Contacts of the helix formed by residues 734 - 753 (chain B) in PDB entry 3H44
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 734 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B LEU* 3.5 30.8 - - + +
539B PRO 5.2 2.0 - - - +
541B GLU* 3.5 26.2 - - + +
561B PHE* 3.5 6.7 - - - -
563B GLN* 4.5 6.3 - - - +
733B ILE* 1.3 78.2 - - - +
735B LYS* 1.3 68.8 + - - +
736B GLN* 4.0 5.7 + - - +
737B ALA* 2.8 21.6 + - - +
738B ALA* 2.8 21.5 + - - +
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Residues in contact with LYS 735 (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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541B GLU* 3.2 20.6 + - - +
543B GLU* 5.7 5.6 - - - -
551B ILE* 3.5 40.6 + - + +
561B PHE* 3.2 21.6 - - + -
734B THR* 1.3 71.6 - - - +
736B GLN* 1.3 71.6 + - - +
738B ALA* 3.2 2.4 + - - +
739B LEU* 3.0 41.5 + - + +
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Residues in contact with GLN 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B GLU* 4.2 3.2 + - - +
734B THR* 3.1 7.1 + - - +
735B LYS* 1.3 86.9 - - - +
737B ALA* 1.3 60.8 - - - +
739B LEU* 3.6 29.0 + - - +
740B GLY* 3.0 24.1 + - - -
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Residues in contact with ALA 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B LEU* 5.8 1.1 - - + -
733B ILE* 3.6 26.9 - - + -
734B THR* 2.8 22.9 + - - +
736B GLN* 1.3 77.7 - - - +
738B ALA* 1.3 52.7 + - - +
740B GLY* 3.2 3.0 + - - -
741B ILE* 2.8 40.9 + - + +
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Residues in contact with ALA 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ILE* 4.4 7.0 - - + -
559B LEU* 4.3 1.8 - - - -
561B PHE* 3.6 29.4 - - + -
729B LEU* 3.7 23.9 - - + +
733B ILE* 4.8 4.5 - - + -
734B THR 2.8 14.5 + - - +
735B LYS* 3.5 4.9 - - - +
737B ALA* 1.3 74.6 - - - +
739B LEU* 1.3 66.8 + - - +
741B ILE* 2.9 7.3 + - - +
742B MET* 2.9 23.9 + - - +
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Residues in contact with LEU 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ILE* 3.8 32.5 - - + +
552B LYS* 4.3 24.7 - - + -
559B LEU* 4.3 5.8 - - + -
735B LYS* 3.0 30.4 + - + +
736B GLN* 3.6 35.9 - - - +
738B ALA* 1.3 75.6 - - - +
740B GLY* 1.3 52.7 + - - +
742B MET* 3.2 3.0 + - - +
743B GLN* 2.8 36.0 + - - +
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Residues in contact with GLY 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B GLN 3.0 16.3 + - - -
737B ALA* 3.4 4.9 - - - -
738B ALA 3.1 0.2 - - - -
739B LEU* 1.3 77.2 - - - +
741B ILE* 1.3 55.9 + - - +
743B GLN* 3.5 5.8 + - - +
744B MET* 3.0 28.9 + - - +
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Residues in contact with ILE 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LEU* 4.2 31.4 - - + -
576B PHE* 4.6 4.7 - - + -
638B GLN* 5.7 0.9 - - - +
639B PRO* 4.5 24.0 - - + -
642B LEU* 3.8 25.1 - - + -
729B LEU* 4.2 13.5 - - + -
733B ILE* 5.0 16.4 - - + -
737B ALA* 2.8 23.7 + - + +
738B ALA* 2.9 6.9 + - - +
740B GLY* 1.3 68.9 - - - +
742B MET* 1.3 68.2 + - - +
744B MET* 3.2 13.4 + - + +
745B VAL* 3.0 28.6 + - + +
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Residues in contact with MET 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B LYS* 4.5 7.0 - - + +
557B SER* 3.9 22.2 - - - +
558B LYS 5.4 0.2 - - - +
559B LEU* 3.5 35.4 - - + -
576B PHE* 4.3 12.3 - - + -
725B ILE* 3.8 38.4 - - + -
727B ALA* 4.0 23.3 - - - -
729B LEU* 4.7 2.3 - - - +
738B ALA 2.9 5.8 + - - +
739B LEU* 3.4 8.1 - - - +
741B ILE* 1.3 75.7 - - - +
743B GLN* 1.3 63.0 + - - +
745B VAL* 2.9 19.1 + - + +
746B GLU* 3.0 28.9 + - + +
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Residues in contact with GLN 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B LYS* 3.7 22.4 + - - +
739B LEU 2.8 20.5 + - - +
740B GLY* 3.8 7.4 - - - +
742B MET* 1.3 73.2 - - - +
744B MET* 1.3 53.2 + - - +
746B GLU* 3.3 16.3 + - - +
747B ASP* 2.6 78.8 + - - +
750B ILE* 6.1 0.2 - - - +
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Residues in contact with MET 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B PRO* 4.0 32.1 - - + +
