Contacts of the helix formed by residues 746 - 760 (chain B) in PDB entry 3JS2
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 746 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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762A SER* 5.3 6.1 - - - +
764A GLN 4.7 3.8 - - - +
765A GLU* 4.1 16.4 - - + -
680B GLN* 3.8 21.5 - - - +
683B VAL* 4.4 0.7 - - - -
744B ARG 4.9 1.8 - - - +
745B PRO* 1.3 78.0 - - + +
747B PHE* 1.3 63.7 + - - +
748B LYS* 3.4 10.4 + - - +
749B GLN* 3.0 34.2 + - - +
750B LEU* 3.0 22.1 + - - +
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Residues in contact with PHE 747 (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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765A GLU 4.0 10.8 + - - +
608B ALA* 4.3 10.5 - - - +
611B MET* 3.7 47.6 - - + -
612B GLU* 3.9 20.0 - - + -
615B ALA* 4.6 9.9 - - + -
624B LEU* 4.4 0.4 - - + -
679B HIS* 3.7 23.1 - - - -
682B ASP* 3.7 32.3 - - + -
683B VAL* 3.8 7.6 - - + +
686B PHE* 3.8 29.2 - + + -
746B THR* 1.3 74.8 - - - +
748B LYS* 1.3 56.9 + - - +
750B LEU* 3.7 16.2 - - + +
751B VAL* 3.0 34.0 + - - +
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Residues in contact with LYS 748 (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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765A GLU* 4.5 6.7 + - + +
612B GLU* 3.2 27.1 - - + +
746B THR* 3.0 11.2 + - - +
747B PHE* 1.3 80.8 - - - +
749B GLN* 1.3 63.5 + - + +
751B VAL* 3.5 2.6 + - - +
752B GLU* 3.2 49.0 + - + +
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Residues in contact with GLN 749 (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 ARG 4.5 0.9 - - - +
745B PRO* 3.2 18.6 - - + +
746B THR* 3.0 39.9 + - - +
748B LYS* 1.3 79.3 - - + +
750B LEU* 1.3 58.9 + - - +
752B GLU* 3.8 12.9 - - - +
753B ASP* 3.0 40.3 + - - +
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Residues in contact with LEU 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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608B ALA* 4.5 9.9 - - + -
683B VAL* 4.3 13.5 - - + -
686B PHE* 3.6 28.3 - - + -
732B MET* 3.8 35.7 - - + -
736B CYS* 4.2 9.6 - - - -
745B PRO* 3.8 20.6 - - + -
746B THR 3.0 16.8 + - - +
747B PHE* 3.8 25.8 - - + +
748B LYS 3.3 0.2 - - - -
749B GLN* 1.3 74.6 - - - +
751B VAL* 1.3 60.4 + - - +
753B ASP* 4.0 3.7 - - - +
754B LEU* 2.9 38.0 + - + +
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Residues in contact with VAL 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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605B TYR* 3.8 24.1 - - + +
608B ALA* 3.3 39.5 - - + +
609B ARG* 3.5 12.6 - - + +
612B GLU* 3.9 20.0 - - + +
747B PHE 3.0 20.4 + - - +
748B LYS 3.8 4.7 - - - +
749B GLN 3.3 0.2 - - - -
750B LEU* 1.3 77.4 - - - +
752B GLU* 1.3 60.6 + - + +
754B LEU* 3.9 2.4 - - - -
755B ASP* 2.9 29.1 + - + +
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Residues in contact with GLU 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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612B GLU* 5.9 0.2 - - - +
748B LYS* 3.2 45.9 + - + +
749B GLN* 3.8 12.7 - - - +
750B LEU 3.3 0.2 - - - -
751B VAL* 1.3 78.9 - - + +
753B ASP* 1.3 62.5 + - - +
755B ASP* 3.3 7.3 + - - +
756B ARG* 3.1 21.3 + - - +
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Residues in contact with ASP 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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732B MET* 3.6 22.6 - - + +
745B PRO* 5.8 1.9 - - - +
749B GLN* 3.0 26.4 + - - +
750B LEU* 4.0 2.2 - - - +
752B GLU* 1.3 74.8 - - - +
754B LEU* 1.3 61.0 + - - +
756B ARG* 2.7 34.7 + - - +
757B ILE* 2.8 34.7 + - + +
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Residues in contact with LEU 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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601B VAL* 4.6 11.0 - - + -
604B ALA* 3.5 43.5 - - + +
605B TYR* 3.6 15.9 - - + +
608B ALA* 3.9 10.8 - - + -
686B PHE* 4.0 11.4 - - + -
690B LEU* 5.2 0.9 - - + -
729B LEU* 4.2 16.4 - - + -
732B MET* 3.4 29.8 - - + -
750B LEU 2.9 21.9 + - - +
751B VAL 4.1 2.2 - - - +
753B ASP* 1.3 74.1 - - - +
755B ASP* 1.3 61.0 + - - +
757B ILE* 4.2 3.4 - - + -
758B VAL* 2.8 37.1 + - + +
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Residues in contact with ASP 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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605B TYR* 3.6 31.1 + - + -
751B VAL* 2.9 21.0 + - + +
752B GLU* 3.4 8.3 - - - +
753B ASP 3.2 0.2 - - - -
754B LEU* 1.3 79.4 - - - +
756B ARG* 1.3 61.9 + - - +
758B VAL* 3.4 4.7 + - - +
759B ALA* 3.3 19.9 + - - +
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Residues in contact with ARG 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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728B GLU* 3.0 28.7 + - - -
752B GLU 3.1 9.0 + - - +
753B ASP* 2.7 43.4 + - - +
755B ASP* 1.3 80.2 - - - +
757B ILE* 1.3 71.7 + - - +
759B ALA* 3.3 7.8 + - - +
760B LEU* 3.2 43.0 + - + +
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Residues in contact with ILE 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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601B VAL* 4.3 11.9 - - + -
726B THR* 6.5 0.9 - - + -
728B GLU* 3.5 42.2 - - + +
729B LEU* 4.3 24.2 - - + -
732B MET* 3.7 26.5 - - + -
753B ASP 2.8 23.0 + - - +
754B LEU* 3.9 6.1 - - + +
756B ARG* 1.3 84.3 - - - +
758B VAL* 1.3 60.2 + - - +
760B LEU* 3.1 15.9 + - + +
761B THR* 2.5 33.1 + - - +
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Residues in contact with VAL 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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598B LYS* 3.0 40.6 + - + +
601B VAL* 3.1 39.5 - - + +
602B SER* 4.2 7.9 - - - +
605B TYR* 4.1 15.3 - - + -
754B LEU 2.8 31.8 + - - +
755B ASP* 3.8 5.8 - - - +
757B ILE* 1.3 71.8 - - - +
759B ALA* 1.3 64.6 + - - +
761B THR* 3.1 11.7 + - - -
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Residues in contact with ALA 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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598B LYS* 3.5 12.9 + - - +
755B ASP 3.3 10.4 + - - +
756B ARG* 3.5 11.4 - - - +
757B ILE 3.2 0.2 - - - -
758B VAL* 1.3 81.7 - - - +
760B LEU* 1.3 64.4 + - + +
761B THR 3.3 4.5 + - - +
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Residues in contact with LEU 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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728B GLU* 6.0 1.3 - - - +
756B ARG* 3.3 39.7 - - + +
757B ILE* 3.1 9.8 + - + +
759B ALA* 1.3 81.2 - - + +
761B THR* 1.3 57.7 + - - +
762B SER 4.2 0.5 + - - -
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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