Contacts of the helix formed by residues 745 - 754 (chain A) in PDB entry 5MJ6
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 PRO 745 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739A ALA* 4.4 0.2 - - - -
744A VAL* 1.3 90.9 - - + +
746A LEU* 1.3 60.7 + - - +
747A LYS* 4.2 23.6 - - + +
748A ARG* 2.9 51.9 + - + +
749A ALA 3.8 1.6 + - - -
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Residues in contact with LEU 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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736A PHE* 4.4 17.7 - - + +
739A ALA* 3.7 24.7 - - + +
744A VAL 3.6 2.4 + - - -
745A PRO* 1.3 70.5 - - - +
747A LYS* 1.3 62.4 + - - +
749A ALA* 3.0 17.1 + - + +
750A PHE* 3.4 25.4 + - + -
775A ILE* 4.8 1.3 - - + -
1013A TRP* 3.6 37.9 - - + +
1017A ASN* 3.6 34.5 + - + +
1020A SER* 5.3 8.7 - - - -
1021A LEU* 4.1 23.1 - - + +
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Residues in contact with LYS 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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745A PRO* 4.2 18.8 - - + +
746A LEU* 1.3 78.9 - - - +
748A ARG* 1.3 77.2 + - - +
750A PHE* 3.0 10.3 + - - +
751A ASP* 2.9 53.9 + - - +
1020A SER* 6.0 3.4 - - - -
1024A TRP* 5.2 20.6 - - + +
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Residues in contact with ARG 748 (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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706A ASP* 2.6 50.8 + - - +
709A TRP* 4.1 27.2 - - - +
710A GLU* 5.7 4.5 + - - +
713A ILE* 4.1 16.0 - - + +
735A ILE* 4.3 7.3 - - + +
744A VAL* 4.3 22.6 - - + +
745A PRO* 2.9 34.7 + - + +
747A LYS* 1.3 95.7 - - - +
749A ALA* 1.3 57.4 + - - +
751A ASP* 3.4 7.8 + - - +
752A LEU* 3.1 25.8 + - - +
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Residues in contact with ALA 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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735A ILE* 3.8 31.5 - - + +
736A PHE* 3.9 33.0 - - + -
739A ALA* 4.5 2.2 - - + -
745A PRO 3.8 0.8 + - - -
746A LEU* 3.0 18.3 + - + +
748A ARG* 1.3 79.6 - - - +
750A PHE* 1.3 62.5 + - - +
752A LEU* 3.4 4.9 + - - +
753A ILE* 3.3 24.9 + - - +
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Residues in contact with PHE 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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736A PHE* 3.7 23.6 - + - -
746A LEU* 3.4 35.3 + - + -
747A LYS* 3.0 7.9 + - + +
749A ALA* 1.3 75.1 - - - +
751A ASP* 1.3 67.6 + - - +
753A ILE* 3.4 25.5 + - + +
754A ASN* 3.3 24.7 + - - +
772A THR* 4.9 9.6 - - - -
775A ILE* 4.1 11.7 - - + -
791A LEU* 4.0 22.2 - - + -
795A VAL* 5.2 3.4 - - + -
1021A LEU* 3.9 16.2 - - + -
1024A TRP* 3.4 53.7 - + + +
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Residues in contact with ASP 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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713A ILE* 4.5 14.8 - - + -
717A LYS* 3.6 17.9 + - - +
747A LYS* 2.9 45.4 + - - +
748A ARG* 3.4 11.6 - - - +
749A ALA 3.3 0.2 - - - -
750A PHE* 1.3 77.7 - - - +
752A LEU* 1.3 61.4 + - - +
754A ASN* 3.2 29.5 + - - +
1024A TRP* 5.8 1.7 + - - -
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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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709A TRP* 3.8 29.6 - - + -
712A LEU* 6.0 0.4 - - + -
713A ILE* 3.8 28.6 - - + +
716A LEU* 4.1 18.6 - - + +
717A LYS* 5.7 0.5 - - - -
731A LEU* 4.4 11.4 - - + +
732A ILE* 3.7 39.7 - - + +
735A ILE* 4.2 17.0 - - + -
748A ARG 3.1 10.4 + - - +
749A ALA 3.7 8.1 - - - +
750A PHE 3.3 0.4 - - - -
751A ASP* 1.3 81.8 - - - +
753A ILE* 1.3 60.1 + - + +
754A ASN 3.5 0.3 + - - -
755A TYR* 3.0 27.2 + - + +
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Residues in contact with ILE 753 (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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732A ILE* 4.0 26.7 - - + -
736A PHE* 3.9 26.0 - - + -
749A ALA 3.3 5.7 + - - +
750A PHE* 3.4 44.2 - - + +
751A ASP 3.2 0.2 - - - -
752A LEU* 1.3 76.7 - - + +
754A ASN* 1.3 56.3 + - - +
755A TYR* 3.0 9.6 - - - -
756A LEU* 2.9 43.3 + - + +
768A ALA* 4.4 7.6 - - + -
772A THR* 5.1 7.0 - - - +
795A VAL* 5.4 5.6 - - + -
798A LEU* 3.2 19.1 - - + +
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Residues in contact with ASN 754 (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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717A LYS* 3.9 24.1 - - - +
750A PHE 3.3 15.3 + - - +
751A ASP* 3.2 21.4 + - - +
753A ILE* 1.3 76.7 - - - +
755A TYR* 1.3 61.3 + - - +
756A LEU 3.1 0.7 + - - -
757A GLY* 4.0 2.8 + - - -
794A ARG* 6.1 1.0 - - - -
798A LEU* 3.7 28.3 - - - +
1024A TRP* 5.6 6.8 - - - -
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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