Contacts of the helix formed by residues 749 - 766 (chain B) in PDB entry 2PY3
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 THR 749 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683B GLN* 3.9 18.8 - - - +
747B ARG 5.0 1.8 - - - +
748B PRO* 1.3 77.9 - - - +
750B PHE* 1.3 64.9 + - - +
751B LYS* 3.5 10.5 + - - +
752B GLN* 2.9 46.9 + - - +
753B LEU* 3.0 13.1 + - - +
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Residues in contact with PHE 750 (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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611B ALA* 4.3 6.6 - - - +
614B MET* 3.4 48.7 - - + -
615B GLU* 3.7 20.9 - - + +
618B ALA* 4.4 11.9 - - + -
682B HIS* 3.6 25.6 - - + -
683B GLN* 4.9 1.0 - - - +
685B ASP* 3.6 13.5 - - + -
686B VAL* 3.5 28.4 - - + +
689B PHE* 3.7 27.6 - + + -
748B PRO 4.1 0.2 + - - -
749B THR* 1.3 73.4 - - - +
751B LYS* 1.3 62.5 + - - +
753B LEU* 3.1 16.2 + - + +
754B VAL* 2.9 28.8 + - - +
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Residues in contact with LYS 751 (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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615B GLU* 3.5 29.2 + - + +
749B THR* 3.1 9.3 + - - +
750B PHE* 1.3 78.5 - - - +
752B GLN* 1.3 63.2 + - + +
754B VAL* 3.3 4.6 + - + +
755B GLU* 3.1 47.7 + - + +
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Residues in contact with GLN 752 (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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747B ARG 4.5 1.4 - - - +
748B PRO* 3.3 15.3 - - + +
749B THR* 2.9 45.6 + - - +
751B LYS* 1.3 80.3 - - + +
753B LEU* 1.3 62.1 + - - +
755B GLU* 3.4 13.3 + - - +
756B ASP* 3.0 34.9 + - - +
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Residues in contact with LEU 753 (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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611B ALA* 4.4 9.6 - - + -
686B VAL* 4.6 7.2 - - + -
689B PHE* 3.8 27.4 - - + -
735B MET* 3.6 34.1 - - + -
739B CYS* 4.1 17.3 - - - -
748B PRO* 4.0 19.5 - - + -
749B THR 3.0 17.6 + - - +
750B PHE* 3.1 27.3 + - + +
752B GLN* 1.3 77.7 - - - +
754B VAL* 1.3 56.5 + - - +
756B ASP* 3.8 5.1 - - - +
757B LEU* 2.9 40.1 + - + +
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Residues in contact with VAL 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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608B TYR* 4.0 8.6 - - + -
611B ALA* 3.5 35.9 - - + +
612B ARG* 3.3 47.1 - - + +
615B GLU* 3.7 16.8 - - + +
750B PHE 2.9 17.7 + - - +
751B LYS* 3.5 8.7 - - - +
753B LEU* 1.3 76.5 - - - +
755B GLU* 1.3 57.4 + - + +
757B LEU* 3.7 3.0 - - - +
758B ASP* 2.7 37.6 + - + +
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Residues in contact with GLU 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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751B LYS* 3.1 43.4 + - + +
752B GLN* 3.8 12.3 - - - +
753B LEU 3.3 0.2 - - - -
754B VAL* 1.3 81.8 - - + +
756B ASP* 1.3 64.6 + - - +
758B ASP* 3.3 7.2 + - - +
759B ARG* 3.1 23.4 + - - +
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Residues in contact with ASP 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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735B MET* 3.6 24.2 - - + +
748B PRO* 5.8 1.7 - - - +
752B GLN* 3.0 28.8 + - - +
753B LEU* 3.9 4.3 - - - +
755B GLU* 1.3 76.5 - - - +
757B LEU* 1.3 63.9 + - - +
759B ARG* 3.2 35.3 + - - +
760B ILE* 3.1 27.6 + - - +
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Residues in contact with LEU 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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604B VAL* 4.1 11.8 - - + +
607B THR* 3.7 47.8 - - + +
608B TYR* 4.1 14.5 - - + -
611B ALA* 3.9 15.0 - - + -
689B PHE* 4.4 5.4 - - + -
