Contacts of the helix formed by residues 752 - 762 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744B TRP* 4.0 11.8 - - - -
749B VAL 4.9 1.8 + - - -
750B ASP* 3.3 4.2 - - - +
751B ASN* 1.3 93.0 + - - +
753B LEU* 1.3 64.1 + - - -
754B TRP* 3.6 12.1 - - - -
755B ARG 4.5 0.2 - - - -
756B VAL* 3.8 16.8 + - - +
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Residues in contact with LEU 753 (chain B).
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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936A PHE* 6.0 6.5 - - + -
744B TRP* 5.1 4.9 - - + -
752B GLY* 1.3 73.3 - - - -
754B TRP* 1.3 84.0 + - + +
755B ARG 3.3 0.4 - - - -
756B VAL* 3.1 8.6 + - - +
757B THR* 3.0 34.1 + - + +
800B HIS* 5.4 9.0 + - + +
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Residues in contact with TRP 754 (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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751B ASN 5.3 0.2 - - - -
752B GLY* 5.0 7.6 - - - -
753B LEU* 1.3 100.8 - - + +
755B ARG* 1.3 112.1 + - + +
757B THR* 2.4 29.6 + - - +
758B LEU* 2.9 32.7 + - + +
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Residues in contact with ARG 755 (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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750B ASP 5.3 1.0 + - - -
751B ASN* 3.1 44.1 + - + +
752B GLY 4.4 0.9 - - - +
753B LEU 3.3 0.2 - - - -
754B TRP* 1.3 126.4 - - + +
756B VAL* 1.3 56.4 + - - +
758B LEU* 3.3 10.2 + - + +
759B CYS* 3.0 32.6 + - - +
770B LEU 4.0 20.9 + - - +
771B ILE* 4.6 6.4 - - + +
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Residues in contact with VAL 756 (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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744B TRP* 4.8 14.6 - - + -
751B ASN* 5.7 4.2 - - - +
752B GLY 3.8 11.9 + - - +
753B LEU* 3.1 13.0 + - - +
755B ARG* 1.3 79.4 - - - +
757B THR* 1.3 56.3 + - + +
759B CYS* 3.4 12.6 - - - -
760B MET* 2.9 30.1 + - - +
771B ILE* 5.3 1.3 - - - -
791B PHE* 4.7 5.8 - - + -
796B VAL* 5.3 4.0 - - + -
797B VAL* 6.0 4.1 - - + +
800B HIS* 5.2 13.0 - - + +
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Residues in contact with THR 757 (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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753B LEU* 3.0 17.9 + - + +
754B TRP* 2.4 32.5 + - - +
756B VAL* 1.3 79.1 - - - +
758B LEU* 1.3 62.8 + - - +
760B MET* 3.3 26.0 + - + +
761B LEU* 2.9 26.9 + - - +
800B HIS* 4.9 15.7 - - + +
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Residues in contact with LEU 758 (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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754B TRP* 2.9 37.2 + - + +
755B ARG* 3.3 9.6 + - + +
757B THR* 1.3 82.8 + - - +
759B CYS* 1.3 57.1 + - - +
761B LEU* 3.0 10.2 + - + +
762B ALA* 2.9 29.3 + - - +
765B LEU* 5.6 1.3 - - - -
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Residues in contact with CYS 759 (chain B).
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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755B ARG 3.0 26.4 + - - +
756B VAL* 3.4 13.5 - - - -
758B LEU* 1.3 73.0 - - - +
760B MET* 1.3 62.3 + - - +
762B ALA 2.9 22.9 - - - +
763B PHE* 4.9 0.9 - - - -
765B LEU* 4.8 7.9 - - + -
766B LEU* 4.8 18.3 - - + +
771B ILE* 3.3 31.6 - - + -
791B PHE* 3.5 30.1 - - + -
792B PHE* 5.8 0.7 - - - -
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Residues in contact with MET 760 (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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756B VAL 2.9 17.6 + - - +
757B THR* 3.3 31.2 - - + +
758B LEU 3.2 0.2 - - - -
759B CYS* 1.3 80.2 - - - +
761B LEU* 1.3 61.4 + - + +
762B ALA 4.8 0.9 - - - -
763B PHE* 5.1 8.5 - - - -
791B PHE* 4.7 10.1 - - + -
792B PHE* 5.9 4.6 - - + -
797B VAL* 5.3 6.3 - - + +
800B HIS* 3.7 36.1 - - + +
801B LEU* 3.7 28.3 - - + -
804B LEU* 4.7 16.8 - - + -
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Residues in contact with LEU 761 (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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757B THR 2.9 13.2 + - - +
758B LEU* 3.0 13.0 + - + +
760B MET* 1.3 81.3 - - - +
762B ALA* 1.3 59.8 + - + +
763B PHE* 3.9 6.9 + - - -
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Residues in contact with ALA 762 (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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758B LEU 2.9 13.2 + - - +
759B CYS* 2.9 23.7 - - - +
761B LEU* 1.3 77.6 - - + +
763B PHE* 1.3 67.2 + - - +
764B PRO* 4.5 5.8 - - + -
765B LEU* 3.8 24.0 + - + +
766B LEU* 4.4 1.2 + - - +
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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