Contacts of the helix formed by residues 561 - 572 (chain B) in PDB entry 5NV6
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 ASP 561 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557B ARG* 3.1 39.4 + - - +
558B LEU 3.0 17.2 - - - +
560B GLY* 1.4 72.8 - - - +
562B ALA* 1.3 61.2 + - - +
563B LYS* 3.8 13.8 + - - +
564B GLU* 3.3 27.0 + - + +
565B LEU 3.2 17.7 + - - -
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Residues in contact with ALA 562 (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 SER* 4.8 14.4 - - - +
525B ALA* 4.8 4.2 - - - -
558B LEU 4.6 1.1 - - - -
559B LEU 4.7 3.3 + - - +
560B GLY 3.8 4.8 + - - +
561B ASP* 1.3 70.5 + - - +
563B LYS* 1.4 59.8 + - - +
564B GLU 3.4 0.2 - - - -
565B LEU* 3.6 13.0 + - + +
566B ALA* 3.2 27.0 + - - +
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Residues in contact with LYS 563 (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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561B ASP* 3.3 13.9 + - - +
562B ALA* 1.4 75.5 - - - +
564B GLU* 1.4 60.6 + - - +
566B ALA* 3.7 7.9 + - - +
567B ASN* 2.9 34.1 + - - +
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Residues in contact with GLU 564 (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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554B GLU* 6.0 2.1 - - - +
557B ARG* 3.0 49.7 + - - +
558B LEU* 4.7 12.3 - - + +
561B ASP* 3.3 24.2 + - + +
562B ALA 3.4 0.2 - - - -
563B LYS* 1.4 77.0 - - - +
565B LEU* 1.4 63.7 + - - +
567B ASN* 3.3 11.3 + - + +
568B ILE* 3.2 37.9 + - + +
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Residues in contact with LEU 565 (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 ALA* 3.8 34.8 - - + +
524B SER* 4.0 17.9 - - - -
525B ALA 4.6 4.9 - - - +
547B PHE* 6.2 3.4 - - + -
558B LEU* 3.3 56.7 + - + +
559B LEU* 4.9 3.8 - - - +
561B ASP 3.2 8.1 + - - +
562B ALA* 3.7 11.0 - - + +
564B GLU* 1.4 73.4 - - - +
566B ALA* 1.4 62.2 + - - +
568B ILE* 3.5 3.2 + - + +
569B LEU* 3.2 32.4 + - + +
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Residues in contact with ALA 566 (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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525B ALA* 3.8 31.4 - - + +
527B LEU* 4.0 2.7 - - + +
562B ALA 3.2 16.5 + - - +
563B LYS* 3.7 9.2 - - - +
564B GLU 3.3 0.2 - - - -
565B LEU* 1.4 77.0 - - - +
567B ASN* 1.4 58.0 + - - +
569B LEU* 3.6 2.4 + - - +
570B LYS* 3.0 45.2 + - - +
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Residues in contact with ASN 567 (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 LYS* 2.9 28.9 + - - +
564B GLU* 3.3 12.3 + - + +
566B ALA* 1.4 76.3 - - - +
568B ILE* 1.4 65.4 + - + +
570B LYS* 3.4 15.9 + - - +
571B TYR* 3.2 18.4 + - - +
593B GLN* 3.3 33.6 + - + +
634B PRO* 5.3 1.8 - - + -
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Residues in contact with ILE 568 (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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547B PHE* 6.5 0.2 - - + -
554B GLU* 5.9 1.6 - - - +
558B LEU* 3.7 25.4 - - + -
564B GLU* 3.2 28.6 + - + +
565B LEU* 3.8 6.1 - - + +
566B ALA 3.4 0.4 - - - -
567B ASN* 1.4 75.1 - - + +
569B LEU* 1.4 58.0 + - + +
571B TYR* 3.3 15.9 + - - +
572B HIS* 2.8 32.3 + - + -
631B VAL* 4.1 12.6 - - + -
632B LEU 3.7 18.8 - - - +
633B GLN* 5.0 7.2 - - + -
634B PRO* 3.7 26.9 - - + -
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Residues in contact with LEU 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B LEU* 3.8 28.9 - - + -
521B ALA* 3.4 44.2 - - + +
522B ILE* 3.9 13.8 - - + +
525B ALA* 3.8 14.4 - - + -
527B LEU* 3.8 13.0 - - + -
542B PRO* 5.8 0.7 - - + -
547B PHE* 5.0 8.7 - - + -
565B LEU* 3.2 25.5 + - + +
566B ALA 3.9 0.7 - - - +
567B ASN 3.4 0.2 - - - -
568B ILE* 1.4 75.3 - - + +
570B LYS* 1.4 63.1 + - - +
572B HIS* 3.1 25.1 + - + +
573B ILE* 3.4 17.9 - - - +
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Residues in contact with LYS 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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527B LEU* 4.1 27.1 - - + -
566B ALA* 3.0 34.2 + - - +
567B ASN* 3.6 18.1 + - - +
568B ILE 3.4 0.2 - - - -
569B LEU* 1.4 74.4 - - - +
571B TYR* 1.4 56.7 + - - +
573B ILE* 3.1 18.8 + - - +
592B LEU* 3.1 48.4 + - + +
593B GLN* 3.6 14.1 - - - +
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Residues in contact with TYR 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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567B ASN 3.2 13.2 + - - +
568B ILE 3.3 12.8 - - - +
569B LEU 3.2 0.4 - - - -
570B LYS* 1.4 77.5 - - - +
572B HIS* 1.4 56.4 + - - +
591B SER* 3.4 14.7 - - - -
593B GLN* 3.3 19.7 - - + +
595B ASP* 3.4 29.2 - - + -
596B LYS 2.9 20.0 + - - -
597B LEU* 3.4 35.0 - - + +
609B ASN* 3.1 32.5 + - - -
632B LEU* 4.0 17.7 - - + -
633B GLN 3.7 12.8 - - - -
634B PRO* 3.7 26.5 - - + -
635B PRO* 3.5 13.9 - - + +
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Residues in contact with HIS 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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518B LEU* 6.5 0.2 - - + -
538B THR 3.0 5.7 - - - +
539B VAL* 5.2 2.9 - - + -
540B PHE* 2.8 62.9 + - - +
542B PRO* 3.6 22.0 - - + +
568B ILE* 2.8 31.7 + - + -
569B LEU* 3.1 17.9 + - + +
571B TYR* 1.4 76.7 - - + +
573B ILE* 1.4 58.4 + - + +
628B ILE* 3.7 2.5 - - + -
631B VAL* 3.9 11.9 - - + -
632B LEU* 2.9 61.9 + - + -
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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