Contacts of the strand formed by residues 559 - 578 (chain A) in PDB entry 4QDR
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 ASP 559 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A PRO 5.7 0.5 - - - +
403A LEU* 4.9 1.1 - - - -
502A ILE* 3.3 5.1 - - - -
503A ILE* 2.8 42.6 + - + +
551A GLY 4.0 6.3 - - - +
552A ASN* 2.7 34.4 + - - +
553A MET* 4.3 14.9 + - - +
557A THR* 3.6 5.6 - - - +
558A PRO* 1.3 79.2 - - - +
560A ILE* 1.3 61.5 + - - +
561A ARG* 3.5 35.0 + - - +
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Residues in contact with ILE 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A MET* 3.7 28.3 - - + -
403A LEU* 4.5 7.3 - - + +
429A VAL* 3.9 13.9 - - + -
501A VAL 3.4 3.8 - - - +
502A ILE* 4.3 9.4 - - + +
559A ASP* 1.3 72.5 - - - +
561A ARG* 1.3 82.3 + - - +
562A ARG* 3.4 51.5 + - + +
590A LEU* 3.6 26.2 - - + -
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Residues in contact with ARG 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLY* 3.2 2.7 - - - -
501A VAL* 2.8 47.5 + - + -
503A ILE* 5.0 1.3 - - + -
524A PHE* 3.9 14.4 - - + -
549A PHE* 3.8 23.8 - - + -
550A GLU* 2.8 41.6 + - - +
551A GLY 3.3 22.0 + - - -
553A MET* 5.5 3.8 - - - +
559A ASP* 3.5 29.5 + - - +
560A ILE* 1.3 85.5 + - - +
562A ARG* 1.3 62.5 - - - +
563A PHE* 3.8 4.0 - - - -
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Residues in contact with ARG 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A MET* 4.6 15.2 - - - -
429A VAL* 2.9 32.5 + - - +
432A ALA* 3.4 18.6 - - - +
433A PRO 5.2 1.4 + - - -
434A CYS 5.3 0.4 + - - -
435A SER* 2.7 27.5 + - - -
499A LYS* 3.4 20.2 + - + +
500A GLY* 4.0 0.4 - - - -
549A PHE* 4.3 6.8 - - - -
560A ILE* 3.4 34.0 + - + +
561A ARG* 1.3 75.5 - - - +
563A PHE* 1.3 65.8 + - - +
590A LEU* 4.5 5.7 - - + +
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Residues in contact with PHE 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A VAL* 3.7 28.0 - - + -
499A LYS* 2.9 26.3 + - - +
500A GLY* 3.4 37.2 - - - -
501A VAL* 4.0 13.7 - - + -
526A VAL* 4.7 6.1 - - + -
538A ILE* 3.6 34.3 - - + -
547A LYS* 6.1 0.4 - - + -
549A PHE* 3.7 30.5 - + + -
561A ARG 3.8 5.2 - - - -
562A ARG* 1.3 78.7 - - - +
564A ASP* 1.3 79.9 + - - +
565A PRO 3.5 1.9 - - - -
566A ILE* 4.0 4.7 - - + -
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Residues in contact with ASP 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ILE* 5.9 0.2 - - - +
563A PHE* 1.3 87.2 - - - +
565A PRO* 1.3 76.6 - - + +
566A ILE* 3.5 9.2 + - - +
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Residues in contact with PRO 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A THR* 3.6 24.0 - - + -
498A VAL 3.2 9.9 - - - +
499A LYS* 4.3 24.9 - - + +
563A PHE 3.5 4.2 - - - +
564A ASP* 1.3 90.1 - - + +
566A ILE* 1.3 62.2 + - - +
567A PRO* 4.7 0.9 - - - +
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Residues in contact with ILE 566 (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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497A THR* 3.5 6.4 - - - -
498A VAL* 2.8 49.4 + - + +
526A VAL* 5.4 1.1 - - + -
