Contacts of the strand formed by residues 427 - 448 (chain A) in PDB entry 5C58
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 ALA 427 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A SER 3.4 5.4 - - - +
414A ASP* 3.9 23.1 - - - +
426A TYR* 1.3 72.8 - - - +
428A THR* 1.3 61.5 + - - +
469A ASP* 4.5 0.5 - - - +
470A SER* 3.3 13.4 + - - -
471A SER* 3.3 21.5 + - - +
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Residues in contact with THR 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LYS* 4.5 15.8 + - - +
411A ASP 3.8 0.5 - - - +
412A ASP* 3.7 3.8 - - - +
413A SER* 3.0 47.4 + - - +
415A THR* 5.6 3.4 - - + -
426A TYR* 3.9 11.1 + - + +
427A ALA* 1.3 74.7 - - - +
429A ARG* 1.3 68.9 + - - +
430A THR* 4.4 7.8 - - - +
468A SER* 4.9 0.7 + - - -
469A ASP 3.9 4.6 + - - -
470A SER* 3.7 15.8 - - - -
475A MET* 3.9 30.5 + - + +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN* 3.2 35.1 - - + +
411A ASP 3.3 7.0 - - - +
412A ASP* 3.3 20.9 + - - +
427A ALA 5.6 0.4 - - - +
428A THR* 1.3 78.5 + - - +
430A THR* 1.3 67.7 + - - +
431A ARG* 5.0 4.9 - - + +
467A THR 5.7 0.4 - - - +
468A SER* 3.3 9.9 + - - -
469A ASP* 2.9 61.6 + - - +
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Residues in contact with THR 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 3.8 18.0 - - - -
185A GLN 5.1 1.6 - - - -
186A LYS* 3.9 26.4 - - + +
410A GLN* 3.5 0.7 - - - -
411A ASP* 2.7 52.3 + - - +
428A THR* 4.4 7.6 - - - +
429A ARG* 1.3 79.2 - - - +
431A ARG* 1.3 58.9 + - - +
467A THR 3.9 4.0 - - - -
468A SER* 4.0 11.2 - - - +
479A THR* 4.1 24.2 - - + +
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Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 5.0 0.7 - - - -
382A ARG* 5.0 5.8 - - - +
406A TYR* 3.8 3.2 + - - -
408A ASP* 2.7 39.5 + - - +
409A THR 3.5 3.8 - - - +
410A GLN* 3.5 35.5 + - + +
429A ARG* 5.1 5.6 - - + +
430A THR* 1.3 76.7 - - - +
432A LEU* 1.3 63.4 + - - +
433A ARG* 3.4 35.2 - - + +
465A LYS 3.7 0.9 - - - +
466A ALA* 3.7 1.7 - - - +
467A THR* 3.0 51.5 + - - +
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN* 3.2 48.0 - - + +
184A PHE* 3.6 19.6 - - + +
185A GLN 5.0 1.8 - - - +
407A VAL* 3.9 1.7 - - - +
408A ASP* 3.9 1.0 - - - -
409A THR* 3.0 32.9 + - - -
431A ARG* 1.3 73.9 - - - +
433A ARG* 1.3 66.6 + - - +
434A THR* 4.2 5.9 + - - +
464A ASP* 4.0 14.4 - - + +
465A LYS 3.3 31.9 - - - +
466A ALA* 3.7 15.7 - - + +
593A ILE* 4.6 4.0 - - + -
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Residues in contact with ARG 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 3.4 20.9 - - + +
407A VAL 3.2 4.5 - - - +
408A ASP* 3.5 16.4 - - - +
431A ARG* 3.4 42.4 - - - +
432A LEU* 1.3 74.5 - - - +
434A THR* 1.3 60.8 + - - +
435A TYR* 3.9 26.5 + - + +
463A TYR 3.3 3.6 - - - +
464A ASP* 3.5 1.7 - - - -
465A LYS* 3.0 60.4 + - + +
467A THR* 3.3 35.0 + - - +
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Residues in contact with THR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG* 4.2 6.8 + - + +
183A ASN* 3.9 20.5 + - - +
405A TYR* 4.2 20.1 - - + +
406A TYR* 3.2 9.2 - - - -
407A VAL* 2.8 54.1 + - - +
432A LEU* 4.3 6.2 + - - +
433A ARG* 1.3 74.9 - - - +
435A TYR* 1.3 63.1 + - - +
436A GLY 4.0 0.5 + - - -
462A TYR* 4.2 15.7 - - + -
463A TYR 3.6 3.1 - - - +
464A ASP* 3.2 23.0 + - - +
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Residues in contact with TYR 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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405A TYR 3.9 4.5 - - - +
406A TYR* 3.4 34.0 + + + -
433A ARG* 3.9 38.3 + - + -
434A THR* 1.3 72.9 - - - +
436A GLY* 1.3 58.5 + - - +
461A PHE* 3.8 5.4 - - + +
462A TYR* 3.2 3.7 - - - -
463A TYR* 2.8 65.6 + + + +
465A LYS* 4.4 15.7 - - + +
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Residues in contact with GLY 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 3.5 5.0 - - - +
405A TYR* 2.9 64.4 + - - +
434A THR 4.0 1.4 + - - -
435A TYR* 1.3 75.6 - - - +
437A ALA* 1.3 61.6 + - - +
461A PHE* 3.3 7.0 - - - -
462A TYR* 4.2 0.9 - - - -
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Residues in contact with ALA 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LYS 3.4 6.5 - - - +
