.9 10.7 - - - +
464A TYR 3.1 12.1 - - - -
465A ASP* 3.3 15.1 + - - -
466A TRP* 4.8 1.1 - - - -
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY 3.4 6.3 - - - +
378A VAL* 3.6 22.7 - - + -
443A THR* 5.5 2.5 - - + -
444A GLY* 1.3 79.0 - - - +
446A TYR* 1.3 61.4 + - - +
447A VAL* 5.8 0.4 - - - -
463A ARG* 3.3 1.3 - - - +
464A TYR* 2.9 40.6 + - + +
466A TRP* 4.2 21.1 - - + -
1103A GOL 5.0 9.9 - - - +
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Residues in contact with TYR 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.6 7.1 + - + -
138A VAL 3.9 4.5 - - - +
139A LEU* 4.0 22.7 - - + -
358A ASP* 2.6 29.3 + - - -
360A GLN* 3.1 22.3 + - - +
375A LEU* 4.1 30.3 - - + -
376A THR* 3.5 0.3 - - - -
377A GLY* 3.0 52.8 + - - +
378A VAL 4.0 0.7 - - - -
379A ASP* 4.1 3.8 - - + -
444A GLY 4.6 0.7 - - - -
445A VAL* 1.3 78.1 - - - +
447A VAL* 1.3 73.8 + - - +
448A GLN* 5.9 0.4 - - + -
462A GLY 3.2 13.7 - - - +
463A ARG* 3.4 42.8 - - + -
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 4.2 16.8 - - + -
375A LEU 3.1 11.2 - - - +
376A THR* 4.4 12.6 - - + -
445A VAL 5.8 0.4 - - - -
446A TYR* 1.3 83.4 - - - +
448A GLN* 1.3 70.1 + - - +
449A ASP* 6.1 0.2 - - + -
461A GLY* 3.0 3.7 - - - -
462A GLY 2.9 33.2 + - - +
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Residues in contact with GLN 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 3.5 20.9 + - - +
39A THR* 4.7 0.2 - - - +
138A VAL* 6.2 2.2 - - + -
139A LEU* 4.2 9.8 - - + +
373A THR 3.6 1.3 + - - +
374A LEU* 3.3 6.0 - - - +
375A LEU* 2.4 86.7 + - + +
446A TYR* 5.9 0.4 - - + -
447A VAL* 1.3 81.0 - - - +
449A ASP* 1.3 68.7 + - - +
450A GLN* 4.5 11.3 + - - +
459A THR* 4.0 13.1 - - + +
460A LEU 3.4 14.4 - - - +
461A GLY* 3.8 5.2 - - - -
490A ARG* 3.3 25.0 + - - +
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Residues in contact with ASP 449 (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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365A PHE* 5.0 0.5 - - - -
372A HIS* 3.1 28.2 + - - +
373A THR 3.1 11.0 - - - +
374A LEU* 3.6 16.8 - - + +
447A VAL* 6.1 0.2 - - + -
448A GLN* 1.3 75.7 - - - +
450A GLN* 1.3 67.0 + - - +
451A ALA* 3.0 35.5 + - - +
458A VAL* 3.3 5.5 - - + +
459A THR* 3.4 1.9 - - - +
460A LEU* 2.9 36.8 + - + +
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Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 3.8 16.5 - - - +
39A THR* 2.9 32.5 + - - +
41A THR* 2.7 34.3 + - - +
45A LYS 4.7 5.3 + - - -
371A ASP 3.6 0.7 - - - +
372A HIS* 3.2 2.6 - - - -
373A THR* 2.6 54.0 + - - +
448A GLN* 4.5 7.4 + - - +
449A ASP* 1.3 76.4 - - - +
451A ALA* 1.3 59.7 + - - +
452A GLN 4.2 0.4 + - - -
457A LEU* 4.2 8.8 - - + +
458A VAL 3.4 5.2 - - - -
459A THR* 4.0 20.1 + - + +
1106A GOL 4.2 18.2 + - - +
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 4.5 8.1 - - + -
371A ASP 3.1 8.1 - - - +
372A HIS* 3.9 10.3 - - + +
449A ASP* 3.0 17.5 - - - +
450A GLN* 1.3 73.7 - - - +
452A GLN* 1.3 61.5 + - - +
453A TRP* 4.2 1.0 + - - +
456A VAL* 3.7 1.6 - - - +
457A LEU* 3.4 2.3 - - - +
458A VAL* 2.7 55.4 + - + +
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Residues in contact with GLN 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 3.0 37.4 + - - +
369A ASP 3.9 1.4 - - - +
370A ILE* 3.6 1.4 - - - -
371A ASP* 2.8 48.4 + - + +
450A GLN 4.2 0.4 - - - -
451A ALA* 1.3 74.7 - - - +
453A TRP* 1.3 61.4 + - - +
454A ASP 3.6 19.8 + - - +
455A LYS* 5.5 1.8 - - - +
456A VAL 3.0 18.8 - - - +
457A LEU* 4.2 11.1 - - + +
496A LEU* 5.2 5.6 - - - +
1106A GOL 3.9 12.7 + - - +
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Residues in contact with TRP 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP* 3.1 36.5 + - + +
370A ILE* 3.4 33.0 - - + -
451A ALA 4.2 1.1 + - - -
452A GLN* 1.3 74.0 - - - +
454A ASP* 1.3 84.4 + - - +
455A LYS 3.2 2.6 + - - -
456A VAL* 2.9 37.2 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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