Contacts of the helix formed by residues 740 - 754 (chain A) in PDB entry 4K33
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 740 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674A GLN* 4.3 19.1 - - - +
677A VAL* 4.5 0.7 - - - -
738A ARG 5.1 1.3 - - - +
739A PRO* 1.3 77.7 - - - +
741A PHE* 1.3 59.4 + - - +
742A LYS* 3.4 11.1 + - - +
743A GLN* 2.9 39.7 + - - +
744A LEU* 2.8 27.1 + - - +
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Residues in contact with PHE 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A ALA* 4.2 9.8 - - - +
605A MET* 3.5 59.2 - - + -
606A GLU* 3.8 20.9 - - - +
609A ALA* 4.7 11.7 - - + -
673A HIS* 3.8 8.7 - - + -
674A GLN* 5.4 0.4 - - - +
676A ASP* 3.7 15.5 - - + -
677A VAL* 3.6 30.5 - - + +
680A PHE* 3.7 25.8 - + + -
740A THR* 1.3 71.3 - - - +
742A LYS* 1.3 55.5 + - - +
744A LEU* 3.1 19.6 + - + +
745A VAL* 2.7 39.9 + - - +
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Residues in contact with LYS 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A GLU* 3.4 33.8 - - + +
740A THR* 3.4 9.3 + - - +
741A PHE* 1.3 79.8 - - - +
743A GLN* 1.3 61.8 + - + +
745A VAL* 3.2 4.9 + - - +
746A GLU* 3.1 42.8 + - + +
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Residues in contact with GLN 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A ARG 4.5 1.0 - - - +
739A PRO* 3.2 17.5 - - + +
740A THR* 2.9 49.6 + - + +
742A LYS* 1.3 76.3 - - + +
744A LEU* 1.3 58.4 + - - +
746A GLU* 3.1 19.4 + - - +
747A ASP* 2.9 38.8 + - - +
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Residues in contact with LEU 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A ALA* 4.4 9.6 - - + -
677A VAL* 3.9 19.7 - - + -
680A PHE* 3.6 26.5 - - + -
726A ILE* 3.8 22.7 - - + -
730A CYS* 3.8 19.1 - - - -
739A PRO* 3.8 16.2 - - + -
740A THR 2.8 15.6 + - - +
741A PHE* 3.1 36.5 + - + +
743A GLN* 1.3 77.2 - - - +
745A VAL* 1.3 61.4 + - - +
747A ASP* 3.9 5.5 - - + +
748A LEU* 3.0 33.0 + - + +
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Residues in contact with VAL 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A TYR* 3.5 29.5 - - + +
602A ALA* 3.4 36.1 - - + +
603A ARG* 3.6 17.9 - - + +
606A GLU* 3.8 20.2 - - - +
741A PHE 2.7 23.0 + - - +
742A LYS* 3.2 5.8 + - - +
744A LEU* 1.3 73.7 - - - +
746A GLU* 1.3 57.5 + - + +
749A ASP* 2.9 29.8 + - + +
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Residues in contact with GLU 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742A LYS* 3.1 41.5 + - + +
743A GLN* 3.3 18.5 - - - +
745A VAL* 1.3 77.0 - - + +
747A ASP* 1.3 68.0 + - - +
749A ASP* 3.1 8.3 + - - +
750A ARG* 3.0 24.2 + - - +
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Residues in contact with ASP 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A ILE* 4.0 24.6 - - + +
739A PRO* 5.1 5.5 - - - +
743A GLN* 2.9 30.3 + - - +
744A LEU* 4.1 6.5 - - - +
746A GLU* 1.3 78.1 - - - +
748A LEU* 1.3 59.0 + - - +
750A ARG* 2.5 41.4 + - - +
751A VAL* 3.2 30.5 + - - +
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Residues in contact with LEU 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL* 4.0 20.2 - - + +
598A ALA* 4.0 23.6 - - + +
599A TYR* 4.0 19.9 - - + +
602A ALA* 4.1 6.3 - - + -
680A PHE* 3.8 33.0 - - + -
684A LEU* 4.9 2.0 - - + -
723A LEU* 3.6 30.5 - - + -
726A ILE* 4.2 13.0 - - + -
744A LEU* 3.0 22.8 + - + +
747A ASP* 1.3 78.0 - - - +
749A ASP* 1.3 63.6 + - - +
750A ARG 3.3 0.4 - - - -
751A VAL* 3.6 5.3 + - + +
752A LEU* 3.2 22.7 + - - +
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Residues in contact with ASP 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A TYR* 3.6 27.7 + - + -
745A VAL* 2.9 19.7 + - + +
746A GLU* 3.1 7.8 + - - +
748A LEU* 1.3 74.4 - - - +
750A ARG* 1.3 54.8 + - - +
752A LEU* 3.1 7.5 + - - +
753A THR* 2.7 67.0 + - - -
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Residues in contact with ARG 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722A ASP* 5.8 2.2 + - - +
726A ILE* 5.6 2.8 - - - +
746A GLU 3.0 10.9 + - - +
747A ASP* 2.5 49.7 + - - +
748A LEU 3.3 0.2 - - - -
749A ASP* 1.3 76.7 - - - +
751A VAL* 1.3 69.9 + - - +
752A LEU 2.9 1.4 + - - -
753A THR* 3.0 15.0 + - - -
754A VAL* 3.1 29.9 + - + +
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Residues in contact with VAL 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A PHE* 4.1 23.6 - - + -
595A VAL* 3.9 20.0 - - + -
720A THR* 5.7 0.9 - - - +
722A ASP* 4.8 16.2 - - + -
723A LEU* 4.2 9.4 - - + -
726A ILE* 4.1 18.8 - - + -
747A ASP 3.2 17.6 + - - +
748A LEU* 3.8 9.0 - - + +
750A ARG* 1.3 84.4 - - - +
752A LEU* 1.3 49.6 - - - +
754A VAL* 3.5 7.9 - - - +
755A THR* 2.2 29.8 + - - +
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Residues in contact with LEU 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A LYS* 3.8 47.0 + - + +
595A VAL* 3.6 28.3 - - + -
596A SER* 3.9 12.1 - - - +
599A TYR* 4.3 33.9 - - + -
748A LEU 3.2 13.2 + - - +
749A ASP* 3.1 6.2 + - - +
750A ARG 3.0 0.6 - - - -
751A VAL* 1.3 76.0 - - - +
753A THR* 1.3 63.1 + - - +
754A VAL 3.3 1.3 - - - -
755A THR* 3.3 14.4 + - - +
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Residues in contact with THR 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A ASP* 2.7 42.3 + - - -
750A ARG* 3.0 7.9 + - - -
752A LEU* 1.3 74.4 - - - +
754A VAL* 1.3 62.8 + - + +
755A THR 3.7 2.3 + - - -
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Residues in contact with VAL 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ARG* 3.1 29.8 + - + +
751A VAL* 3.5 6.7 - - - +
753A THR* 1.3 81.0 - - + +
755A THR* 1.3 63.1 + - - +
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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