Contacts of the helix formed by residues 508 - 516 (chain B) in PDB entry 2QY0
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 508 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B HIS* 3.0 20.5 + - + +
507B THR* 1.3 79.4 + - - +
509B VAL* 1.3 51.7 + - - +
510B GLU* 2.9 19.0 + - - +
511B GLU* 2.7 36.3 + - + +
512B LEU* 2.7 35.1 + - - +
588B HIS* 3.6 9.9 + - - +
589B ASP* 2.9 27.6 + - - +
314C ARG* 5.6 2.4 - - - +
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B PHE* 4.0 19.7 - - + -
469B ARG* 4.1 17.3 - - - +
507B THR 3.7 0.2 + - - -
508B ASN* 1.3 68.2 - - - +
510B GLU* 1.3 66.9 + - - +
512B LEU* 3.5 8.6 - - - +
513B MET* 3.2 48.5 + - + +
579B PHE* 3.8 25.8 - - + -
587B ALA 4.5 0.2 - - - +
588B HIS* 3.1 34.5 + - + +
314C ARG* 5.9 5.4 - - + +
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Residues in contact with GLU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B ASN* 2.9 14.8 + - - +
509B VAL* 1.3 79.9 - - - +
511B GLU* 1.3 60.9 + - + +
513B MET* 3.2 9.9 + - - +
514B LYS* 3.1 54.8 + - + +
313C PHE* 4.1 27.6 - - + -
314C ARG* 5.0 18.9 + - + +
340C VAL* 4.1 17.4 - - + +
342C GLN* 4.1 15.1 - - - +
343C ASP* 4.7 1.0 + - - -
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Residues in contact with GLU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B HIS* 3.6 33.9 + - + +
508B ASN* 2.7 26.9 + - + +
510B GLU* 1.3 71.6 - - + +
512B LEU* 1.3 64.2 + - - +
513B MET 3.2 0.2 - - - -
514B LYS* 3.9 27.3 + - + +
515B LEU* 3.1 29.8 + - - +
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Residues in contact with LEU 512 (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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461B GLN 5.6 1.8 - - - +
463B PHE* 3.5 24.9 - - + +
503B PHE* 3.4 24.0 - - + +
504B LEU* 3.4 41.7 - - - +
505B GLY 3.7 0.4 - - - +
506B HIS* 3.3 28.9 - - - +
508B ASN 2.7 14.4 + - - +
509B VAL* 3.5 14.1 - - - +
510B GLU 3.3 0.2 - - - -
511B GLU* 1.3 73.6 - - - +
513B MET* 1.3 61.7 + - + +
515B LEU* 3.5 13.0 + - - +
516B GLY 3.6 3.8 + - - +
579B PHE* 3.3 38.1 - - + -
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Residues in contact with MET 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B PHE* 3.7 30.3 - - + -
465B ASN* 5.7 0.4 - - - +
469B ARG* 5.5 1.8 - - - +
503B PHE* 3.7 22.9 - - + -
509B VAL* 3.2 29.2 + - + +
510B GLU* 3.2 7.6 + - - +
512B LEU* 1.3 76.1 - - + +
514B LYS* 1.3 61.5 + - - +
516B GLY* 3.1 14.6 + - - -
314C ARG 3.9 18.8 - - - +
316C TYR* 3.6 35.2 - - + -
338C THR* 3.4 22.0 - - + +
340C VAL* 3.4 20.9 - - + -
802C GOL 5.6 1.8 - - - +
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Residues in contact with LYS 514 (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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510B GLU* 3.1 44.7 + - + +
511B GLU* 3.9 30.2 + - - +
512B LEU 3.4 0.2 - - - -
513B MET* 1.3 73.8 - - - +
515B LEU* 1.3 64.8 + - - +
516B GLY* 3.1 2.3 + - - -
338C THR 5.3 0.7 - - - +
340C VAL* 3.9 9.9 - - + -
342C GLN* 3.1 32.8 - - - +
348C HIS* 3.7 45.0 + - + +
349C ARG* 4.6 9.4 + - - -
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Residues in contact with LEU 515 (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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504B LEU 3.4 24.2 - - - +
505B GLY* 3.6 24.0 - - - +
506B HIS* 4.0 15.7 - - + -
511B GLU* 3.1 17.3 + - - +
512B LEU* 3.6 9.0 - - - +
513B MET 3.3 0.4 - - - -
514B LYS* 1.3 76.9 - - - +
516B GLY* 1.3 60.2 + - - +
518B HIS* 5.2 4.0 + - - +
349C ARG* 5.7 1.6 + - - -
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Residues in contact with GLY 516 (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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503B PHE* 3.6 11.5 - - - -
504B LEU 5.0 0.3 + - - -
512B LEU 3.6 3.4 + - - +
513B MET 3.1 15.3 + - - -
514B LYS 4.0 1.8 - - - -
515B LEU* 1.3 81.5 - - - +
517B ASN* 1.3 68.4 + - - -
518B HIS* 3.3 18.0 + - - -
336C SER* 4.7 3.8 - - - -
337C PHE* 6.0 0.2 - - - -
338C THR* 3.8 10.3 - - - -
349C ARG* 6.0 2.9 - - - -
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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