Contacts of the strand formed by residues 569 - 580 (chain C) in PDB entry 4YZ9
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 ILE 569 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565C ILE* 3.5 5.7 - - - +
566C VAL* 2.5 47.2 + - + +
567C GLY 3.3 0.2 - - - -
568C LYS* 1.3 79.4 - - - +
570C SER* 1.3 74.1 + - - +
571C PHE* 4.8 4.5 - - + -
590C MET 3.8 7.2 - - - +
591C PHE* 4.2 10.3 - - + -
598C VAL* 4.1 26.0 - - + -
630C CYS* 4.0 15.7 - - - +
632C GLU* 3.7 27.4 - - + -
639C TYR* 3.8 22.7 - - + +
641C ALA* 4.1 20.6 - - + +
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Residues in contact with SER 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563C VAL* 4.1 10.6 - - - +
564C VAL 3.3 11.0 - - - -
565C ILE* 4.1 17.0 - - - -
569C ILE* 1.3 77.5 - - - +
571C PHE* 1.3 65.9 + - - +
589C GLY* 3.0 2.6 - - - -
590C MET* 2.8 55.0 + - - +
598C VAL* 3.9 4.0 - - - +
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Residues in contact with PHE 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563C VAL* 3.3 6.8 - - - +
564C VAL* 2.9 56.5 + - + -
566C VAL* 4.7 5.8 - - + -
569C ILE* 4.8 3.4 - - + -
570C SER* 1.3 78.5 - - - +
572C CYS* 1.3 74.2 + - - +
573C PRO* 4.0 22.0 - - + -
587C TYR* 3.9 26.7 - + + -
588C ARG 3.2 16.6 - - - +
589C GLY* 3.7 2.0 - - - -
598C VAL* 3.9 28.7 - - + -
600C ARG* 5.8 0.7 - - - -
639C TYR* 3.4 41.5 - + - -
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Residues in contact with CYS 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C SER 3.4 13.9 - - - +
563C VAL* 4.2 13.5 - - - -
571C PHE* 1.3 82.9 - - - +
573C PRO* 1.3 69.7 - - - +
574C LYS* 3.2 3.1 - - + +
575C ASP* 3.1 37.3 + - + +
587C TYR* 3.6 5.2 - - - +
588C ARG* 3.1 16.2 + - - +
589C GLY* 5.6 0.9 - - - -
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Residues in contact with PRO 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C SER* 3.4 23.3 - - - +
564C VAL* 3.3 34.8 - - + -
571C PHE* 3.8 11.4 - - + +
572C CYS* 1.3 82.7 - - - +
574C LYS* 1.3 61.8 + - + +
575C ASP 3.4 0.5 + - - -
576C VAL* 3.8 6.6 - - - +
587C TYR* 3.7 27.8 - - + -
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Residues in contact with LYS 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C SER* 4.2 32.3 - - - +
572C CYS* 3.2 3.7 - - + -
573C PRO* 1.3 80.7 - - + +
575C ASP* 1.3 58.7 + - - +
576C VAL* 3.7 5.4 + - - +
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Residues in contact with ASP 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C CYS* 3.1 31.3 + - + +
574C LYS* 1.3 76.5 - - + +
576C VAL* 1.3 69.4 + - - +
577C LEU* 4.0 3.5 - - - +
587C TYR* 3.4 16.6 - - - +
588C ARG* 3.1 47.3 + - + -
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Residues in contact with VAL 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573C PRO 3.8 8.5 - - - +
574C LYS 3.7 6.0 + - - +
575C ASP* 1.3 80.6 + - - +
577C LEU* 1.3 63.7 + - - +
578C GLY* 3.7 18.2 - - - +
585C ILE* 4.1 12.3 - - + -
586C VAL 3.6 11.4 - - - +
587C TYR* 3.8 23.3 - - + -
715C CYS* 4.4 14.0 - - - +
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Residues in contact with LEU 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C ASP* 4.0 5.1 + - - +
576C VAL* 1.3 75.0 - - - +
578C GLY* 1.3 57.8 + - - +
586C VAL* 2.9 14.3 + - + +
587C TYR 3.9 4.9 - - - +
588C ARG* 3.4 63.9 - - + +
597C ALA* 4.0 8.5 - - + -
644C LEU* 3.3 33.4 - - + -
714C LEU* 3.4 22.6 - - + +
715C CYS* 2.8 28.7 + - - +
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Residues in contact with GLY 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C VAL* 3.5 11.7 - - - +
577C LEU* 1.3 82.2 - - - +
579C HIS* 1.3 63.1 + - - +
585C ILE* 3.9 1.4 - - - -
586C VAL* 3.0 31.3 + - - +
713C GLY 3.3 14.4 - - - -
715C CYS* 3.8 15.7 - - - -
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Residues in contact with HIS 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C GLY* 1.3 77.2 - - - +
580C GLY* 1.3 71.6 + - - +
584C THR 3.3 13.5 - - - +
585C ILE* 4.1 12.8 - - + -
586C VAL* 4.4 2.2 - - - +
690C LYS* 6.1 2.1 + - - -
693C ASN* 4.9 0.2 - - - +
712C PHE* 3.2 6.4 - - - -
713C GLY* 3.0 29.7 + - - -
715C CYS* 6.0 2.2 - - - -
734C THR* 6.1 4.7 - - + -
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Residues in contact with GLY 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579C HIS* 1.3 88.3 - - - +
581C ALA* 1.3 68.6 + - - +
582C GLU 3.8 0.5 + - - -
583C GLY* 3.8 3.1 + - - -
584C THR* 2.9 26.6 + - - +
688C ASP* 4.9 2.0 - - - -
693C ASN* 5.4 0.2 - - - -
711C ASP* 3.5 17.3 - - - -
712C PHE* 4.0 4.9 - - - +
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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