Contacts of the strand formed by residues 560 - 569 (chain A) in PDB entry 3S3J
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 LEU 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A THR* 3.5 8.1 - - - -
514A VAL* 2.8 49.3 + - + +
515A SER 4.2 4.9 - - - +
516A TYR* 3.8 22.9 - - + -
555A LEU* 4.0 4.6 - - - +
556A THR* 4.5 1.3 + - - -
558A SER* 3.5 24.5 - - - +
559A ASN* 1.3 75.6 - - - +
561A ILE* 1.3 66.3 + - - +
581A ASP* 5.0 10.8 - - + +
582A LEU 3.3 24.5 - - - +
583A TYR* 3.9 20.4 - - + -
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Residues in contact with ILE 561 (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 PHE* 4.6 5.8 - - + -
511A ALA* 3.8 25.8 - - + -
512A ARG 3.2 18.8 - - - +
513A THR* 4.6 2.5 - - + -
514A VAL* 3.6 3.8 - - - -
524A CYS* 3.9 9.0 - - - -
546A ILE* 4.4 22.4 - - + -
551A TYR* 4.4 10.5 - - + -
555A LEU* 4.4 8.3 - - + -
560A LEU* 1.3 80.3 - - - +
562A LYS* 1.3 61.9 + - - +
563A VAL* 3.9 5.5 + - + +
580A ARG 3.8 0.3 - - - +
581A ASP* 3.4 0.7 - - - -
582A LEU* 2.8 45.7 + - + +
584A LEU* 3.3 35.4 - - + -
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Residues in contact with LYS 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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510A CYS 3.8 0.5 - - - +
511A ALA* 3.3 4.7 - - - -
512A ARG* 2.7 35.0 + - + +
514A VAL* 3.4 15.5 - - + +
518A GLY 5.2 2.5 - - - -
520A LEU* 3.5 33.0 - - + -
561A ILE* 1.3 74.4 - - - +
563A VAL* 1.3 64.1 + - - +
564A ARG* 3.7 21.3 + - + +
579A GLU* 2.7 46.8 + - - +
580A ARG 3.6 3.1 - - - +
581A ASP* 3.0 35.7 + - - +
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Residues in contact with VAL 563 (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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477A ILE* 3.5 34.8 - - + +
491A VAL* 4.2 21.3 - - + -
509A LEU* 3.8 18.6 - - + -
510A CYS 3.5 7.6 - - - +
511A ALA* 4.7 8.5 - - + -
546A ILE* 5.8 0.7 - - + -
561A ILE* 4.8 2.7 - - + +
562A LYS* 1.3 75.8 - - - +
564A ARG* 1.3 64.6 + - - +
578A ALA 3.9 0.7 - - - +
579A GLU* 3.3 2.9 - - - -
580A ARG 2.7 43.5 + - - +
582A LEU* 3.5 31.4 - - + -
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Residues in contact with ARG 564 (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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310A ASN* 3.8 7.2 - - - +
311A LEU* 3.4 53.9 - - + +
314A GLU* 3.0 33.5 + - - -
509A LEU* 3.6 0.5 - - - +
510A CYS* 2.9 41.7 + - - +
512A ARG* 3.4 32.1 - - - +
520A LEU* 3.9 19.1 - - - +
562A LYS* 3.7 21.4 + - + +
563A VAL* 1.3 77.1 - - - +
565A ALA* 1.3 59.5 + - - +
578A ALA 3.5 2.7 - - - -
579A GLU* 3.3 32.3 - - + -
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Residues in contact with ALA 565 (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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311A LEU* 3.7 4.7 - - - +
475A MET* 3.5 25.1 - - + -
477A ILE* 3.9 13.0 - - + +
493A ALA* 4.4 4.7 - - + -
507A LEU* 4.5 1.8 - - + -
508A LEU 3.2 8.7 - - - +
509A LEU* 3.9 18.6 - - + -
564A ARG* 1.3 74.1 - - - +
566A LEU* 1.3 60.2 + - - +
577A LEU* 3.5 6.1 - - - +
578A ALA* 2.8 30.6 + - + +
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Residues in contact with LEU 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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311A LEU* 4.1 20.9 - - + +
312A LEU* 3.6 22.0 - - + -
315A TYR* 3.5 43.5 - - + -
475A MET* 3.9 1.8 - - - -
506A ARG 3.7 0.7 - - - +
507A LEU* 3.4 6.4 - - - +
508A LEU* 2.8 34.9 + - + +
565A ALA* 1.3 76.2 - - - +
567A LEU* 1.3 62.3 + - - +
568A VAL* 3.8 20.3 - - + +
575A TYR* 4.1 7.6 - - + -
576A LEU 3.2 2.7 - - - +
577A LEU* 3.1 30.5 - - + -
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Residues in contact with LEU 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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473A MET* 3.9 27.8 - - + -
475A MET* 3.6 14.8 - - + +
495A ILE* 4.0 25.8 - - + -
505A CYS* 3.7 21.5 - - + -
506A ARG 3.4 14.6 - - - +
507A LEU* 3.8 22.2 - - + -
532A LEU* 3.9 11.9 - - + -
534A LEU* 4.8 1.3 - - + -
566A LEU* 1.3 74.1 - - - +
568A VAL* 1.3 60.1 + - - +
574A SER 3.8 0.9 - - - +
575A TYR* 3.4 4.7 - - - +
576A LEU* 2.8 56.0 + - + +
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Residues in contact with VAL 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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315A TYR* 4.1 24.9 - - + +
505A CYS* 3.1 9.2 - - - -
506A ARG* 2.8 48.3 + - + +
566A LEU* 3.8 22.4 - - + +
567A LEU* 1.3 76.0 - - - +
569A GLU* 1.3 63.9 + - - +
570A PRO* 3.6 22.9 - - + +
574A SER 3.6 3.1 - - - +
575A TYR* 3.6 39.5 - - + +
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Residues in contact with GLU 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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473A MET* 5.3 4.5 - - + -
503A TYR* 4.0 19.5 - - + +
504A VAL* 3.3 26.6 + - - +
505A CYS* 4.0 11.4 - - - -
567A LEU 4.2 0.4 + - - -
568A VAL* 1.3 73.8 - - - +
570A PRO* 1.3 65.1 - - - +
571A VAL* 2.9 44.6 + - - +
572A ILE* 2.9 30.3 - - + +
573A ASN 3.0 19.2 + - - -
574A SER* 2.9 29.7 + - - +
576A LEU* 6.5 0.7 - - + -
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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