Contacts of the helix formed by residues 562 - 568 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560C PHE 3.7 1.2 + - - -
561C PRO* 1.3 68.9 - - - +
563C ILE* 1.3 58.4 + - - +
564C VAL* 3.1 22.7 + - - +
565C GLN* 3.2 24.7 + - + +
566C LEU* 3.1 30.5 + - - +
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Residues in contact with ILE 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C LEU* 4.2 38.1 - - + +
510C ILE* 4.2 4.5 - - + -
511C LYS* 3.3 46.9 - - + +
514C THR* 4.0 11.7 - - - +
515C GLU* 5.3 3.8 - - + +
547C PHE* 4.0 13.5 - - + -
555C LEU* 4.0 20.9 - - + -
561C PRO* 3.3 13.3 + - + +
562C ASN* 1.3 71.8 + - - +
564C VAL* 1.4 61.2 + - + +
566C LEU* 3.7 9.5 - - + +
567C GLY* 3.0 23.7 + - - -
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Residues in contact with VAL 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C LEU* 4.7 6.5 - - + -
562C ASN* 3.1 10.2 + - - +
563C ILE* 1.4 75.4 - - + +
565C GLN* 1.3 65.3 + - - +
567C GLY 3.2 1.0 + - - -
568C LEU* 3.0 28.7 + - + +
580C ALA* 3.5 27.5 - - - +
583C GLN* 3.0 38.4 - - + +
584C ALA* 4.2 18.8 - - + +
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Residues in contact with GLN 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C ASN* 3.2 30.9 + - + +
564C VAL* 1.3 77.5 - - - +
566C LEU* 1.3 66.2 + - + +
568C LEU* 3.2 31.8 + - - +
569C CYS* 3.5 21.9 + - - -
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Residues in contact with LEU 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C PHE* 3.7 19.4 - - + -
551C ASN* 3.6 34.8 + - + +
554C LEU* 4.2 14.8 - - + -
555C LEU* 4.5 9.4 - - + -
561C PRO* 3.7 31.2 - - + -
562C ASN 3.1 15.0 + - - +
563C ILE* 3.7 11.4 - - + +
564C VAL 3.3 0.2 - - - -
565C GLN* 1.3 82.8 - - + +
567C GLY* 1.3 62.2 + - - +
569C CYS* 3.2 24.8 + - - +
570C GLU* 3.9 5.2 + - - +
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Residues in contact with GLY 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C LEU* 5.5 0.7 - - - -
547C PHE* 3.7 12.5 - - - -
563C ILE 3.0 16.2 + - - -
564C VAL 3.2 3.5 + - - -
566C LEU* 1.3 71.8 - - - +
568C LEU* 1.3 57.1 + - - +
569C CYS 3.0 5.6 - - - -
570C GLU* 3.0 17.4 + - - +
576C VAL* 4.0 11.7 - - - -
577C TYR* 3.4 18.0 - - - -
580C ALA* 3.6 13.9 - - - -
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Residues in contact with LEU 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564C VAL* 3.0 28.3 + - + +
565C GLN* 3.2 26.4 + - - +
567C GLY* 1.3 75.7 - - - +
569C CYS* 1.3 58.5 + - - +
570C GLU 3.3 0.9 - - - +
577C TYR* 3.3 28.6 - - + -
580C ALA* 3.9 4.0 - - + +
581C LYS* 3.7 53.6 - - + +
584C ALA* 4.6 10.1 - - + -
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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