528A TYR* 3.4 63.3 - - + +
538A ILE* 4.1 11.0 - - + -
563A PHE* 4.0 20.2 - - + -
564A ASP 3.9 6.7 - - - +
565A PRO* 1.3 78.6 - - - +
567A PRO* 1.3 69.4 - - + +
568A ALA* 3.8 0.8 + - + -
571A VAL* 5.9 0.7 - - + -
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Residues in contact with PRO 567 (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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496A LYS 3.5 7.9 - - - +
497A THR* 4.8 1.3 - - - +
528A TYR* 3.7 17.9 - - + -
529A SER 5.0 0.7 - - - -
530A LEU* 4.4 21.8 - - + +
565A PRO 4.7 1.6 - - - +
566A ILE* 1.3 87.4 - - + +
568A ALA* 1.3 63.9 + - - +
594A TRP* 4.6 16.4 - - + +
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Residues in contact with ALA 568 (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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492A LEU* 3.7 8.4 - - - +
495A PRO* 4.2 2.9 - - - -
496A LYS* 2.8 33.1 + - - +
498A VAL* 4.0 19.5 - - + +
528A TYR* 3.8 17.9 - - + -
529A SER 3.6 7.2 - - - +
530A LEU* 4.1 6.2 - - - +
566A ILE* 3.8 1.2 + - + +
567A PRO* 1.3 77.0 - - - +
569A GLN* 1.3 60.1 + - - +
570A TYR 3.7 18.4 - - - +
571A VAL* 4.5 1.6 - - + -
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Residues in contact with GLN 569 (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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491A ASP* 3.0 24.8 + - - +
492A LEU* 2.6 40.1 + - - +
493A GLY* 3.1 24.5 + - - +
494A THR* 3.5 23.2 - - - +
495A PRO* 3.5 20.8 - - + +
529A SER 2.9 5.1 + - - -
530A LEU* 3.9 14.6 - - - +
568A ALA* 1.3 74.6 - - - +
570A TYR* 1.3 86.2 + - + +
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Residues in contact with TYR 570 (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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489A GLN* 3.8 22.0 - - + +
490A VAL 3.3 4.0 - - - +
491A ASP* 3.4 38.4 + - + -
528A TYR* 3.2 5.9 - - - +
529A SER 3.0 33.6 + - - +
530A LEU 3.4 18.4 - - - -
531A ASN 4.0 3.1 + - - -
532A GLY* 3.5 31.5 - - - -
535A TRP* 3.3 22.7 - + + -
568A ALA* 3.7 1.2 - - - +
569A GLN* 1.3 96.9 + - + +
571A VAL* 1.3 65.5 + - - +
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Residues in contact with VAL 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LEU 3.9 0.7 - - - +
489A GLN* 3.3 2.6 - - - +
490A VAL* 2.8 36.9 + - + +
492A LEU* 4.4 7.9 - - + -
498A VAL* 4.0 32.3 - - + -
501A VAL* 4.8 11.4 - - + -
526A VAL* 4.1 18.6 - - + -
527A SER 3.5 9.2 - - - +
528A TYR* 4.8 3.1 - - + -
535A TRP* 4.4 0.2 - - - -
566A ILE* 6.3 0.2 - - + -
568A ALA* 4.5 3.6 - - + -
570A TYR* 1.3 80.2 - - - +
572A ARG* 1.3 67.7 + - - +
573A VAL* 4.2 9.0 - - + -
587A LEU* 6.1 0.9 - - + -
589A VAL* 4.3 22.4 - - + -
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Residues in contact with ARG 572 (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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487A TRP* 3.6 37.9 - - + -
488A LEU 3.3 4.7 - - - +
489A GLN* 2.9 40.9 + - + +
526A VAL* 3.4 6.6 - - - +
527A SER* 2.7 51.6 + - - +
532A GLY 5.7 0.2 + - - -
535A TRP* 3.2 43.9 - - + +
571A VAL* 1.3 73.0 - - - +
