Contacts of the helix formed by residues 744 - 761 (chain B) in PDB entry 3ODX
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 744 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723B LYS* 4.1 8.7 - - - +
742B ALA* 3.8 5.1 - - - +
743B GLN* 1.3 75.3 - - - +
745B VAL* 1.3 67.0 + - - +
746B SER* 3.3 25.4 + - - +
747B GLU* 2.8 36.1 + - + +
748B ARG* 3.3 16.8 + - - +
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Residues in contact with VAL 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B HIS* 3.0 35.2 - - + +
723B LYS* 4.0 17.0 - - + +
744B THR* 1.3 76.6 + - - +
746B SER* 1.3 61.3 + - - +
748B ARG* 3.2 37.7 + - - +
749B LYS* 3.2 26.3 + - - +
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Residues in contact with SER 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B THR* 3.3 19.0 + - - +
745B VAL* 1.3 78.9 - - - +
747B GLU* 1.3 60.6 + - - +
749B LYS* 3.3 16.5 - - - +
750B ASN* 3.1 25.3 + - - +
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Residues in contact with GLU 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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742B ALA* 3.5 10.8 - - + -
743B GLN* 3.1 19.3 + - - +
744B THR* 2.8 45.5 + - + +
746B SER* 1.3 77.8 + - - +
748B ARG* 1.3 63.7 + - - +
749B LYS 3.2 0.9 - - - -
750B ASN* 3.7 13.9 - - + +
751B TRP* 2.8 38.1 + - + +
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Residues in contact with ARG 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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717B GLU* 2.8 48.9 + - - +
722B HIS* 2.8 31.8 + - - +
723B LYS* 3.7 15.3 - - - +
724B ALA 3.2 25.1 + - - -
725B PHE* 3.7 22.5 - - + +
742B ALA* 3.6 11.4 - - + +
744B THR 3.3 7.2 + - - +
745B VAL* 3.2 32.2 + - - +
747B GLU* 1.3 75.6 - - - +
749B LYS* 1.3 87.5 + - - +
751B TRP* 3.6 2.8 + - - +
752B CYS* 3.2 22.7 + - - -
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Residues in contact with LYS 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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717B GLU* 5.0 4.9 + - - -
745B VAL* 3.2 31.1 + - - +
746B SER* 3.3 15.9 - - - +
747B GLU 3.2 0.6 - - - -
748B ARG* 1.3 100.1 - - - +
750B ASN* 1.3 64.8 + - - +
751B TRP 3.1 0.7 + - - -
752B CYS* 3.1 6.4 + - - +
753B ALA* 3.0 23.9 + - - +
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Residues in contact with ASN 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650B HIS* 3.6 28.5 + - - -
746B SER 3.1 13.5 + - - +
747B GLU* 3.7 15.3 + - - +
749B LYS* 1.3 79.3 - - - +
751B TRP* 1.3 55.9 + - - +
753B ALA* 3.4 7.0 - - - +
754B LEU* 3.0 37.9 + - - +
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Residues in contact with TRP 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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650B HIS* 3.7 31.8 - + - -
651B GLU* 3.9 1.3 - - - -
652B GLY* 3.6 41.7 - - - -
653B PRO 4.4 1.8 + - - -
654B LEU* 3.6 34.1 - - + +
668B VAL* 3.5 35.9 - - + -
670B LEU* 4.5 16.6 - - + -
675B LEU* 5.1 0.9 - - + -
725B PHE* 3.8 19.7 - + + -
742B ALA* 4.5 1.4 - - + +
747B GLU* 2.8 33.7 + - + +
748B ARG 3.8 5.6 - - - +
749B LYS 3.1 0.8 + - - -
750B ASN* 1.3 74.3 - - - +
752B CYS* 1.3 68.6 + - - +
754B LEU* 2.8 18.2 + - + +
755B ILE* 2.8 36.2 + - + +
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Residues in contact with CYS 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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715B THR* 3.2 28.3 - - - +
716B ARG 4.9 2.9 - - - -
717B GLU* 6.1 0.7 - - - -
725B PHE* 3.4 40.4 - - - -
748B ARG* 3.2 20.2 - - - -
749B LYS* 3.1 7.5 + - - +
751B TRP* 1.3 77.8 - - - +
