Contacts of the helix formed by residues 571 - 584 (chain B) in PDB entry 5ZR1
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 ASN 571 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560B ASN* 3.6 13.9 - - - +
569B ALA* 3.5 2.6 - - - +
570B SER* 1.3 82.4 - - - +
572B GLU* 1.3 64.9 + - - +
573B ILE* 4.1 15.7 - - - +
574B ALA* 3.2 25.2 + - - +
575B LEU* 3.3 21.5 + - - +
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Residues in contact with GLU 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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556B LEU* 3.6 25.0 - - - +
557B LYS* 5.0 16.6 + - - +
560B ASN* 2.8 39.3 + - - +
571B ASN* 1.3 76.0 - - - +
573B ILE* 1.3 64.6 + - + +
575B LEU* 3.4 6.1 + - - +
576B ARG* 2.9 63.4 + - - +
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Residues in contact with ILE 573 (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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571B ASN* 3.4 12.6 + - - +
572B GLU* 1.3 80.9 - - + +
574B ALA* 1.3 61.3 + - - +
576B ARG* 3.2 9.7 + - - +
577B SER* 2.8 39.8 + - - +
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Residues in contact with ALA 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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569B ALA* 4.7 1.1 - - + -
570B SER* 4.7 13.0 - - - +
571B ASN* 3.2 22.0 + - - +
573B ILE* 1.3 75.3 - - - +
575B LEU* 1.3 63.1 + - - +
577B SER* 4.0 6.4 - - - -
578B MET* 3.3 37.3 + - + +
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Residues in contact with LEU 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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524B MET* 3.7 24.9 - - - -
556B LEU* 3.9 23.1 - - + -
559B PHE* 3.7 12.1 - - + -
560B ASN* 3.7 38.8 - - + +
563B CYS* 3.7 18.4 - - - -
569B ALA* 3.9 10.7 - - + +
571B ASN 3.3 14.7 + - - +
572B GLU* 3.4 11.7 - - - +
574B ALA* 1.3 79.0 - - - +
576B ARG* 1.3 58.2 + - - +
577B SER 3.3 0.3 + - - -
578B MET* 3.3 5.2 + - - +
579B LEU* 2.9 39.9 + - + +
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Residues in contact with ARG 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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556B LEU* 3.4 21.0 - - + +
572B GLU* 2.9 46.6 + - - +
573B ILE* 3.2 9.4 + - + +
575B LEU* 1.3 75.4 - - - +
577B SER* 1.3 61.5 + - - +
579B LEU* 3.8 12.6 - - + +
580B ARG* 3.4 24.3 + - - +
590B ILE* 5.4 6.7 - - + +
598B GLU* 3.2 35.4 + - - -
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Residues in contact with SER 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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573B ILE* 2.8 27.5 + - - +
574B ALA* 4.0 8.0 - - - -
575B LEU 3.2 0.2 - - - -
576B ARG* 1.3 78.6 - - - +
578B MET* 1.3 57.1 + - - +
580B ARG* 3.4 26.7 + - - +
581B GLU* 4.3 5.0 + - - +
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Residues in contact with MET 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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520B ASN* 4.2 18.4 - - + +
521B SER* 4.5 9.2 - - - +
524B MET* 3.3 35.9 - - + +
568B ILE* 3.9 31.4 - - - +
569B ALA* 5.1 2.5 - - - -
574B ALA* 3.3 27.5 + - + +
575B LEU* 3.5 9.4 - - - +
577B SER* 1.3 76.9 - - - +
579B LEU* 1.3 62.3 + - - +
581B GLU* 3.3 33.2 - - - +
582B PHE* 3.4 1.9 - - - -
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Residues in contact with LEU 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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524B MET* 3.7 21.3 - - + -
528B LEU* 5.0 9.9 - - + -
556B LEU* 3.7 30.3 - - + -
559B PHE* 4.6 3.8 - - + -
575B LEU* 2.9 33.2 + - + +
576B ARG* 4.0 8.7 - - + +
577B SER 3.4 0.2 - - - -
578B MET* 1.3 77.2 - - - +
580B ARG* 1.3 54.6 + - - +
581B GLU 3.1 0.4 - - - -
582B PHE* 2.7 32.5 + - + +
583B ILE* 3.2 23.8 + - + +
588B ALA* 5.5 4.0 - - + -
590B ILE* 4.3 15.0 - - + -
600B ILE* 4.3 21.1 - - + -
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Residues in contact with ARG 580 (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 ARG 3.4 13.2 + - - +
577B SER* 3.4 21.3 + - - +
579B LEU* 1.3 77.9 - - - +
581B GLU* 1.3 61.4 + - - +
582B PHE 3.2 0.2 - - - -
583B ILE* 3.6 17.2 - - + +
584B GLU* 2.9 61.2 + - - +
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Residues in contact with GLU 581 (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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521B SER* 3.1 30.4 + - - -
577B SER 4.8 4.2 - - - +
578B MET* 3.3 34.1 - - - +
580B ARG* 1.3 86.6 - - - +
582B PHE* 1.3 63.0 + - + +
584B GLU* 3.4 28.4 - - - +
585B HIS* 3.5 4.3 - - - +
15C PHE* 3.2 52.4 - - + -
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Residues in contact with PHE 582 (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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517B LEU* 4.0 22.2 - - + -
521B SER* 3.4 22.2 - - - -
524B MET* 3.6 20.9 - - + -
525B TYR* 3.6 33.2 - + + -
578B MET 3.4 26.5 - - - -
579B LEU* 2.7 18.8 + - + +
581B GLU* 1.3 85.1 - - + +
583B ILE* 1.3 56.8 + - - -
585B HIS* 3.5 2.8 + - - +
586B LYS 2.8 21.8 + - - -
587B MET* 2.8 47.8 + - + -
588B ALA* 3.5 20.3 + - + -
15C PHE* 5.0 3.6 - + - -
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Residues in contact with ILE 583 (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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579B LEU* 3.2 37.7 + - + +
580B ARG* 3.2 13.6 + - + +
582B PHE* 1.3 75.7 - - - +
584B GLU* 1.3 62.0 + - - +
586B LYS* 2.9 25.1 + - - +
588B ALA* 3.3 29.2 - - + +
589B ASN* 5.3 2.0 - - - +
590B ILE* 3.7 41.3 - - + +
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Residues in contact with GLU 584 (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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580B ARG* 2.9 40.1 + - - +
581B GLU* 3.4 29.0 - - - +
583B ILE* 1.3 78.4 - - - +
585B HIS* 1.3 74.8 + - + +
586B LYS* 4.6 4.4 - - - +
15C PHE* 4.7 6.1 - - - +
20C ARG* 4.1 36.7 + - - +
21C SER* 5.0 6.6 + - - +
22C HIS* 5.7 2.8 - - - -
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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