Contacts of the strand formed by residues 569 - 579 (chain B) in PDB entry 4YZC
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B VAL 4.1 0.3 - - - +
565B ILE* 3.5 2.4 - - - +
566B VAL* 2.8 40.3 + - + +
567B GLY 4.7 0.4 - - - -
568B LYS* 1.3 78.4 - - - +
570B SER* 1.3 62.5 + - - +
571B PHE* 4.5 7.2 - - + -
590B MET 3.5 4.7 - - - +
591B PHE* 4.4 10.3 - - + -
598B VAL* 3.6 36.3 - - + -
630B CYS* 4.2 4.7 - - + +
631B THR 4.6 1.1 - - - -
632B GLU* 3.8 20.4 - - + +
639B TYR* 3.6 33.9 - - + +
640B ILE 4.6 0.2 - - - -
641B ALA* 3.8 30.7 - - + +
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Residues in contact with SER 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B VAL* 4.8 5.8 - - - -
564B VAL 3.3 10.1 - - - -
565B ILE* 4.0 19.5 - - - -
568B LYS 3.7 2.7 + - - -
569B ILE* 1.3 76.3 - - - +
571B PHE* 1.3 60.6 + - - +
589B GLY* 3.3 1.7 - - - -
590B MET* 2.6 58.3 + - - +
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Residues in contact with PHE 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B VAL* 3.8 5.5 - - - +
564B VAL* 3.0 63.9 + - + +
566B VAL* 5.1 1.8 - - + -
569B ILE* 4.5 5.6 - - + -
570B SER* 1.3 76.5 - - - +
572B CYS* 1.3 65.9 + - - +
573B PRO* 4.1 10.5 - - + -
587B TYR* 3.6 49.4 - + + -
588B ARG 3.8 12.3 - - - +
589B GLY* 3.9 9.6 - - - -
598B VAL* 4.0 20.6 - - + -
600B ARG* 5.0 4.7 - - - -
639B TYR* 3.5 33.9 - + - -
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Residues in contact with CYS 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562B SER 3.2 26.5 - - - +
563B VAL* 4.9 5.4 - - + +
571B PHE* 1.3 76.1 - - - +
573B PRO* 1.3 69.4 - - - +
574B LYS* 3.5 29.6 - - - -
575B ASP* 3.1 39.9 + - - +
587B TYR* 3.7 3.5 - - - +
588B ARG 4.0 4.0 + - - -
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Residues in contact with PRO 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B SER* 3.2 40.8 - - - +
564B VAL* 4.5 12.8 - - + -
571B PHE* 3.9 11.4 - - + +
572B CYS* 1.3 82.9 - - - +
574B LYS* 1.3 62.2 + - + +
576B VAL* 3.1 20.6 - - - +
587B TYR* 3.5 20.0 - - + +
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Residues in contact with LYS 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562B SER 6.3 0.4 - - - +
572B CYS* 3.5 22.7 - - - -
573B PRO* 1.3 82.5 - - + +
575B ASP* 1.3 74.2 + - - +
576B VAL* 3.2 9.1 + - - +
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Residues in contact with ASP 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B CYS* 3.1 29.8 + - - +
574B LYS* 1.3 89.3 - - - +
576B VAL* 1.3 56.8 + - - +
577B LEU 4.3 0.4 - - - -
587B TYR* 3.0 29.6 - - - +
588B ARG* 4.0 32.9 - - + +
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Residues in contact with VAL 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B PRO 3.1 25.8 - - - +
574B LYS 3.2 8.8 + - - +
575B ASP* 1.3 72.8 - - - +
577B LEU* 1.3 67.0 + - - +
578B GLY* 3.6 15.9 - - - +
579B HIS* 4.0 17.5 - - + +
585B ILE* 3.8 17.5 - - + -
586B VAL 3.5 12.3 - - - +
587B TYR* 3.8 11.7 - - + -
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Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B VAL* 1.3 74.9 - - - +
578B GLY* 1.3 58.3 + - - +
586B VAL* 2.9 13.6 + - + +
587B TYR 3.7 18.8 - - - +
588B ARG* 3.9 26.0 - - + +
597B ALA* 3.8 12.8 - - + -
644B LEU* 3.6 28.3 - - + -
1001B STU 3.3 65.6 - - + +
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Residues in contact with GLY 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B VAL* 3.4 9.1 - - - +
577B LEU* 1.3 80.7 - - - +
579B HIS* 1.3 68.6 + - - -
585B ILE* 3.8 0.3 - - - +
586B VAL* 3.1 30.1 + - - +
1001B STU 3.5 18.7 + - - -
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Residues in contact with HIS 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B VAL* 4.0 15.0 - - + +
578B GLY* 1.3 77.7 - - - -
580B GLY* 1.3 65.9 + - - +
584B THR 3.8 4.2 + - - +
585B ILE* 4.0 31.6 - - + +
1001B STU 4.0 12.3 - - - +
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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