Contacts of the helix formed by residues 752 - 762 (chain D) in PDB entry 6PUO
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 GLY 752 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744D TRP* 4.0 12.0 - - - -
749D VAL 4.9 1.8 + - - -
750D ASP 3.3 5.5 - - - -
751D ASN* 1.3 91.3 + - - +
753D LEU* 1.3 63.9 + - - -
754D TRP* 3.6 11.4 - - - -
755D ARG 4.5 0.4 - - - -
756D VAL* 3.8 16.3 + - - +
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Residues in contact with LEU 753 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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936C PHE* 5.9 6.5 - - + -
744D TRP* 5.1 4.9 - - + -
752D GLY* 1.3 74.6 - - - -
754D TRP* 1.3 82.7 + - + +
755D ARG 3.3 0.4 - - - -
756D VAL* 3.1 8.7 + - - +
757D THR* 3.0 33.0 + - + +
800D HIS* 5.4 9.9 + - + +
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Residues in contact with TRP 754 (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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751D ASN 5.3 0.2 - - - -
752D GLY* 5.0 7.6 - - - -
753D LEU* 1.3 102.4 - - + +
755D ARG* 1.3 113.2 + - + +
757D THR* 2.4 29.4 + - - +
758D LEU* 2.9 32.7 + - + +
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Residues in contact with ARG 755 (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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750D ASP 5.3 1.2 + - - -
751D ASN* 3.1 43.9 + - + +
752D GLY 4.4 0.6 - - - +
753D LEU 3.3 0.6 - - - -
754D TRP* 1.3 126.4 - - + +
756D VAL* 1.3 56.9 + - - +
758D LEU* 3.3 8.9 + - + +
759D CYS* 3.0 33.1 + - - +
770D LEU 4.0 20.6 + - - +
771D ILE* 4.6 6.5 - - + +
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Residues in contact with VAL 756 (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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744D TRP* 4.8 14.1 - - + -
751D ASN* 5.7 4.6 - - - +
752D GLY 3.8 11.7 + - - +
753D LEU* 3.1 13.6 + - - +
755D ARG* 1.3 79.4 - - - +
757D THR* 1.3 56.7 + - + +
759D CYS* 3.4 12.4 - - - -
760D MET* 2.9 29.4 + - - +
771D ILE* 5.3 1.3 - - - +
791D PHE* 4.7 6.4 - - + -
796D VAL* 5.3 3.6 - - + -
797D VAL* 6.0 4.2 - - + +
800D HIS* 5.2 12.8 - - + +
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Residues in contact with THR 757 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753D LEU* 3.0 18.2 + - + +
754D TRP* 2.4 33.0 + - - +
756D VAL* 1.3 77.3 - - - +
758D LEU* 1.3 63.0 + - - +
760D MET* 3.3 26.5 + - + +
761D LEU* 2.9 26.9 + - - +
800D HIS* 4.9 15.7 - - + +
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Residues in contact with LEU 758 (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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754D TRP* 2.9 38.0 + - + +
755D ARG* 3.3 8.7 + - + +
757D THR* 1.3 83.7 + - - +
759D CYS* 1.3 57.8 + - - +
761D LEU* 3.0 10.0 + - + +
762D ALA* 2.9 29.9 + - - +
765D LEU* 5.6 1.3 - - - -
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Residues in contact with CYS 759 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755D ARG 3.0 27.5 + - - +
756D VAL* 3.4 13.9 - - - -
758D LEU* 1.3 73.9 - - - +
760D MET* 1.3 63.3 + - - +
762D ALA 2.9 23.9 - - - +
763D PHE* 5.0 0.9 - - - -
765D LEU* 4.8 7.4 - - + -
766D LEU* 4.8 18.0 - - + +
771D ILE* 3.3 31.0 - - + -
791D PHE* 3.5 31.7 - - + -
792D PHE* 5.8 0.5 - - - -
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Residues in contact with MET 760 (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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756D VAL 2.9 16.9 + - - +
757D THR* 3.3 31.2 - - + +
759D CYS* 1.3 79.9 - - - +
761D LEU* 1.3 61.6 + - + +
762D ALA 4.8 0.9 - - - -
763D PHE* 5.1 8.7 - - - -
791D PHE* 4.7 9.9 - - + -
792D PHE* 5.9 3.8 - - + -
797D VAL* 5.3 5.6 - - + +
800D HIS* 3.7 35.7 - - + +
801D LEU* 3.7 29.6 - - + -
804D LEU* 4.7 18.8 - - + -
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Residues in contact with LEU 761 (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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757D THR 2.9 13.2 + - - +
758D LEU* 3.0 12.1 + - + +
760D MET* 1.3 79.3 - - + +
762D ALA* 1.3 59.4 + - + +
763D PHE* 3.9 7.1 + - - -
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Residues in contact with ALA 762 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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758D LEU 2.9 13.1 + - - +
759D CYS* 2.9 23.9 - - - +
761D LEU* 1.3 76.9 - - + +
763D PHE* 1.3 66.8 + - - +
764D PRO* 4.5 6.1 - - + -
765D LEU* 3.8 24.6 + - + +
766D LEU 4.4 1.0 + - - -
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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