753B ALA* 1.3 55.7 + - - +
755B ILE* 4.5 0.2 - - - -
756B THR* 2.7 39.0 + - - +
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Residues in contact with ALA 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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749B LYS 3.0 13.0 + - - +
750B ASN* 3.4 13.9 - - - +
752B CYS* 1.3 74.3 - - - +
754B LEU* 1.3 58.7 + - + +
756B THR* 2.9 19.0 + - - -
757B GLU* 3.0 31.2 + - - +
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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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649B VAL* 4.4 17.7 - - + +
650B HIS* 3.3 48.0 - - + +
670B LEU* 4.0 9.6 - - + -
750B ASN* 3.0 37.0 + - - +
751B TRP* 2.8 8.2 + - - +
753B ALA* 1.3 74.0 - - + +
755B ILE* 1.3 65.0 + - - +
757B GLU* 3.3 16.5 + - - +
758B THR* 2.8 27.9 + - - -
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Residues in contact with ILE 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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670B LEU* 3.8 25.1 - - + +
675B LEU* 5.1 11.7 - - + -
710B LEU* 4.0 23.1 - - + +
713B ALA* 4.4 10.8 - - + -
714B MET 5.3 0.4 - - - +
715B THR* 3.9 28.9 - - + -
725B PHE* 4.1 21.5 - - + -
727B VAL* 4.5 10.3 - - + -
740B LEU* 6.3 0.4 - - + -
751B TRP* 2.8 36.8 + - + +
754B LEU* 1.3 71.3 - - - +
756B THR* 1.3 57.0 + - + +
758B THR* 2.9 4.3 + - - -
759B ALA* 2.8 34.3 + - - +
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Residues in contact with THR 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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714B MET* 4.7 4.7 - - - +
715B THR* 3.0 45.1 - - + +
752B CYS 2.7 19.4 + - - +
753B ALA* 2.9 13.5 + - - -
755B ILE* 1.3 76.2 - - - +
757B GLU* 1.3 56.8 + - - +
759B ALA* 3.8 6.6 - - - +
760B GLY* 2.9 24.9 + - - -
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Residues in contact with GLU 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 ALA* 3.0 29.3 + - - +
754B LEU* 3.3 19.0 - - - +
756B THR* 1.3 77.4 - - - +
758B THR* 1.3 53.9 + - - +
760B GLY* 2.9 4.2 + - - -
761B SER* 2.7 36.1 + - - -
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Residues in contact with THR 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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649B VAL* 3.9 36.2 - - + +
670B LEU* 4.1 4.2 - - - +
671B LEU 3.9 7.4 - - - +
672B ASP* 3.5 21.3 - - - +
710B LEU* 4.4 9.4 - - + -
754B LEU 2.8 15.9 + - - -
755B ILE 2.9 6.9 + - - -
757B GLU* 1.3 70.7 - - - +
759B ALA* 1.3 65.3 + - - +
761B SER* 3.5 16.0 + - - +
762B LEU* 3.3 20.1 - - - +
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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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710B LEU* 3.9 22.8 - - + +
711B THR* 5.0 3.9 - - - -
713B ALA* 4.2 22.9 - - + +
755B ILE 2.8 16.7 + - - +
756B THR* 3.8 8.7 - - - +
758B THR* 1.3 78.2 - - - +
760B GLY* 1.3 60.9 + - - +
762B LEU* 3.1 31.7 + - - +
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Residues in contact with GLY 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 THR 2.9 17.2 + - - -
757B GLU 3.3 4.3 - - - -
759B ALA* 1.3 73.9 - - - +
761B SER* 1.3 56.3 + - - +
762B LEU 3.0 17.1 + - - +
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Residues in contact with SER 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 GLU 2.7 17.6 + - - -
758B THR* 3.5 19.8 - - - +
759B ALA 3.3 0.4 - - - -
760B GLY* 1.3 70.8 - - - +
762B LEU* 1.3 61.1 + - - +
763B LYS* 3.9 4.7 + - - +
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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