Contacts of the helix formed by residues 741 - 749 (chain A) in PDB entry 6BM4
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 ASN 741 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667A GLY 4.3 3.2 + - - -
668A ASP* 3.2 36.5 + - - +
670A ILE 5.3 0.8 + - - -
737A LEU* 3.4 26.6 - - + +
738A LYS* 3.2 24.6 + - + +
739A ASP 3.2 1.4 - - - +
740A LEU* 1.3 81.1 - - + +
742A ASN* 1.3 53.6 + - - +
743A VAL* 3.1 14.9 + - - +
744A LYS* 3.1 21.8 + - + +
745A GLN* 2.8 34.8 + - - +
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Residues in contact with ASN 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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662A PHE* 3.3 28.5 - - + +
663A SER* 3.1 37.6 + - - +
664A THR* 3.5 4.6 - - - +
668A ASP* 2.9 34.5 + - - +
740A LEU 4.0 5.9 + - - +
741A ASN* 1.3 70.3 - - - +
743A VAL* 1.3 58.4 + - - +
745A GLN* 3.2 17.1 + - - +
746A MET* 2.9 28.5 + - - +
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Residues in contact with VAL 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A THR* 4.2 15.0 - - + -
668A ASP* 3.6 30.5 - - + +
669A THR* 4.9 3.4 - - + -
737A LEU* 5.3 0.9 - - + -
741A ASN* 3.1 7.7 + - - +
742A ASN* 1.3 74.7 - - - +
744A LYS* 1.3 58.2 + - - +
746A MET* 3.1 17.4 + - + +
747A VAL* 2.9 34.9 + - + +
752A LYS 4.8 0.2 - - - +
753A GLY* 6.2 2.5 - - - -
754A SER 5.9 0.2 - - - +
757A ASN* 5.9 2.0 - - + -
758A ILE* 3.9 27.6 - - + -
761A MET* 4.4 20.9 - - + -
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Residues in contact with LYS 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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734A GLU* 3.7 20.6 + - + +
735A VAL* 4.5 3.8 + - - +
737A LEU* 2.9 37.8 + - + +
738A LYS 3.3 17.5 - - - +
739A ASP* 4.3 9.2 + - - -
741A ASN* 3.1 21.1 + - + +
743A VAL* 1.3 79.4 - - - +
745A GLN* 1.3 58.3 + - - +
747A VAL* 3.3 10.4 + - + +
748A MET* 2.9 61.9 + - + +
758A ILE* 4.7 7.1 - - + +
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Residues in contact with GLN 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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529A CYS* 5.3 2.5 - - - -
532A ARG* 3.4 26.3 + - - +
533A LYS* 3.1 33.3 + - + +
662A PHE* 3.7 16.7 - - + -
739A ASP 3.3 18.2 - - - +
740A LEU* 2.8 34.6 + - - +
741A ASN 2.8 14.7 + - - +
742A ASN* 3.3 18.5 - - - +
743A VAL 3.1 0.2 - - - -
744A LYS* 1.3 74.7 - - - +
746A MET* 1.3 59.5 + - - +
748A MET* 3.2 3.1 + - - -
749A ALA* 2.9 28.3 + - - +
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Residues in contact with MET 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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529A CYS* 4.3 4.3 - - + -
662A PHE* 3.5 29.4 - - + -
664A THR* 3.4 29.6 - - + +
742A ASN 2.9 15.4 + - - +
743A VAL* 3.1 18.6 + - + +
745A GLN* 1.3 76.4 - - - +
747A VAL* 1.3 55.9 + - - +
749A ALA* 4.4 1.1 - - - -
750A GLY* 3.0 21.3 + - - -
751A SER* 3.1 30.5 + - - +
752A LYS* 3.3 25.8 + - - +
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Residues in contact with VAL 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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734A GLU* 5.4 7.0 - - - +
743A VAL* 2.9 26.2 + - + +
744A LYS* 3.5 12.6 - - + +
746A MET* 1.3 74.4 - - - +
748A MET* 1.3 68.2 + - + +
750A GLY* 3.1 13.4 + - - -
752A LYS 3.9 5.2 - - - +
753A GLY* 3.9 28.3 - - - +
754A SER* 4.2 18.2 - - - +
755A PHE* 5.2 1.6 - - - +
758A ILE* 4.2 14.8 - - + -
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Residues in contact with MET 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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532A ARG* 4.1 32.0 - - - +
618A GLU* 4.1 16.3 - - - +
620A LYS* 5.9 0.3 + - - -
739A ASP* 4.0 28.7 - - - +
744A LYS* 2.9 55.7 + - + +
745A GLN* 3.5 4.9 - - - +
747A VAL* 1.3 78.7 - - + +
749A ALA* 1.3 62.4 + - - +
750A GLY* 3.3 1.0 + - - -
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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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528A LEU* 3.4 10.4 - - - +
529A CYS* 3.7 22.2 - - + +
532A ARG* 3.6 32.5 - - + +
618A GLU* 3.6 3.1 - - - +
619A LYS* 3.3 24.2 + - - -
745A GLN 2.9 17.0 + - - +
746A MET* 3.9 4.5 - - - +
747A VAL 3.3 0.2 - - - -
748A MET* 1.3 76.4 - - - +
750A GLY* 1.3 58.8 + - - +
751A SER* 3.1 7.2 - - - +
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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