Contacts of the helix formed by residues 581 - 592 (chain F) in PDB entry 5ZCS
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 TYR 581 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534F ASP* 5.4 4.3 - - + -
577F LEU 3.9 12.8 + - - +
578F LEU* 4.4 2.3 - - - -
579F TYR 3.9 0.4 - - - -
580F PHE* 1.3 77.8 - - - +
582F LYS* 1.3 64.2 + - - +
583F PRO 4.9 0.2 - - - -
584F SER* 3.8 25.1 - - - +
585F SER* 3.3 21.5 + - - -
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Residues in contact with LYS 582 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471F ALA 6.5 0.7 - - - -
472F ALA* 6.1 4.9 - - + +
580F PHE 4.1 2.2 + - - -
581F TYR* 1.3 71.8 - - - +
583F PRO* 1.3 62.1 - - - +
585F SER* 3.4 4.9 + - - -
586F LYS* 2.9 28.1 + - - +
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Residues in contact with PRO 583 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534F ASP* 5.3 9.0 - - + +
581F TYR* 3.5 1.0 - - + -
582F LYS* 1.3 77.8 - - - +
584F SER* 1.3 59.6 + - - +
586F LYS* 3.3 6.4 + - + +
587F LEU* 2.9 28.9 + - - +
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Residues in contact with SER 584 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530F ILE* 4.7 12.5 - - - +
531F ASN* 5.7 1.3 - - - -
534F ASP* 3.8 27.1 - - - +
577F LEU* 4.8 12.5 - - - +
581F TYR* 3.8 19.5 + - - +
582F LYS 3.4 0.4 - - - -
583F PRO* 1.3 79.6 - - - +
585F SER* 1.3 56.7 + - - +
587F LEU* 3.4 6.5 + - - +
588F TYR* 2.9 29.6 + - - +
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Residues in contact with SER 585 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468F ARG* 5.4 5.3 - - - +
475F CYS* 6.0 4.9 - - - -
574F VAL 5.3 1.8 - - - -
577F LEU* 4.7 2.8 + - - -
578F LEU* 3.7 30.5 - - - +
581F TYR 3.3 19.9 + - - -
582F LYS* 3.8 4.9 - - - -
583F PRO 3.3 0.2 - - - -
584F SER* 1.3 76.3 - - - +
586F LYS* 1.3 58.3 + - - +
588F TYR* 3.4 6.4 + - - +
589F ALA* 2.9 30.0 + - - +
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Residues in contact with LYS 586 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468F ARG 4.9 2.6 + - - +
469F ALA* 4.2 31.0 - - + +
582F LYS 2.9 17.3 + - - +
583F PRO* 3.7 7.9 - - + +
584F SER 3.3 0.2 - - - -
585F SER* 1.3 78.4 - - - +
587F LEU* 1.3 56.1 + - - +
589F ALA* 3.4 5.8 + - - +
590F ASN* 2.9 30.5 + - - +
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Residues in contact with LEU 587 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544F LEU* 5.5 16.2 - - + +
547F ASN* 6.3 2.9 - - + -
548F TRP* 5.2 5.6 - - + +
583F PRO 2.9 16.1 + - - +
584F SER* 3.8 7.4 - - - +
585F SER 3.3 0.2 - - - -
586F LYS* 1.3 76.3 - - - +
588F TYR* 1.3 58.6 + - - +
590F ASN* 3.4 5.3 + - - +
591F LEU* 2.9 30.1 + - - +
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Residues in contact with TYR 588 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574F VAL* 4.0 29.6 - - + +
577F LEU* 5.8 4.0 - - + -
584F SER 2.9 17.4 + - - +
585F SER* 3.8 6.7 - - - +
587F LEU* 1.3 76.4 - - - +
589F ALA* 1.3 60.0 + - - +
591F LEU* 4.0 5.8 - - - +
592F ASP* 3.5 22.2 + - - +
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Residues in contact with ALA 589 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465F LYS* 4.4 13.8 - - - +
468F ARG* 4.0 26.7 - - + -
469F ALA* 5.3 0.9 - - + +
585F SER 2.9 17.9 + - - +
586F LYS* 3.8 6.5 - - - +
588F TYR* 1.3 78.4 - - - +
590F ASN* 1.3 61.5 + - - +
592F ASP* 3.6 3.5 + - - +
593F LEU* 3.3 23.0 + - - +
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Residues in contact with ASN 590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465F LYS* 5.5 2.2 - - - -
469F ALA* 6.3 1.6 - - + -
548F TRP* 5.7 3.1 - - + +
586F LYS 2.9 18.7 + - - +
587F LEU* 4.0 5.2 - - - +
588F TYR 3.4 0.2 - - - -
589F ALA* 1.3 75.0 - - - +
591F LEU* 1.3 62.9 + - - +
592F ASP 3.6 0.2 + - - -
593F LEU* 3.7 16.5 + - - +
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Residues in contact with LEU 591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547F ASN 3.6 24.7 - - - +
548F TRP* 3.8 22.6 - - - +
551F ILE* 4.9 12.3 - - - +
587F LEU 2.9 19.3 + - - +
588F TYR* 4.0 7.4 - - - +
589F ALA 3.3 0.2 - - - -
590F ASN* 1.3 79.5 - - - +
592F ASP* 1.3 57.0 + - + +
593F LEU 3.4 1.4 + - - -
594F ASP* 4.9 5.7 + - - +
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Residues in contact with ASP 592 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571F HIS* 5.6 10.5 - - + -
588F TYR 3.5 14.9 + - - +
589F ALA* 3.6 4.2 + - - +
590F ASN 3.4 0.6 - - - -
591F LEU* 1.3 77.3 - - + +
593F LEU* 1.3 55.2 + - - +
594F ASP* 3.3 10.7 + - - +
598F ALA* 5.8 2.3 - - - +
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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