Contacts of the strand formed by residues 564 - 573 (chain A) in PDB entry 4TZ1
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 VAL 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526A VAL* 4.3 3.8 - - + -
530A VAL* 4.3 3.6 - - + +
531A THR 3.4 29.6 - - - +
532A THR 3.8 3.1 - - - +
533A HIS* 3.3 20.4 - - + +
558A ALA* 4.1 9.2 - - + -
559A PRO* 3.4 50.3 - - + +
561A LYS* 3.1 22.0 + - + +
562A PRO 3.5 0.6 - - - -
563A GLY* 1.3 74.8 - - - +
565A LYS* 1.3 60.2 + - - +
566A PHE* 5.2 4.5 - - + -
604A PHE* 3.9 10.4 - - + -
605A PRO* 3.8 9.4 - - - +
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Residues in contact with LYS 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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533A HIS 2.9 8.1 + - - +
534A GLU* 3.1 35.4 + - - +
535A GLY 3.1 21.3 + - - -
562A PRO 3.5 26.0 - - - +
563A GLY* 4.2 4.7 - - - -
564A VAL* 1.3 75.9 - - - +
566A PHE* 1.3 69.1 + - - +
567A HIS* 4.4 14.1 - - + +
604A PHE 3.1 7.9 - - - +
605A PRO* 3.8 14.1 - - + -
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Residues in contact with PHE 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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524A TYR* 3.6 25.6 - + - -
526A VAL* 4.3 4.9 - - + -
533A HIS* 3.8 18.4 - + - -
535A GLY* 3.3 32.1 - - - -
538A MET* 3.7 17.7 - - - -
556A PHE* 5.1 4.5 - + + -
557A GLN 5.5 0.9 - - - -
558A ALA* 4.2 15.9 - - + -
564A VAL* 5.2 3.1 - - + -
565A LYS* 1.3 78.7 - - - +
567A HIS* 1.3 77.4 + - - +
569A LEU* 3.9 18.4 - - + -
584A ILE* 3.5 20.9 - - + -
602A VAL 4.5 0.7 - - - -
603A SER* 3.8 3.2 - - - -
604A PHE* 3.0 56.7 + + + +
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Residues in contact with HIS 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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247A GLN* 6.2 0.2 - - - +
255A THR* 5.6 0.2 - - + -
534A GLU* 2.4 32.3 + - - +
535A GLY 2.9 11.7 + - - +
536A TRP* 3.3 37.6 + + + -
537A GLY 2.9 25.6 + - - -
538A MET 4.7 0.2 + - - -
565A LYS* 4.4 18.7 + - + +
566A PHE* 1.3 90.6 + - - +
568A ASP* 1.3 70.6 + - - +
569A LEU* 3.7 2.3 - - - +
602A VAL 3.4 8.6 + - - +
603A SER* 4.8 7.0 + - - -
604A PHE 5.6 0.2 - - - -
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Residues in contact with ASP 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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247A GLN* 2.9 26.8 + - - -
249A PHE* 3.1 46.1 - - + +
255A THR* 2.5 34.7 + - - +
537A GLY* 3.5 1.8 - - - +
538A MET 3.0 24.3 + - - +
567A HIS* 1.3 78.6 - - - +
569A LEU* 1.3 61.5 + - - +
570A LEU* 4.0 4.7 - - - +
601A VAL 3.7 1.5 + - - -
602A VAL* 3.0 21.9 + - - +
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Residues in contact with LEU 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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249A PHE* 3.8 4.3 - - - -
538A MET* 3.3 35.7 - - + -
556A PHE* 4.0 21.3 - - + -
566A PHE* 3.9 26.7 - - + -
567A HIS 5.0 0.9 - - - +
568A ASP* 1.3 78.3 - - - +
570A LEU* 1.3 64.3 + - - +
583A VAL* 3.8 11.9 - - + -
584A ILE* 3.7 46.0 - - + -
600A GLN* 3.3 3.1 - - - -
601A VAL* 2.9 41.8 + - + +
603A SER 6.1 0.2 - - - -
604A PHE* 4.8 0.9 - - + -
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Residues in contact with LEU 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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234A TRP* 3.8 35.9 - - + +
235A ASN* 3.9 12.3 - - + -
249A PHE* 4.3 9.2 - - + -
538A MET 2.9 29.8 + - - +
539A GLY* 3.2 5.9 - - - -
540A SER 3.1 22.3 + - - -
541A TYR* 4.0 17.3 - - + +
556A PHE* 3.8 3.1 - - - -
568A ASP 4.0 6.7 - - - +
569A LEU* 1.3 79.7 - - - +
571A VAL* 1.3 66.8 + - - +
572A VAL* 3.9 24.7 - - + -
583A VAL* 4.5 2.0 - - - -
598A PRO* 4.6 6.7 - - + -
599A SER 3.2 11.0 - - - +
600A GLN* 4.4 10.5 - - + +
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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
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540A SER* 3.1 10.1 - - - +
555A GLY* 3.9 19.3 - - - +
556A PHE* 4.3 4.7 - - + -
570A LEU* 1.3 79.0 - - - +
572A VAL* 1.3 67.1 + - - +
580A TYR* 3.6 48.5 - - + -
582A HIS 3.9 7.6 - - - +
583A VAL* 4.0 16.4 - - + +
589A ASP 4.9 0.2 - - - +
591A THR* 3.8 9.5 - - + +
599A SER* 2.9 45.8 + - - +
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Residues in contact with VAL 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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234A TRP* 4.0 18.2 - - + -
540A SER 3.1 5.7 + - - -
541A TYR* 3.1 28.3 - - + +
542A CYS 2.8 25.5 + - - -
570A LEU* 3.9 12.6 - - + -
571A VAL* 1.3 83.0 - - - +
573A SER* 1.3 63.1 + - - +
574A LEU* 4.0 3.4 - - + -
580A TYR* 3.4 5.6 - - - -
591A THR* 4.3 2.0 - - - -
596A THR* 3.4 39.3 - - + -
597A ILE 4.8 0.4 - - - -
598A PRO* 3.8 24.0 - - + -
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Residues in contact with SER 573 (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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542A CYS* 3.8 11.5 - - - -
572A VAL* 1.3 73.6 - - - +
574A LEU* 1.3 61.3 + - - +
575A GLY 3.3 6.2 + - - -
576A GLY* 3.4 17.9 + - - -
577A LYS 3.4 2.4 + - - -
578A GLY 2.7 23.4 + - - -
579A GLN* 3.4 21.8 - - - -
591A THR* 3.9 15.0 - - - +
593A GLY 5.7 0.2 - - - -
596A THR* 3.5 23.0 + - - +
597A ILE 5.3 1.6 + - - +
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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
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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