Contacts of the helix formed by residues 508 - 516 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ARG* 5.9 2.4 - - - +
506D HIS* 3.1 20.4 + - + +
507D THR* 1.3 78.9 + - - +
509D VAL* 1.3 65.6 + - - +
510D GLU* 2.8 17.9 + - - +
511D GLU* 2.9 35.9 + - + +
512D LEU* 2.9 22.0 + - - +
588D HIS* 3.6 9.3 + - - +
589D ASP* 3.0 27.3 + - - +
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Residues in contact with VAL 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ARG* 5.6 3.6 - - + +
463D PHE* 3.7 20.9 - - + -
469D ARG* 3.7 31.2 - - - +
507D THR 3.7 1.8 + - - -
508D ASN* 1.3 69.3 - - - +
510D GLU* 1.3 60.2 + - - +
512D LEU* 3.6 10.8 - - - +
513D MET* 3.2 42.0 + - + +
579D PHE* 3.8 20.4 - - + -
587D ALA 4.2 0.2 - - - +
588D HIS* 3.1 33.3 + - + +
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Residues in contact with GLU 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 3.7 30.9 - - - -
314A ARG* 4.8 17.4 + - + +
340A VAL* 4.0 15.9 - - + +
342A GLN* 4.2 13.3 - - - +
508D ASN* 3.0 13.0 + - - +
509D VAL* 1.3 77.8 - - - +
511D GLU* 1.3 69.6 + - - +
513D MET* 3.5 7.9 + - - +
514D LYS* 3.1 51.4 + - - +
588D HIS 4.7 0.4 + - - -
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Residues in contact with GLU 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D HIS* 3.6 43.1 + - + +
508D ASN* 2.9 17.7 + - - +
510D GLU* 1.3 77.5 - - + +
512D LEU* 1.3 64.3 + - - +
514D LYS* 3.1 32.1 + - - +
515D LEU* 3.1 28.2 + - - +
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Residues in contact with LEU 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D GLN 5.7 1.8 - - - +
463D PHE* 3.9 19.3 - - + +
503D PHE* 3.6 20.2 - - + +
504D LEU* 3.3 31.1 - - - +
505D GLY 3.6 0.7 - - - +
506D HIS* 3.1 44.1 - - - +
508D ASN 2.9 8.2 + - - +
509D VAL* 3.6 13.7 - - - +
511D GLU* 1.3 74.5 - - - +
513D MET* 1.3 64.1 + - + +
515D LEU* 3.3 17.3 + - - +
516D GLY 3.6 4.5 + - - +
579D PHE* 3.3 39.0 - - + -
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Residues in contact with MET 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ARG 3.9 19.1 - - - +
316A TYR* 3.5 37.5 - - + -
338A THR* 3.5 20.4 - - + +
340A VAL* 3.4 21.5 - - + -
463D PHE* 3.6 35.0 - - + -
465D ASN* 6.0 0.4 - - - -
469D ARG* 5.4 1.6 - - - +
503D PHE* 3.7 26.0 - - + -
509D VAL* 3.2 26.0 + - + +
510D GLU* 3.5 3.8 + - - +
511D GLU 3.3 0.2 - - - -
512D LEU* 1.3 81.4 - - + +
514D LYS* 1.3 61.8 + - - +
516D GLY* 3.1 12.5 + - - -
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Residues in contact with LYS 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A THR 5.0 0.9 - - - +
340A VAL* 3.8 11.4 - - + -
342A GLN* 3.0 27.8 + - - -
348A HIS* 3.6 45.5 + - + +
349A ARG* 4.7 9.2 + - - -
510D GLU* 3.1 41.8 + - - +
511D GLU* 3.1 36.0 + - - +
513D MET* 1.3 76.7 - - - +
515D LEU* 1.3 61.5 + - - +
516D GLY* 3.3 1.4 + - - -
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Residues in contact with LEU 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ARG* 5.7 1.4 + - - -
504D LEU 3.6 17.5 - - - +
505D GLY* 3.5 26.9 - - - +
506D HIS* 4.0 17.3 - - + -
511D GLU* 3.1 15.5 + - - +
512D LEU* 3.6 8.7 - - - +
513D MET 3.2 0.4 - - - -
514D LYS* 1.3 77.5 - - + +
516D GLY* 1.3 60.2 + - - +
518D HIS* 5.0 6.1 + - - +
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Residues in contact with GLY 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A SER* 4.8 4.0 - - - -
338A THR* 4.0 10.5 - - - -
349A ARG* 5.7 4.3 - - - -
503D PHE* 3.7 11.2 - - - -
504D LEU 4.9 0.3 + - - -
512D LEU 3.6 2.8 + - - +
513D MET 3.1 13.8 + - - -
514D LYS 3.2 2.0 - - - -
515D LEU* 1.3 78.7 - - - +
517D ASN* 1.3 68.2 + - - -
518D HIS* 3.1 21.2 + - - -
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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