Contacts of the helix formed by residues 562 - 568 (chain B) in PDB entry 1Z6T
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 562 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560B PHE 3.7 1.2 + - - -
561B PRO* 1.3 68.8 - - - +
563B ILE* 1.3 59.6 + - - +
564B VAL* 3.1 22.1 + - - +
565B GLN* 3.3 24.7 + - + +
566B LEU* 3.1 29.3 + - - +
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Residues in contact with ILE 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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507B LEU* 4.1 38.6 - - + +
510B ILE* 4.3 4.3 - - + -
511B LYS* 3.3 49.7 - - + +
514B THR* 4.2 3.8 - - - +
515B GLU* 5.2 3.1 - - + +
547B PHE* 4.1 11.8 - - + -
555B LEU* 4.1 28.7 - - + -
561B PRO* 3.3 12.6 + - + +
562B ASN* 1.3 71.6 + - - +
564B VAL* 1.3 60.7 + - + +
566B LEU* 3.6 9.0 + - + +
567B GLY* 3.0 23.9 + - - -
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Residues in contact with VAL 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 4.7 6.7 - - + -
562B ASN* 3.1 9.9 + - - +
563B ILE* 1.3 76.1 - - + +
565B GLN* 1.3 64.3 + - - +
567B GLY 3.2 0.9 + - - -
568B LEU* 3.0 33.4 + - + +
580B ALA* 3.4 28.6 - - - +
583B GLN* 3.4 37.0 - - + +
584B ALA* 4.1 14.4 - - + +
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Residues in contact with GLN 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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562B ASN* 3.3 31.7 + - + +
564B VAL* 1.3 77.9 - - - +
566B LEU* 1.3 66.3 + - + +
568B LEU* 3.2 29.3 + - - +
569B CYS* 3.5 25.0 + - - -
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Residues in contact with LEU 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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547B PHE* 3.7 19.2 - - + -
551B ASN* 3.6 36.5 + - + +
554B LEU* 3.9 16.6 - - + -
555B LEU* 4.3 10.8 - - + -
561B PRO* 3.8 30.3 - - + -
562B ASN 3.1 13.2 + - - +
563B ILE* 3.7 12.1 - - + +
564B VAL 3.3 0.2 - - - -
565B GLN* 1.3 81.1 - - + +
567B GLY* 1.3 62.6 + - - +
569B CYS* 3.2 25.5 + - + +
570B GLU* 3.9 5.4 + - - +
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Residues in contact with GLY 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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507B LEU* 5.5 0.7 - - - -
547B PHE* 3.7 13.7 - - - -
563B ILE 3.0 14.4 + - - -
564B VAL 3.2 3.3 + - - -
566B LEU* 1.3 71.6 - - - +
568B LEU* 1.3 55.8 + - - +
569B CYS 3.1 5.4 - - - -
570B GLU* 3.1 16.9 + - - +
576B VAL* 3.9 11.2 - - - -
577B TYR* 3.3 20.4 - - - -
580B ALA* 3.6 15.3 - - - -
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Residues in contact with LEU 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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564B VAL* 3.0 32.3 + - + +
565B GLN* 3.2 24.1 + - - +
567B GLY* 1.3 76.6 - - - +
569B CYS* 1.3 58.8 + - - +
570B GLU 3.3 0.9 - - - +
577B TYR* 3.4 28.8 - - + +
580B ALA* 3.9 3.1 - - + -
581B LYS* 3.7 53.6 - - + +
584B ALA* 4.4 11.4 - - + -
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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