Contacts of the helix formed by residues 567 - 573 (chain B) in PDB entry 1QCO
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 LEU 567 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519B TYR* 3.7 36.1 - - + +
520B GLY* 4.3 2.5 - - - +
521B VAL* 4.5 5.4 - - + -
532B ILE* 3.6 39.0 - - + -
566B THR* 1.3 72.3 - - - +
568B ASN* 1.3 64.7 + - - +
569B ASN 3.4 1.1 - - - -
570B PHE* 3.0 24.7 + - + +
571B MET* 2.8 45.7 + - + +
618B PRO* 2.9 39.3 + - + +
726B PHE* 5.0 2.5 - - + -
763B VAL* 4.3 3.8 - - + -
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Residues in contact with ASN 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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566B THR* 3.3 17.7 + - - +
567B LEU* 1.3 75.6 - - - +
569B ASN* 1.3 62.6 + - - +
571B MET* 3.1 11.0 + - - +
572B GLY* 2.9 25.3 + - - -
619B ALA* 3.3 8.7 - - - +
620B THR* 2.9 52.2 + - - +
842B PRO* 3.3 33.0 + - + +
843B GLY* 3.9 2.4 - - - -
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Residues in contact with ASN 569 (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 VAL* 3.9 21.6 - - + +
564B GLU* 3.1 37.5 + - + -
566B THR* 4.6 2.6 + - - -
567B LEU 3.4 0.6 - - - -
568B ASN* 1.3 83.5 - - - +
570B PHE* 1.3 62.0 + - - +
572B GLY* 3.3 3.7 + - - -
573B LEU* 3.2 25.8 + - - +
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Residues in contact with PHE 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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519B TYR* 3.7 30.5 - + - -
532B ILE* 5.4 0.2 - - + -
555B LEU* 4.4 5.8 - - + -
561B VAL* 4.2 24.4 + - + +
562B PHE* 3.8 32.3 - + + -
566B THR 5.4 0.2 + - - -
567B LEU* 3.0 28.3 + - + +
569B ASN* 1.3 77.8 - - - +
571B MET* 1.3 62.9 + - - +
573B LEU* 3.2 16.9 + - + +
577B ALA* 4.3 7.0 - - + -
578B TRP* 3.1 34.9 + + - -
581B ALA* 3.7 26.0 - - + -
726B PHE* 3.8 26.7 - + - -
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Residues in contact with MET 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 LEU* 2.8 43.9 + - + +
568B ASN* 3.5 7.2 - - - +
570B PHE* 1.3 76.3 - - - +
572B GLY* 1.3 61.5 + - - +
578B TRP* 3.0 30.4 - - - +
618B PRO 5.3 0.2 - - - -
619B ALA* 4.2 9.6 - - + -
705B PHE* 3.8 35.4 - - + -
706B VAL 3.9 14.8 - - - +
707B GLY* 3.1 11.3 - - - -
708B PRO 3.5 0.2 - - - -
726B PHE* 3.9 32.5 - - + -
763B VAL* 4.7 2.2 - - + -
842B PRO* 4.5 2.7 - - + -
843B GLY* 3.9 26.5 - - - -
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Residues in contact with GLY 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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568B ASN 2.9 13.7 + - - -
569B ASN* 3.3 6.0 + - - -
570B PHE 3.2 0.6 - - - -
571B MET* 1.3 76.7 - - - +
573B LEU* 1.3 62.9 + - - +
574B GLY 3.3 1.1 + - - -
708B PRO* 3.7 17.0 - - - +
842B PRO* 3.8 23.1 - - - +
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Residues in contact with LEU 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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554B ALA 5.4 0.4 - - - +
555B LEU* 4.2 7.2 - - + -
558B HIS* 4.0 41.1 - - + +
561B VAL* 3.9 32.5 - - + -
569B ASN 3.2 13.8 + - - +
570B PHE* 3.2 14.1 + - + +
572B GLY* 1.3 77.2 - - - +
574B GLY* 1.3 59.3 + - - +
576B ALA* 5.4 1.0 + - - +
577B ALA* 3.6 28.1 + - + +
708B PRO* 4.6 0.4 - - - -
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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