404A LEU* 4.7 9.2 - - + +
405A TYR* 4.2 0.6 - - - -
436A GLY* 1.3 74.3 - - - +
438A GLN* 1.3 64.7 + - - +
459A LEU* 5.3 4.5 - - + +
460A GLU* 3.4 4.2 - - - +
461A PHE* 2.8 49.1 + - + +
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Residues in contact with GLN 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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179A GLY* 3.1 29.7 + - - -
216A MET* 3.7 33.4 - - + +
217A GLY* 5.6 1.8 - - - -
401A GLN 4.8 0.2 - - - -
402A ALA* 3.3 5.0 - - - +
403A LYS* 2.8 61.5 + - + +
404A LEU* 5.9 0.2 - - - +
405A TYR* 3.8 16.6 + - + -
437A ALA* 1.3 81.4 - - - +
439A ALA* 1.3 64.2 + - - +
459A LEU* 3.8 5.8 - - - -
460A GLU* 3.4 20.7 + - + -
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A MET* 4.7 1.3 - - - +
400A PHE* 4.3 17.9 - - + -
401A GLN 3.7 7.9 - - - -
402A ALA* 4.6 2.5 - - + -
438A GLN* 1.3 76.8 - - - +
440A GLN* 1.3 64.3 + - - +
458A GLY* 4.1 0.9 - - - -
459A LEU* 2.7 60.1 + - + +
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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
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216A MET* 3.6 32.6 - - - +
399A ASP 4.1 0.9 - - - +
400A PHE* 3.3 11.5 - - - -
401A GLN* 2.9 66.1 + - + +
439A ALA* 1.3 78.6 - - - +
441A ASN* 1.3 60.7 + - - +
442A THR* 5.0 4.8 - - + +
456A ASN* 3.1 31.2 + - - +
457A TYR 3.4 11.0 - - - +
458A GLY* 3.8 6.1 - - - -
490A PHE* 3.8 10.7 - - + -
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Residues in contact with ASN 441 (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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397A TRP* 3.0 24.3 + - - -
398A LEU* 3.4 26.0 - - - +
399A ASP 3.5 10.5 + - - +
400A PHE* 3.6 16.8 - - + +
440A GLN* 1.3 74.1 - - - +
442A THR* 1.3 83.9 + - - +
443A SER 3.7 0.6 - - - +
455A ALA 3.7 0.7 - - - +
456A ASN* 3.2 4.2 - - - +
457A TYR* 2.8 63.9 + - + +
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Residues in contact with THR 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP 3.7 6.4 - - - +
399A ASP* 2.7 46.8 + - - +
440A GLN* 5.0 6.3 - - + +
441A ASN* 1.3 79.6 + - - +
443A SER* 1.3 60.5 + - - +
444A ARG* 3.6 17.2 + - - +
454A ARG* 5.1 7.6 - - - +
455A ALA 3.2 7.6 - - - -
456A ASN* 3.3 32.3 - - + +
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP 3.6 4.5 - - - -
397A TRP* 3.7 28.0 - - - +
441A ASN* 3.7 1.8 - - - +
442A THR* 1.3 72.5 - - - +
444A ARG* 1.3 61.5 + - - +
445A PHE* 4.2 9.4 - - - -
454A ARG* 3.7 0.5 - - - -
455A ALA* 2.8 55.3 + - - +
457A TYR* 3.5 18.9 + - - -
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Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP* 3.1 43.8 + - + +
397A TRP* 4.6 0.5 + - - -
399A ASP* 3.2 32.3 + - - +
442A THR* 3.6 20.8 + - - +
443A SER* 1.3 74.4 - - - +
445A PHE* 1.3 64.4 + - - +
453A PHE 3.8 7.4 - - - +
454A ARG* 3.6 40.3 - - + +
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Residues in contact with PHE 445 (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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396A ASP* 5.7 1.1 - - - -
443A SER* 4.2 12.8 - - - -
444A ARG* 1.3 78.9 - - - +
446A SER* 1.3 63.4 + - - +
447A LEU* 3.5 30.7 - - + -
452A ASP* 4.0 0.2 - - - -
453A PHE* 2.9 58.6 + + + +
455A ALA* 4.4 21.5 - - + -
493A LEU* 4.6 7.2 - - + -
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Residues in contact with SER 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PHE* 1.3 78.3 + - - +
447A LEU* 1.3 64.8 + - - +
448A ALA 4.3 8.1 - - - -
449A PRO* 6.0 0.4 - - - -
451A HIS 3.5 10.5 - - - -
452A ASP* 2.6 26.8 + - - +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PHE* 3.5 35.4 - - + -
446A SER* 1.3 73.1 - - - +
448A ALA* 1.3 63.2 + - + +
451A HIS* 3.5 8.6 + - + +
453A PHE* 3.5 26.0 - - + -
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A SER* 3.5 8.0 - - - -
447A LEU* 1.3 83.0 - - + +
449A PRO* 1.3 71.4 - - + +
450A GLY 3.1 0.7 + - - -
451A HIS* 2.8 48.3 + - + +
452A ASP* 4.5 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
------------------------------------------------------------
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