Contacts of the helix formed by residues 536 - 539 (chain A) in PDB entry 3QFS
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 PRO 536 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A VAL 4.1 1.1 - - - -
535A GLY* 1.3 85.4 - - - +
537A GLY* 1.3 66.9 + - - +
538A THR 3.5 0.2 + - - -
539A GLY* 3.0 14.0 + - - -
566A TYR 4.5 0.2 - - - -
568A GLY* 3.6 20.6 - - - +
608A VAL* 4.2 18.6 - - + -
632A CYS 3.9 8.4 - - - +
633A GLY* 4.8 3.0 - - - -
634A ASP* 5.6 0.8 + - + +
638A MET* 3.7 36.8 - - + -
753A NAP 3.7 29.0 - - - +
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Residues in contact with GLY 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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301A ARG* 6.2 0.7 - - - -
303A LEU* 6.0 0.9 - - - -
536A PRO* 1.3 66.9 - - - +
538A THR* 1.3 60.0 + - - -
539A GLY 2.9 10.1 + - - -
540A VAL* 3.1 13.7 + - - +
567A TYR* 3.4 17.2 - - - -
568A GLY 2.9 17.4 + - - -
569A CYS* 5.6 1.1 - - - -
577A LEU* 3.7 8.4 - - - +
753A NAP 3.6 25.9 - - - -
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Residues in contact with THR 538 (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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303A LEU* 4.1 12.3 - - + -
475A CYS* 4.3 11.4 - - - -
476A ALA* 4.2 5.6 - - - -
477A VAL* 3.8 33.5 - - + +
536A PRO 3.5 0.4 + - - -
537A GLY* 1.3 66.5 - - - -
539A GLY* 1.3 57.8 + - - +
540A VAL 2.9 11.2 + - - -
541A ALA* 3.0 23.1 + - - +
577A LEU* 4.1 5.8 - - - +
679A TRP* 3.7 20.9 + - - -
752A FAD 3.9 18.3 + - - +
753A NAP 3.0 27.7 + - - +
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Residues in contact with GLY 539 (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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535A GLY* 3.7 7.3 - - - -
536A PRO 3.0 11.1 + - - -
537A GLY 2.9 3.4 - - - -
538A THR* 1.3 81.2 + - - +
540A VAL* 1.3 60.6 + - - +
541A ALA 3.1 0.8 + - - -
542A PRO* 3.4 1.9 - - - +
543A PHE* 3.6 6.4 - - - -
632A CYS* 3.2 48.3 - - - +
633A GLY* 3.8 8.9 - - - -
679A TRP* 4.1 1.7 - - - -
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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