Contacts of the strand formed by residues 557 - 572 (chain A) in PDB entry 3F8I
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 ASN 557 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A MET* 3.2 7.1 - - - +
435A TRP* 2.7 44.9 + - + +
436A ARG 3.4 15.2 + - - -
437A PHE* 3.7 18.6 - - - +
438A ARG* 3.9 15.0 - - - +
441A VAL* 3.9 17.7 - - + -
466A VAL* 4.8 0.2 - - - +
540A VAL* 3.8 16.1 - - + +
541A ARG 3.4 4.7 - - - -
542A ASN* 2.9 33.1 + - - +
553A PRO* 4.7 0.9 - - - -
555A GLU 3.8 1.3 + - - -
556A GLY* 1.3 75.7 - - - -
558A ARG* 1.3 61.0 + - - +
609A MET* 4.9 0.2 - - - +
409D C 5.3 0.6 + - - -
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Residues in contact with ARG 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLY 4.1 6.5 - - - +
433A THR 3.4 10.5 - - - +
434A MET* 3.9 18.8 - - + -
435A TRP* 4.5 0.4 - - - -
540A VAL* 3.4 6.5 - - - +
541A ARG* 2.8 39.9 + - - +
551A TYR 2.9 27.4 + - - -
552A ALA 4.6 0.4 + - - -
553A PRO* 3.9 31.3 - - + +
557A ASN* 1.3 76.0 - - - +
559A TYR* 1.3 68.8 + - - +
560A ASP* 2.8 36.9 + - - +
593A PRO* 3.5 29.9 + - - +
594A TRP* 3.7 18.2 - - - +
599A LYS* 6.2 0.2 - - - +
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Residues in contact with TYR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A PRO* 4.2 14.2 - - + +
426A ILE 5.8 0.9 - - - -
429A VAL* 3.9 21.5 - - + -
430A PRO 3.8 5.8 - - - -
431A VAL* 3.7 35.9 - - + +
432A GLY* 2.9 29.1 + - - -
433A THR* 2.9 15.0 + - - +
435A TRP* 3.8 24.2 - + + -
446A VAL* 3.9 19.1 - - + -
538A ARG* 4.0 24.2 - - + +
539A VAL 3.4 15.5 - - - -
540A VAL* 4.5 1.6 - - - -
558A ARG* 1.3 68.0 - - - +
560A ASP* 1.3 64.0 + - - +
561A GLY* 3.5 33.0 - - - -
562A ILE* 3.9 17.3 - - - +
588A ASP* 4.5 1.4 + - - -
593A PRO* 4.3 0.2 - - - +
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Residues in contact with ASP 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A VAL* 3.9 5.4 - - - -
539A VAL 3.0 14.0 + - - +
541A ARG* 2.9 49.0 + - + +
558A ARG* 2.8 44.1 + - - +
559A TYR* 1.3 77.5 - - - +
561A GLY* 1.3 57.3 + - - +
563A TYR* 4.1 6.4 - - + +
586A ARG* 2.8 31.2 + - - -
593A PRO* 3.3 12.6 - - + +
594A TRP* 3.6 5.1 - - + -
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Residues in contact with GLY 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A VAL* 4.0 5.8 - - - -
537A VAL 3.7 0.3 - - - +
538A ARG* 3.9 0.3 - - - -
539A VAL 3.1 25.5 + - - -
559A TYR* 3.5 29.0 - - - -
560A ASP* 1.3 81.2 - - - +
562A ILE* 1.3 61.7 + - - -
563A TYR* 3.8 5.3 - - - -
588A ASP* 3.2 14.4 - - - -
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Residues in contact with ILE 562 (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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424A GLY* 4.0 7.4 - - - -
425A PRO* 4.0 36.8 - - + -
536A PRO* 3.6 25.4 - - + -
537A VAL 3.6 7.2 - - - +
538A ARG* 4.0 15.9 - - + -
559A TYR* 3.9 12.8 - - - +
561A GLY* 1.3 72.5 - - - -
563A TYR* 1.3 64.7 + - - +
564A LYS* 4.4 7.0 - - - -
586A ARG* 3.5 7.4 - - - +
587A ASP 2.8 47.4 + - - +
588A ASP* 2.9 17.3 + - - +
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Residues in contact with TYR 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLY 3.0 25.3 + - - -
479A ASN 3.7 4.3 - - - -
481A PHE* 3.6 22.0 - + - -
537A VAL* 3.1 32.0 + - - +
539A VAL* 3.3 43.5 - - + -
541A ARG* 3.1 19.3 + - - -
560A ASP* 4.1 11.4 - - - +
561A GLY 3.8 1.8 - - - -
562A ILE* 1.3 78.6 - - - +
564A LYS* 1.3 70.9 + - - +
584A LEU* 4.3 11.4 - - + -
585A ARG* 3.2 11.9 - - - +
586A ARG* 3.2 55.0 + - + +
587A ASP 4.1 0.7 - - - +
594A TRP* 3.6 3.8 - - - -
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Residues in contact with LYS 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A TRP* 3.7 33.2 - - + +
532A ARG* 3.0 21.6 + - - +
534A GLY* 3.5 27.1 - - - +
535A LYS 3.7 10.3 - - - +