573A VAL* 1.3 62.4 + - - +
574A TYR* 3.4 33.0 + - + -
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Residues in contact with VAL 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A TRP* 3.3 4.2 - - - -
488A LEU* 2.9 32.4 + - + +
501A VAL* 4.6 9.0 - - + -
503A ILE* 4.8 2.9 - - + -
524A PHE* 3.9 24.7 - - + -
525A LYS 3.6 2.9 - - - -
526A VAL* 4.4 14.1 - - + -
571A VAL* 4.8 4.9 - - + -
572A ARG* 1.3 77.6 - - - +
574A TYR* 1.3 62.0 + - - +
575A PRO* 3.4 4.5 - - - +
585A MET* 3.7 31.9 - - + -
587A LEU* 3.8 35.2 - - + -
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Residues in contact with TYR 574 (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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484A GLY* 3.9 28.3 - - - -
486A GLU 3.3 16.2 - - - +
487A TRP* 3.4 23.3 + + + -
524A PHE* 3.1 4.8 - - - -
525A LYS* 2.9 47.5 + - + +
527A SER* 3.2 26.2 + - - -
535A TRP* 5.8 0.3 - - - +
537A TYR* 3.9 31.7 + + - -
572A ARG* 3.4 42.6 + - + -
573A VAL* 1.3 73.2 - - - +
575A PRO* 1.3 71.1 - - - +
576A GLU* 3.4 2.0 + - - +
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Residues in contact with PRO 575 (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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474A TRP* 3.7 22.2 - - + -
484A GLY* 3.5 19.4 + - - -
486A GLU* 3.6 16.2 + - - +
521A VAL* 3.8 18.8 - - + -
523A LYS 3.7 5.8 - - - +
524A PHE* 4.1 1.1 - - + -
573A VAL 3.4 11.7 - - - +
574A TYR* 1.3 84.0 - - - +
576A GLU* 1.3 58.4 - - - +
578A TRP* 3.7 8.8 - - + -
583A ILE* 3.7 25.2 - - + +
585A MET* 3.6 23.1 - - + -
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Residues in contact with GLU 576 (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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483A PRO* 3.3 33.1 - - - +
484A GLY* 3.9 14.6 + - - -
523A LYS* 2.7 25.5 + - + +
524A PHE* 4.2 5.8 - - - +
525A LYS* 3.7 34.3 + - - +
548A LEU* 4.0 18.4 - - + +
574A TYR 3.4 1.2 + - - +
575A PRO* 1.3 74.8 - - - +
577A ARG* 1.3 94.5 + - - +
578A TRP* 3.4 7.0 - - - -
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Residues in contact with ARG 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A PRO* 3.7 17.0 - - - +
521A VAL* 3.6 4.3 - - - +
522A ARG* 3.0 24.8 + - + +
523A LYS* 3.3 42.6 + - + +
548A LEU* 6.5 0.2 - - - -
576A GLU* 1.3 108.5 + - - +
578A TRP* 1.3 70.3 + - - +
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Residues in contact with TRP 578 (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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479A PRO 3.9 7.9 + - - -
480A GLN* 4.5 6.7 - - + +
481A ALA* 3.4 39.3 - - + -
482A GLN 5.0 0.2 - - - -
483A PRO* 4.2 14.6 - - + -
484A GLY 5.4 0.2 - - - -
486A GLU* 6.3 0.2 - - + -
520A PHE 3.6 13.5 - - - +
521A VAL* 4.3 4.9 - - - -
522A ARG* 2.8 28.9 + - - +
575A PRO* 3.7 11.9 - - + -
576A GLU 3.4 26.5 - - - -
577A ARG* 1.3 91.7 - - - +
579A SER* 1.3 85.3 + - - +
580A PRO 5.7 0.2 - - - -
582A GLY* 3.8 20.1 - - - +
583A ILE* 3.4 36.6 - - + +
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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