Contacts of the helix formed by residues 733 - 745 (chain A) in PDB entry 4MS0
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 VAL 733 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635A LEU* 4.0 14.1 - - + -
638A TYR* 3.1 35.2 + - + -
639A PHE* 3.9 21.3 - - + -
675A LEU* 3.5 26.9 - - + -
729A PHE* 2.9 41.0 + - + +
731A ASN 3.6 0.4 - - - -
732A ALA* 1.3 88.5 - - + +
734A ALA* 1.3 64.5 + - - +
735A ILE 3.5 1.3 - - - -
736A PRO* 3.6 1.9 - - - +
737A CYS* 3.1 11.3 + - - +
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Residues in contact with ALA 734 (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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675A LEU* 4.3 11.7 - - + -
678A VAL* 4.2 9.4 - - + -
729A PHE* 3.3 13.9 + - + -
730A TYR* 3.3 13.7 + - + -
733A VAL* 1.3 74.8 - - - +
735A ILE* 1.3 67.8 + - - +
737A CYS* 3.2 4.8 + - - +
738A TYR* 2.9 43.7 + - + -
755A CYS* 3.7 19.3 - - - -
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Residues in contact with ILE 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A TYR* 2.9 27.4 + - + +
731A ASN* 4.7 5.2 - - - +
734A ALA* 1.3 76.9 - - - +
736A PRO* 1.4 67.6 - - + +
738A TYR* 3.2 0.9 + - - -
739A THR* 2.7 39.4 + - - +
752A LEU* 4.1 6.7 - - + +
755A CYS* 3.7 24.5 - - + +
756A ARG* 3.9 36.3 - - + +
759A LEU* 4.4 17.0 - - + -
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Residues in contact with PRO 736 (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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638A TYR* 3.6 7.4 - - - +
642A ARG* 3.5 35.4 - - - +
730A TYR 3.7 1.1 - - - +
731A ASN 3.3 24.2 - - - +
732A ALA 3.7 10.8 - - - +
733A VAL 3.6 11.4 - - - +
735A ILE* 1.4 96.1 - - + +
737A CYS* 1.3 60.6 + - - +
739A THR* 3.5 4.2 - - - +
740A THR* 3.0 28.2 + - - -
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Residues in contact with CYS 737 (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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638A TYR* 3.2 18.9 + - + -
642A ARG* 4.6 0.4 - - - -
668A LEU* 3.8 18.6 - - - +
671A THR* 3.7 26.2 - - + -
672A ALA* 3.7 28.0 - - - -
675A LEU* 5.0 1.6 - - + -
733A VAL 3.1 22.4 + - - +
734A ALA* 3.5 6.5 - - - +
736A PRO* 1.3 76.6 - - - +
738A TYR* 1.3 63.5 + - - +
740A THR* 3.4 0.9 + - - -
741A LEU* 3.0 27.9 + - - +
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Residues in contact with TYR 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ALA* 2.7 51.6 + - + -
675A LEU* 3.2 25.3 + - + +
676A CYS* 3.3 4.3 + - - -
678A VAL* 3.5 21.8 - - + -
679A THR* 3.4 14.5 - - + +
734A ALA* 2.9 41.6 + - + +
737A CYS* 1.3 73.5 - - + +
739A THR* 1.3 61.0 + - - +
741A LEU* 3.8 5.9 - - + +
742A THR* 2.9 35.2 + - - -
751A LEU* 3.7 27.6 - - + -
752A LEU* 3.8 26.2 - - + +
755A CYS* 3.8 11.2 - - + -
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Residues in contact with THR 739 (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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642A ARG* 4.6 8.7 - - - +
735A ILE* 2.7 30.9 + - - +
736A PRO* 3.5 8.2 - - - +
737A CYS 3.2 0.2 - - - -
738A TYR* 1.3 79.5 - - - +
740A THR* 1.3 57.1 + - - +
742A THR* 3.4 3.6 + - - -
743A GLN* 3.1 47.3 + - + +
752A LEU* 3.6 23.5 - - + +
756A ARG* 4.8 7.5 + - - +
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Residues in contact with THR 740 (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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642A ARG* 2.8 35.7 + - + +
645A LEU* 4.1 15.3 - - + -
646A GLU* 3.0 24.7 + - - +
649A TYR* 5.7 0.4 - - + -
668A LEU* 3.9 15.0 - - + -
736A PRO 3.0 6.4 + - - -
739A THR* 1.3 74.5 - - - +
741A LEU* 1.3 65.9 + - - +
743A GLN* 3.3 12.6 + - - +
744A ILE* 3.1 40.7 + - + +
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Residues in contact with LEU 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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540A ILE* 4.3 6.1 - - + -
665A VAL* 4.9 3.8 - - + +
668A LEU* 3.7 19.2 - - + +
669A MET* 3.8 32.3 - - + +
672A ALA* 3.5 28.7 - - + -
737A CYS 3.0 18.8 + - - +
738A TYR* 3.8 7.2 - - + +
740A THR* 1.3 76.0 - - - +
742A THR* 1.3 52.3 + - - +
744A ILE* 3.3 4.8 + - + +
745A LEU* 2.7 44.5 + - + +
748A THR* 3.4 29.6 + - + +
751A LEU* 4.2 10.3 - - + -
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Residues in contact with THR 742 (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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738A TYR 2.9 23.2 + - - -
739A THR 3.6 5.6 - - - +
741A LEU* 1.3 73.9 - - - +
743A GLN* 1.3 66.8 + - + +
745A LEU 3.8 0.9 - - - -
746A PRO* 3.2 24.1 - - + +
748A THR* 3.5 11.8 + - - -
749A GLU* 3.5 50.3 + - + +
752A LEU* 3.5 19.9 + - + +
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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
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646A GLU* 3.0 31.2 + - - +
649A TYR* 3.3 60.6 + - + +
739A THR* 3.1 35.9 + - + +
740A THR* 3.3 11.3 + - - +
742A THR* 1.3 78.8 - - + +
744A ILE* 1.3 63.8 + - - +
746A PRO* 3.9 7.8 - - - +
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Residues in contact with ILE 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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645A LEU* 4.2 26.5 - - + +
649A TYR* 4.7 12.1 - - + -
654A LEU* 3.6 35.0 - - + -
656A LEU* 4.6 8.3 - - + +
665A VAL* 4.3 19.7 - - + -
668A LEU* 4.7 3.8 - - + -
740A THR* 3.1 35.3 + - + +
741A LEU* 3.9 5.2 - - + +
743A GLN* 1.3 79.2 - - - +
745A LEU* 1.3 77.7 + - + +
746A PRO* 3.3 7.9 - - - +
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Residues in contact with LEU 745 (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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540A ILE* 4.3 15.5 - - + -
544A ASN* 3.6 25.4 - - + +
547A LEU* 3.8 23.1 - - + -
548A PHE* 4.6 8.1 - - + -
656A LEU* 5.0 5.2 - - + -
665A VAL* 4.7 3.6 - - + -
669A MET* 4.1 22.0 - - + -
741A LEU* 2.7 34.9 + - + +
742A THR* 3.4 4.1 - - - +
744A ILE* 1.3 90.8 - - + +
746A PRO* 1.3 65.6 - - - +
747A PRO* 3.2 4.3 - - - -
748A THR* 2.7 35.6 + - + -
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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