Contacts of the helix formed by residues 516 - 527 (chain B) in PDB entry 3QNF
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 ASP 516 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483B ALA* 5.0 2.5 - - - -
515B VAL* 1.3 67.1 - - - +
517B VAL* 1.3 62.6 + - - +
518B LYS* 3.6 10.7 + - - +
519B THR* 2.6 40.1 + - - -
520B MET* 3.0 23.0 + - - +
564B HIS* 4.9 5.8 + - + +
581B LEU* 5.5 4.2 - - - +
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Residues in contact with VAL 517 (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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448B LEU* 3.9 23.8 - - + -
452B LEU* 4.5 13.9 - - + -
479B TRP* 3.7 17.3 - - + +
482B MET* 4.0 16.6 - - + +
483B ALA* 3.6 23.2 - - + +
515B VAL* 2.9 28.4 + - + +
516B ASP* 1.3 71.8 - - - +
518B LYS* 1.3 54.3 + - - +
520B MET* 3.1 8.1 + - + +
521B MET* 2.8 51.2 + - + +
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Residues in contact with LYS 518 (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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476B GLU* 3.9 34.5 + - + +
479B TRP* 3.6 23.3 + - + +
480B ASP* 3.2 34.7 + - - +
483B ALA* 4.8 1.9 - - + +
516B ASP* 3.2 7.8 - - - +
517B VAL* 1.3 78.8 - - - +
519B THR* 1.3 60.9 + - - +
521B MET* 4.2 0.7 - - - +
522B ASN* 2.7 47.3 + - - +
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Residues in contact with THR 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B ASP* 2.6 37.7 + - - +
518B LYS* 1.3 78.4 - - - +
520B MET* 1.3 63.7 + - - +
522B ASN* 3.7 9.5 + - + +
523B THR* 3.4 18.6 + - + +
564B HIS* 3.8 24.7 - - + +
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Residues in contact with MET 520 (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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447B MET* 5.9 0.4 - - - -
448B LEU* 4.2 26.9 - - + -
451B TYR* 4.6 11.4 - - + -
452B LEU* 5.4 0.2 - - + -
515B VAL* 4.6 16.6 - - + -
516B ASP 3.0 12.7 + - - +
517B VAL* 3.1 12.5 + - + +
519B THR* 1.3 72.9 - - - +
521B MET* 1.3 68.1 + - - +
522B ASN 3.0 1.3 - - - -
523B THR* 2.5 34.5 + - - -
524B TRP* 3.6 5.8 - - + +
564B HIS* 3.3 42.5 + - + +
566B PRO* 4.2 17.9 - - - -
581B LEU* 3.7 23.8 - - + -
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Residues in contact with MET 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ILE* 3.6 51.1 - - + +
445B LEU* 4.6 0.7 - - - +
447B MET* 5.6 2.0 - - - -
448B LEU* 4.0 26.7 - - + -
479B TRP* 3.6 56.5 - - + +
517B VAL* 2.8 28.6 + - + +
520B MET* 1.3 82.1 - - + +
522B ASN* 1.3 62.5 - - - +
524B TRP* 3.1 12.0 + - + +
525B THR* 2.9 27.5 + - - +
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Residues in contact with ASN 522 (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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475B ASN* 4.8 8.3 - - - +
476B GLU* 6.1 1.3 - - - +
479B TRP* 5.1 4.7 + - - -
518B LYS* 2.7 44.1 + - - +
519B THR* 3.7 10.0 - - + +
520B MET 3.0 0.6 + - - -
521B MET* 1.3 78.2 - - - +
523B THR* 1.3 55.7 + - - +
525B THR* 3.5 7.8 + - - -
526B LEU* 2.9 56.9 + - + +
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Residues in contact with THR 523 (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 THR* 3.4 17.0 - - + +
520B MET 2.5 23.7 + - - +
522B ASN* 1.3 73.0 - - + +
524B TRP* 1.3 69.1 + - - -
527B GLN* 2.8 45.7 + - - +
562B LEU 4.1 8.5 - - - +
563B TRP* 3.4 7.2 + - - -
564B HIS* 3.4 40.2 + - + +
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Residues in contact with TRP 524 (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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419B VAL* 4.8 3.3 + - - +
440B LYS* 3.9 18.8 + - - -
444B ILE* 3.8 24.9 - - + +
447B MET* 3.1 36.8 - - + +
520B MET* 3.6 14.6 - - + -
521B MET* 3.1 14.4 + - - +
523B THR* 1.3 96.5 + - - +
525B THR* 1.3 59.7 + - - +
526B LEU 3.7 0.2 - - - -
527B GLN 3.8 11.2 - - - +
529B GLY 4.7 3.4 - - - -
530B PHE* 4.0 2.0 - - + -
531B PRO* 3.3 28.7 - - + -
563B TRP* 3.5 25.4 - + - +
564B HIS 3.3 18.1 + - - -
565B VAL* 4.2 10.5 - - + -
566B PRO* 4.0 10.1 - - + +
607B TYR* 3.2 47.1 - + + -
608B TYR* 4.6 2.0 - - + -
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Residues in contact with THR 525 (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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373B TRP* 3.5 31.3 - - + -
418B PRO* 3.7 1.2 - - - +
419B VAL* 3.6 13.5 + - + -
420B SER* 3.0 41.1 + - - -
444B ILE* 3.7 20.6 - - + -
475B ASN* 5.0 3.1 + - - -
479B TRP* 4.8 6.8 + - + +
521B MET 2.9 19.0 + - - +
522B ASN* 3.5 13.9 + - - -
524B TRP* 1.3 78.4 - - - +
526B LEU* 1.3 68.2 + - - +
527B GLN 3.6 1.1 - - - -
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Residues in contact with LEU 526 (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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418B PRO* 3.6 17.2 - - - +
420B SER* 4.2 22.9 - - - +
522B ASN* 2.9 41.4 + - + +
525B THR* 1.3 87.1 - - - +
527B GLN* 1.3 60.1 + - + +
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Residues in contact with GLN 527 (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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418B PRO* 4.4 4.7 - - - +
419B VAL 5.5 0.2 + - - -
440B LYS* 4.1 1.7 + - - -
523B THR* 2.8 40.1 + - - +
524B TRP 3.8 15.1 - - - +
525B THR 4.8 0.2 - - - -
526B LEU* 1.3 81.2 - - + +
528B LYS* 1.3 65.8 + - - +
529B GLY 4.0 4.5 - - - +
561B TYR* 3.7 38.1 - - + -
562B LEU 2.6 41.7 + - - +
563B TRP* 3.9 11.2 + - + +
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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