Contacts of the helix formed by residues 571 - 576 (chain B) in PDB entry 5IJ7
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 CYS 571 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B CYS* 3.7 1.6 - - - -
562B CYS* 3.8 6.3 - - - -
566B CYS* 3.6 23.6 - - - -
568B THR* 3.0 15.1 + - - +
569B LYS 4.3 1.3 - - - -
570B GLN* 1.4 77.1 - - - +
572B PRO* 1.4 61.4 - - - +
573B CYS* 3.3 20.6 + - - -
574B TYR* 3.3 9.8 + - + -
575B LEU* 2.9 29.1 + - - +
9005B ZN 2.1 38.1 - - - -
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Residues in contact with PRO 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B PHE* 3.5 15.3 - - + -
558B PRO* 6.1 1.8 - - + -
559B GLY 3.7 12.6 - - - +
560B CYS* 3.6 27.8 - - + -
561B ARG 5.5 0.4 - - - +
562B CYS* 4.7 2.2 - - - -
570B GLN 3.7 8.7 - - - +
571B CYS* 1.4 82.0 - - - +
573B CYS* 1.3 55.9 + - - +
575B LEU* 3.9 13.4 - - + +
576B ALA* 3.0 31.9 + - - +
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Residues in contact with CYS 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B PHE* 3.9 21.5 - - - -
559B GLY 3.9 0.2 - - - -
560B CYS* 3.7 15.3 - - - -
571B CYS* 3.2 5.8 - - - -
572B PRO* 1.3 73.7 - - - +
574B TYR* 1.4 64.3 + - - +
576B ALA 3.1 8.1 + - - -
578B ARG* 3.0 33.6 + - + +
579B GLU 4.1 6.1 - - - +
580B CYS* 3.7 2.9 - - - -
581B ASP 5.2 0.2 - - - -
585B CYS* 3.5 8.5 - - - -
603B ASN* 3.7 10.8 - - - +
9007B ZN 2.2 38.6 - - - -
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Residues in contact with TYR 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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566B CYS 3.3 26.7 - - - +
567B ASN* 3.6 26.1 + - + -
568B THR* 3.3 31.9 - - - +
569B LYS* 3.9 5.2 - - + -
571B CYS* 3.3 6.6 + - + +
573B CYS* 1.4 75.6 - - - +
575B LEU* 1.3 59.1 + - - +
577B VAL* 3.1 20.4 + - - +
578B ARG 3.9 2.7 - - - +
603B ASN* 3.4 15.7 - - + +
635B ASN* 5.7 5.4 + - - +
696B TYR* 5.6 1.9 + - - -
698B LYS* 3.7 29.3 + - - -
700B MET* 6.3 1.1 - - - -
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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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569B LYS* 3.8 37.0 - - + +
571B CYS 2.9 16.7 + - - +
572B PRO* 3.9 13.0 - - + +
574B TYR* 1.3 80.8 - - - +
576B ALA* 1.3 56.8 + - + +
577B VAL* 3.2 10.4 + - - +
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Residues in contact with ALA 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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542B PHE* 4.6 10.0 - - + -
557B PHE* 4.0 9.9 - - + -
572B PRO 3.0 18.8 + - - +
573B CYS 3.1 1.0 + - - +
575B LEU* 1.3 74.9 - - - +
577B VAL* 1.3 70.1 + - - +
578B ARG* 3.3 28.5 - - - +
701B MET* 5.8 0.2 - - - +
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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