732B LEU* 4.0 20.6 - - + -
735B MET* 3.7 26.2 - - + -
753B LEU* 2.9 21.9 + - + +
754B VAL 3.9 3.1 - - - +
756B ASP* 1.3 73.5 - - - +
758B ASP* 1.3 61.5 + - - +
760B ILE* 3.8 4.5 - - + +
761B LEU* 2.9 32.4 + - - +
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Residues in contact with ASP 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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608B TYR* 3.9 28.8 + - + -
612B ARG* 4.9 7.8 + - - -
754B VAL* 2.7 24.6 + - + +
755B GLU* 3.5 8.1 - - - +
756B ASP 3.2 0.2 - - - -
757B LEU* 1.3 73.3 - - - +
759B ARG* 1.3 60.8 + - - +
761B LEU* 3.8 5.8 - - - +
762B THR* 2.8 40.1 + - - -
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Residues in contact with ARG 759 (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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731B GLU* 3.4 24.7 + - - +
735B MET* 5.7 0.6 - - - +
755B GLU 3.1 11.1 + - - +
756B ASP* 3.2 44.5 + - - +
758B ASP* 1.3 74.1 - - - +
760B ILE* 1.3 64.6 + - - +
762B THR* 3.3 5.6 + - - -
763B LEU* 2.9 58.8 + - + +
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Residues in contact with ILE 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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600B PHE* 4.8 6.7 - - + -
604B VAL* 4.0 22.7 - - + -
729B THR* 5.8 0.7 - - - +
731B GLU* 3.6 42.4 - - + +
732B LEU* 3.7 28.9 - - + -
735B MET* 4.0 14.1 - - + -
756B ASP 3.1 16.4 + - - +
757B LEU* 3.8 5.6 - - - +
759B ARG* 1.3 82.3 - - - +
761B LEU* 1.3 56.8 + - - +
763B LEU* 3.5 7.4 + - + +
764B THR* 2.7 39.8 + - - +
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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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601B LYS* 3.7 45.1 - - + +
604B VAL* 3.8 11.6 - - + +
605B SER* 3.9 25.6 - - - +
608B TYR* 4.0 30.5 - - + -
757B LEU 2.9 18.1 + - - +
758B ASP* 3.8 8.1 - - - +
760B ILE* 1.3 75.1 - - - +
762B THR* 1.3 65.0 + - - +
764B THR* 3.2 8.0 + - - -
765B THR* 3.1 25.9 + - - +
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Residues in contact with THR 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 ASP* 2.8 30.2 + - - -
759B ARG* 3.6 5.8 - - - -
761B LEU* 1.3 80.1 - - - +
763B LEU* 1.3 69.3 + - + +
765B THR* 3.1 18.6 + - - -
766B ASN* 3.1 27.0 + - - +
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Residues in contact with LEU 763 (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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759B ARG* 2.9 52.0 + - + +
760B ILE* 4.0 6.1 - - + +
762B THR* 1.3 80.1 - - + +
764B THR* 1.3 61.1 + - - +
766B ASN* 3.4 23.4 + - + +
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Residues in contact with THR 764 (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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600B PHE* 3.7 37.5 - - + -
601B LYS* 4.0 25.4 - - + +
604B VAL* 5.0 0.9 - - - +
760B ILE* 2.7 21.6 + - - +
761B LEU* 3.3 11.3 - - - -
763B LEU* 1.3 74.2 - - - +
765B THR* 1.3 65.9 + - - +
766B ASN 3.5 7.3 + - - +
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Residues in contact with THR 765 (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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601B LYS* 2.9 41.3 + - - +
761B LEU* 3.1 13.2 + - - +
762B THR* 3.1 12.7 + - - -
764B THR* 1.3 79.3 - - - +
766B ASN* 1.3 71.7 + - - +
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Residues in contact with ASN 766 (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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762B THR* 3.1 27.4 + - - +
763B LEU* 3.6 17.5 - - + +
764B THR 3.3 8.6 - - - +
765B THR* 1.3 97.7 + - - +
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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