536A PRO* 3.8 22.7 - - - -
537A VAL* 5.4 0.7 - - - -
562A ILE* 4.4 6.5 - - - -
563A TYR* 1.3 79.0 - - - +
565A VAL* 1.3 63.1 + - - +
566A VAL* 3.4 3.9 + - - +
584A LEU* 3.1 8.2 - - - -
585A ARG 2.8 28.7 + - - -
587A ASP* 2.6 41.1 + - + -
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Residues in contact with VAL 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A LEU* 3.8 26.5 - - + +
516A ASN* 3.8 23.3 + - + +
517A CYS* 3.4 38.3 - - + +
518A HIS 4.6 0.3 + - - -
528A ALA* 4.2 3.5 - - - +
531A TRP* 4.8 4.0 - - - +
534A GLY* 6.0 1.3 - - - -
535A LYS 5.1 1.8 + - - -
537A VAL* 4.8 2.7 - - + -
564A LYS* 1.3 74.9 - - - +
566A VAL* 1.3 60.8 + - - +
567A LYS 3.8 22.4 - - - +
568A TYR* 4.4 2.5 - - + -
582A TYR* 4.4 17.7 - - + -
583A LEU 3.5 6.1 - - - +
584A LEU* 4.1 12.6 - - + -
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Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A TYR* 5.4 2.9 - - + -
517A CYS* 4.1 0.4 - - - -
527A GLU* 3.6 8.8 - - + +
528A ALA* 3.0 26.3 + - + +
531A TRP* 3.9 33.2 - - + -
564A LYS 3.4 1.1 + - - +
565A VAL* 1.3 71.9 - - - +
567A LYS* 1.3 66.1 + - + +
583A LEU* 2.8 35.0 + - + +
585A ARG* 3.8 31.4 - - + +
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Residues in contact with LYS 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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517A CYS* 4.3 5.2 - - - -
526A ALA 3.3 15.3 - - - +
527A GLU* 3.7 28.1 + - + +
565A VAL* 3.3 4.4 - - - +
566A VAL* 1.3 83.7 - - + +
568A TYR* 1.3 65.3 + - - +
569A TRP* 3.7 28.4 - - + -
582A TYR* 3.5 0.7 - - - -
583A LEU* 2.8 53.2 + - + +
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Residues in contact with TYR 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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506A LEU* 4.7 1.8 - - + -
514A ALA* 3.5 41.3 + - + -
517A CYS* 3.7 20.0 - - + -
519A SER 5.0 1.4 + - - -
520A PRO 3.8 5.0 + - - -
521A ILE* 3.5 14.2 - - + +
522A ASN 3.1 40.3 + - - -
525A GLY* 3.2 5.8 - - - -
526A ALA* 3.1 48.7 + - + +
565A VAL* 4.4 2.2 - - + -
567A LYS* 1.3 79.2 - - - +
569A TRP* 1.3 68.5 + - - +
580A TRP* 4.1 17.3 - + + -
581A ARG 3.0 13.2 - - - +
582A TYR* 3.5 22.7 - + + -
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Residues in contact with TRP 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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482A THR* 4.1 15.7 - - + -
524A LYS 4.9 1.3 - - - +
525A GLY* 4.2 3.4 - - - -
567A LYS* 3.7 36.3 - - + -
568A TYR* 1.3 83.6 - - - +
570A PRO* 1.3 85.8 - - + +
571A GLU* 2.8 34.4 + - + +
580A TRP* 3.6 8.4 - - - -
581A ARG* 2.8 70.5 + - + +
583A LEU* 4.2 13.0 - - + -
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Residues in contact with PRO 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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523A GLU 5.0 0.7 - - - +
524A LYS* 3.5 21.1 - - - +
569A TRP* 1.3 96.0 - - + +
571A GLU* 1.3 65.7 + - - +
578A LEU* 4.3 19.1 - - + -
579A VAL 3.5 7.6 - - - +
580A TRP* 3.3 37.7 - - + -
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Residues in contact with GLU 571 (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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569A TRP* 2.8 29.9 + - + +
570A PRO* 1.3 75.4 - - - +
572A ARG* 1.3 75.1 + - - +
578A LEU* 4.3 8.8 - - - +
579A VAL* 3.0 36.1 + - + +
581A ARG* 3.1 39.0 + - - -
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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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571A GLU* 1.3 83.0 - - - +
573A GLY* 1.3 66.6 + - - +
576A GLY* 3.1 32.8 + - - +
577A PHE 3.5 9.0 - - - -
578A LEU* 4.3 15.6 - - + +
579A VAL* 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
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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