Contacts of the helix formed by residues 531 - 544 (chain A) in PDB entry 5Y7G
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 GLN 531 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A GLY* 5.9 0.2 - - - -
524A LYS* 4.2 2.7 - - - +
528A ASP* 4.6 8.4 - - - +
529A ARG 4.1 7.2 - - - +
530A LEU* 1.3 76.5 - - - +
532A ASP* 1.3 60.3 + - - +
533A ASN* 3.4 25.0 + - - +
534A GLN* 3.1 30.1 + - - +
535A LEU* 2.8 28.4 + - - +
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Residues in contact with ASP 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ALA* 5.1 1.9 - - + +
325A GLN* 3.1 42.8 + - - +
326A GLY* 4.8 1.7 + - - -
329A ARG* 2.4 42.4 + - - -
530A LEU 4.9 2.4 - - - +
531A GLN* 1.3 74.7 - - - +
533A ASN* 1.3 58.9 + - - +
535A LEU* 3.0 5.9 + - - +
536A ARG* 2.9 28.2 + - - +
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Residues in contact with ASN 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A ARG* 4.8 0.2 + - - -
500A GLY 5.2 3.1 - - - +
503A ALA* 4.2 17.0 - - - +
504A GLY* 4.0 20.7 - - - +
531A GLN* 3.5 28.7 + - - +
532A ASP* 1.3 76.0 + - - +
534A GLN* 1.3 71.4 + - - +
536A ARG* 3.1 35.0 + - - +
537A TRP* 3.0 24.8 + - - +
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Residues in contact with GLN 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A GLY* 3.2 24.6 - - - +
505A LEU 4.2 9.1 + - - -
507A ASP* 5.2 2.0 + - - -
522A GLU* 4.0 20.5 + - + -
524A LYS* 2.7 36.0 + - - +
530A LEU* 3.9 9.3 - - + +
531A GLN* 3.1 33.3 + - + +
533A ASN* 1.3 91.2 + - - +
535A LEU* 1.3 63.0 + - - +
537A TRP* 3.0 3.6 + - - +
538A LEU* 2.9 29.6 + - + +
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A GLN* 3.7 16.2 - - - +
329A ARG* 6.2 1.1 - - - +
351A ILE* 5.2 9.0 - - + -
530A LEU* 3.4 48.7 - - + +
531A GLN 2.8 13.6 + - - +
532A ASP* 3.0 12.8 + - - +
534A GLN* 1.3 73.8 - - - +
536A ARG* 1.3 57.7 + - - +
538A LEU* 3.8 7.4 - - + +
539A GLN* 2.9 54.3 + - + +
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Residues in contact with ARG 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASP* 4.0 27.1 - - + +
322A ALA* 3.0 31.5 - - - +
325A GLN* 3.0 28.1 + - + +
493A ARG* 3.8 21.6 + - - +
500A GLY* 3.9 21.0 + - - -
501A ASN* 4.3 8.7 + - - -
532A ASP* 2.9 9.7 + - - +
533A ASN* 3.1 40.6 + - - +
535A LEU* 1.3 76.2 - - - +
537A TRP* 1.3 58.2 + - - +
539A GLN* 4.8 2.2 - - - -
540A PHE* 2.9 32.4 + - - +
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Residues in contact with TRP 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ILE* 5.5 4.6 - - + +
490A TRP* 4.4 28.3 - + + -
493A ARG* 3.1 54.0 - - + +
494A LEU* 4.2 9.0 - - + -
501A ASN* 2.8 43.7 - - + -
503A ALA 3.6 11.4 - - - -
504A GLY 3.9 13.0 - - - +
505A LEU* 3.2 38.0 - - + +
506A PRO* 5.1 7.0 - - + -
520A MET* 6.2 1.3 - - - -
533A ASN 3.0 9.3 + - - +
534A GLN 3.0 8.7 + - - +
536A ARG* 1.3 78.0 - - - +
538A LEU* 1.3 64.2 + - + +
540A PHE* 3.3 4.9 + + - +
541A CYS* 3.0 32.2 + - - -
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Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 4.1 15.7 - - + -
506A PRO* 4.2 20.0 - - + -
522A GLU* 4.9 7.2 - - + -
530A LEU* 3.8 26.9 - - + -
534A GLN* 2.9 18.6 + - + +
535A LEU* 3.8 8.7 - - + +
537A TRP* 1.3 76.0 - - + +
539A GLN* 1.3 57.9 + - - +
541A CYS* 3.2 5.9 + - - +
542A ARG* 2.9 28.2 + - - +
548A VAL* 3.7 34.3 - - + +
549A ALA* 5.0 3.1 - - - +
550A VAL* 3.7 30.1 - - + -
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Residues in contact with GLN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ALA* 4.5 13.4 - - - +
349A PRO* 3.9 29.8 - - + +
351A ILE* 4.8 15.2 - - + +
535A LEU* 2.9 43.8 + - + +
536A ARG* 4.2 3.1 - - - +
538A LEU* 1.3 74.5 - - - +
540A PHE* 1.3 57.8 + - - +
542A ARG* 3.7 4.9 - - + +
543A GLU* 2.9 47.8 + - - +
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Residues in contact with PHE 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A ALA* 4.0 25.8 - - + -
490A TRP* 3.7 30.5 - + - -
493A ARG* 3.7 43.5 - - + +
536A ARG 2.9 19.4 + - - +
537A TRP* 3.6 9.0 - - - +
539A GLN* 1.3 78.3 - - - +
541A CYS* 1.3 66.8 + - - +
543A GLU* 3.6 2.9 + - - -
544A ARG* 2.9 85.8 + - + +
546A MET* 4.8 0.9 - - - -
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Residues in contact with CYS 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A TRP* 3.6 30.3 - - - -
520A MET* 5.2 4.7 - - - -
537A TRP* 3.0 30.3 + - - -
538A LEU 3.2 7.2 + - - +
540A PHE* 1.3 76.5 - - - +
542A ARG* 1.3 58.6 + - - +
544A ARG* 2.9 18.4 + - - +
546A MET* 3.0 42.6 + - + -
548A VAL* 3.9 27.6 - - + -
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Residues in contact with ARG 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A PRO* 3.5 32.2 + - + +
350A GLU 3.4 26.7 + - - +
351A ILE* 5.1 7.6 - - + -
352A ASP* 5.4 8.9 + - - +
538A LEU 2.9 17.3 + - - +
539A GLN* 3.0 10.5 + - + +
541A CYS* 1.3 77.9 - - - +
543A GLU* 1.3 59.5 + - - +
545A GLU* 3.2 37.4 + - - +
546A MET 4.4 7.6 - - - +
548A VAL* 4.7 10.1 - - + +
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Residues in contact with GLU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PRO* 4.6 15.8 - - + +
539A GLN* 2.9 35.7 + - - +
540A PHE* 4.0 4.6 - - - +
542A ARG* 1.3 77.9 - - - +
544A ARG* 1.3 83.6 + - - +
545A GLU* 3.2 10.8 + - - +
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Residues in contact with ARG 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A HIS* 4.9 3.5 + - - -
489A ALA* 5.0 5.3 - - + +
540A PHE* 2.9 59.9 + - + +
541A CYS 2.9 9.4 + - - +
543A GLU* 1.3 105.2 + - - +
545A GLU* 1.3 72.9 + - - +
546A MET* 3.4 31.4 + - + +
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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