Contacts of the helix formed by residues 536 - 539 (chain B) in PDB entry 3QFR
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B VAL* 4.2 2.2 - - + -
535B GLY* 1.3 83.4 - - - +
537B GLY* 1.3 57.9 + - - +
539B GLY* 2.7 29.5 + - - -
568B GLY* 3.6 16.4 - - - +
608B VAL* 3.8 31.9 - - + -
632B CYS 3.9 9.6 - - - +
633B GLY* 5.0 1.9 - - - -
638B MET* 4.0 24.5 - - + -
753B NAP 3.6 31.3 + - - +
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Residues in contact with GLY 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 5.7 1.3 - - - -
536B PRO* 1.3 71.4 - - - +
538B THR* 1.3 58.4 + - - -
539B GLY 2.8 5.5 + - - -
540B VAL* 3.1 13.0 + - - +
567B TYR* 3.4 18.7 - - - -
568B GLY 2.8 19.1 + - - -
569B CYS* 5.5 1.3 - - - -
575B ASP* 5.9 1.6 - - - -
577B LEU* 3.8 9.5 - - - +
753B NAP 3.4 23.6 - - - -
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Residues in contact with THR 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 4.2 12.1 - - + +
475B CYS* 4.0 19.7 - - - +
476B ALA* 4.2 1.6 - - - -
477B VAL* 3.8 24.5 - - + +
537B GLY* 1.3 66.3 - - - -
539B GLY* 1.3 60.3 + - - +
540B VAL 2.9 6.5 - - - -
541B ALA* 3.0 23.3 + - - +
577B LEU* 4.1 0.8 - - - +
679B TRP* 3.3 24.7 + - - -
752B FAD 3.6 30.8 + - - +
753B NAP 2.6 30.8 + - - +
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Residues in contact with GLY 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B GLY 3.6 6.5 - - - -
536B PRO 2.7 16.5 + - - -
538B THR* 1.3 81.4 + - - +
540B VAL* 1.3 60.2 + - - +
541B ALA 3.2 0.2 - - - -
542B PRO* 3.1 2.6 - - - +
543B PHE* 3.8 3.1 - - - -
632B CYS* 2.9 41.8 - - - +
633B GLY* 3.8 17.1 - - - -
679B TRP* 4.0 1.1 - - - -
753B NAP 4.4 0.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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