642B LEU* 4.3 18.2 - - + -
643B LYS* 3.5 42.6 - - + +
646B ILE* 6.3 0.7 - - - -
740B GLY 3.0 14.5 + - - +
741B ILE* 3.4 13.9 - - + +
742B MET 3.2 0.2 - - - -
743B GLN* 1.3 74.8 - - - +
745B VAL* 1.3 55.8 + - - +
747B ASP* 3.8 8.1 + - - +
748B THR* 2.5 37.1 + - - +
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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
----------------------------------------------------------
576B PHE* 4.1 23.1 - - + -
578B PHE* 4.6 4.3 - - + -
642B LEU* 3.6 29.8 - - + -
646B ILE* 3.9 28.4 - - + +
725B ILE* 4.4 18.8 - - + -
741B ILE 3.0 17.7 + - - +
742B MET* 2.9 10.5 + - + +
744B MET* 1.3 73.7 - - - +
746B GLU* 1.3 66.0 + - - +
748B THR* 3.1 15.9 + - - -
749B LEU* 3.2 16.1 + - + +
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Residues in contact with GLU 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B LYS* 2.6 32.2 + - - -
554B THR* 4.3 2.4 + - - +
556B MET* 3.5 39.3 - - + +
557B SER* 3.0 23.6 + - - +
725B ILE* 4.8 2.7 - - + -
742B MET* 3.0 29.5 + - + +
743B GLN* 3.5 20.6 + - - +
745B VAL* 1.3 75.6 - - - +
747B ASP* 1.3 63.3 + - - +
749B LEU* 3.1 8.5 + - - +
750B ILE* 3.0 28.2 + - + +
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Residues in contact with ASP 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B GLN* 2.6 63.8 + - - +
744B MET* 3.8 8.4 + - - +
745B VAL 3.2 0.2 - - - -
746B GLU* 1.3 73.7 - - - +
748B THR* 1.3 62.3 + - - +
750B ILE* 3.6 8.1 + - - +
751B GLU* 3.2 24.9 + - - +
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Residues in contact with THR 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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643B LYS* 5.1 9.5 - - + +
646B ILE* 3.7 13.0 - - + +
647B GLU* 3.9 35.0 - - + +
650B ALA* 4.5 0.7 - - - +
744B MET* 2.5 28.8 + - - +
745B VAL* 3.1 6.3 + - - -
747B ASP* 1.3 74.0 - - - +
749B LEU* 1.3 61.4 + - - +
751B GLU* 4.9 1.1 - - - -
752B HIS* 3.0 52.6 + - + +
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Residues in contact with LEU 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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556B MET* 5.4 1.8 - - + -
578B PHE* 4.1 15.9 - - + -
646B ILE* 3.9 16.4 - - + +
649B MET* 5.3 6.1 - - + -
650B ALA* 4.0 21.3 - - + -
720B LEU* 4.6 15.7 - - + -
723B LEU* 4.2 11.9 - - + -
725B ILE* 4.0 26.9 - - + -
745B VAL* 3.2 12.3 + - + +
746B GLU* 3.1 9.4 + - - +
748B THR* 1.3 75.6 - - - +
750B ILE* 1.3 59.1 + - + +
753B ALA* 2.8 39.2 + - + +
754B HIS 3.1 5.5 + - - -
755B THR* 3.4 20.3 + - + +
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Residues in contact with ILE 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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556B MET* 3.3 22.0 - - + -
746B GLU* 3.0 23.0 + - + +
747B ASP* 3.9 9.2 - - - +
749B LEU* 1.3 76.5 - - - +
751B GLU* 1.3 61.4 + - + +
754B HIS* 3.3 23.1 + - - -
755B THR* 3.2 29.8 - - - +
756B LYS* 5.4 0.9 - - - -
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Residues in contact with GLU 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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747B ASP 3.2 16.0 + - - +
748B THR* 4.2 3.1 - - - +
749B LEU 3.2 0.2 - - - -
750B ILE* 1.3 81.9 - - + +
752B HIS* 1.3 91.3 + - + +
753B ALA 3.5 0.2 - - - -
754B HIS* 4.1 15.6 + - - -
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Residues in contact with HIS 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B GLU* 4.4 12.1 - - + +
650B ALA* 3.6 25.4 - - + +
651B THR* 3.1 28.7 - - + +
748B THR* 3.0 39.6 + - + +
751B GLU* 1.3 106.0 + - + +
753B ALA* 1.3 59.6 + - - +
754B HIS* 4.5 7.0 + - - -
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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
----------------------------------------------------------
650B ALA* 3.9 21.1 - - + +
717B PRO* 5.0 7.0 - - + +
720B LEU* 4.0 20.0 - - + -
721B SER* 4.3 11.8 + - - -
749B LEU* 2.8 15.6 + - + +
752B HIS* 1.3 78.1 - - - +
754B HIS* 1.3 74.1 + - - +
755B THR* 3.3 14.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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