Contacts of the helix formed by residues 733 - 747 (chain J) in PDB entry 6H25
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 PHE 733 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730J SER* 3.5 13.4 + - - +
731J PRO 3.4 0.4 - - - -
732J THR* 1.3 83.5 - - - +
734J PRO* 1.3 71.8 - - + +
735J TYR* 3.3 9.3 + - + +
736J LEU* 3.3 40.1 + - + +
737J ASN 4.0 1.6 + - - -
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Residues in contact with PRO 734 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729J GLU* 6.2 2.5 - - + -
730J SER 4.2 11.4 - - - +
731J PRO* 5.3 3.1 - - + +
732J THR 4.8 0.7 - - - -
733J PHE* 1.3 83.0 - - + +
735J TYR* 1.3 59.1 + - - +
736J LEU 3.2 0.4 - - - -
737J ASN* 3.1 14.8 + - + +
738J THR* 3.0 26.8 + - - +
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Residues in contact with TYR 735 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635J PRO* 5.9 1.7 - - - +
733J PHE* 3.1 7.7 - - + +
734J PRO* 1.3 78.2 - - - +
736J LEU* 1.3 63.2 + - + +
738J THR* 3.7 26.6 - - + +
739J LEU* 2.8 53.7 + - + +
851J TYR* 5.2 5.2 - - + -
863J LEU* 3.7 11.9 - - + +
865J PRO* 3.3 40.1 - - + +
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Residues in contact with LEU 736 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730J SER* 5.7 7.9 - - - +
732J THR* 5.5 9.9 - - - -
733J PHE* 3.3 32.1 + - + +
734J PRO 3.2 0.8 - - - -
735J TYR* 1.3 75.8 - - + +
737J ASN* 1.3 58.7 + - - +
739J LEU* 3.3 13.8 + - + +
740J LEU* 3.0 26.9 + - - +
904J PHE* 4.4 35.0 - - + +
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Residues in contact with ASN 737 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725J LEU* 4.0 5.3 + - - +
728J ALA* 2.9 34.9 + - - +
729J GLU* 3.4 13.5 - - + +
730J SER* 5.0 2.8 - - - +
733J PHE 4.0 1.4 + - - +
734J PRO* 3.1 18.6 + - + +
736J LEU* 1.3 79.9 - - - +
738J THR* 1.3 56.1 + - - +
740J LEU* 3.1 10.5 + - - +
741J ARG* 2.9 65.7 + - - +
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Residues in contact with THR 738 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734J PRO* 3.0 14.8 + - - +
735J TYR* 3.2 37.6 + - + +
737J ASN* 1.3 76.2 - - - +
739J LEU* 1.3 57.6 + - + +
741J ARG* 3.2 9.7 + - + +
742J ILE* 3.0 38.9 + - + +
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Residues in contact with LEU 739 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735J TYR* 2.8 43.8 + - + +
736J LEU* 3.6 12.3 - - + +
738J THR* 1.3 72.3 - - + +
740J LEU* 1.3 62.2 + - - +
742J ILE* 3.3 21.9 - - + +
743J LEU* 3.0 30.7 + - - +
851J TYR* 3.8 29.6 - - + -
852J ILE 5.1 1.8 - - - +
853J LEU* 5.1 8.6 - - + +
863J LEU* 5.0 14.1 - - + -
904J PHE* 3.6 40.4 - - + -
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Residues in contact with LEU 740 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702J LEU* 4.6 8.0 - - + +
725J LEU* 4.5 14.9 - - + +
736J LEU 3.0 14.0 + - - +
737J ASN* 3.1 18.4 + - - +
739J LEU* 1.3 77.0 - - - +
741J ARG* 1.3 56.9 + - - +
743J LEU* 3.4 6.7 + - - +
744J ALA* 2.9 28.1 + - - +
904J PHE* 4.1 10.9 - - + -
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Residues in contact with ARG 741 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632J LEU* 3.5 47.7 - - + +
725J LEU* 3.1 33.6 + - - +
726J ASP* 3.1 33.7 + - - +
737J ASN* 2.9 50.2 + - - +
738J THR* 3.2 10.9 + - + +
740J LEU* 1.3 77.7 - - - +
742J ILE* 1.3 54.1 + - + +
744J ALA* 3.2 6.9 + - - +
745J THR* 2.7 36.4 + - - -
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Residues in contact with ILE 742 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633J SER 4.2 12.8 - - - +
635J PRO* 3.7 32.3 - - + -
738J THR* 3.0 25.5 + - + +
739J LEU* 3.3 27.1 - - + +
741J ARG* 1.3 79.7 - - + +
743J LEU* 1.3 62.4 + - + +
745J THR* 3.2 9.2 + - - -
746J ARG* 2.9 24.6 + - - +
853J LEU* 4.7 14.1 - - + -
863J LEU* 4.2 23.3 - - + -
870J GLU* 5.8 2.7 - - - +
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Residues in contact with LEU 743 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702J LEU* 4.2 16.8 - - + +
739J LEU 3.0 19.0 + - - +
740J LEU* 3.8 5.2 - - - +
742J ILE* 1.3 81.2 - - + +
744J ALA* 1.3 63.7 + - - +
746J ARG* 3.4 19.6 + - - +
747J CYS* 3.4 15.9 + - - -
853J LEU* 5.4 9.6 - - + +
904J PHE* 5.4 7.2 - - + -
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Residues in contact with ALA 744 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630J LEU* 6.0 2.5 - - + -
632J LEU* 5.1 4.0 - - + -
699J TYR* 6.0 0.2 - - - -
702J LEU* 4.0 23.2 - - + +
721J LEU* 5.4 5.4 - - + -
725J LEU* 4.1 22.7 - - + -
740J LEU 2.9 14.0 + - - +
741J ARG* 3.2 8.5 + - - +
743J LEU* 1.3 75.7 - - - +
745J THR* 1.3 59.9 + - - +
747J CYS* 3.1 28.2 + - - +
748J MET* 4.3 5.0 - - - +
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Residues in contact with THR 745 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632J LEU* 2.3 38.0 + - - +
633J SER 4.0 0.2 - - - -
634J SER* 3.7 27.6 - - - +
741J ARG 2.7 19.4 + - - -
742J ILE* 3.2 13.6 + - - -
744J ALA* 1.3 74.1 - - - +
746J ARG* 1.3 64.4 + - - +
747J CYS 3.4 2.9 + - - -
748J MET* 4.4 11.8 - - - +
39R U 4.4 9.0 + - - -
40R U 4.2 24.3 - - - +
41R U 6.0 0.2 - - - +
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Residues in contact with ARG 746 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742J ILE 2.9 12.7 + - - +
743J LEU* 3.4 14.8 - - - +
744J ALA 3.2 0.2 - - - -
745J THR* 1.3 77.6 - - - +
747J CYS* 1.3 60.6 + - - +
748J MET 3.4 6.9 + - - +
829J ARG* 5.5 2.4 - - - +
870J GLU* 4.5 22.3 + - - -
39R U 4.1 32.6 + - - -
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Residues in contact with CYS 747 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698J ASN* 3.4 40.4 - - + +
699J TYR* 4.2 13.4 + - + -
701J ILE* 6.1 1.3 - - - -
702J LEU* 4.8 14.4 - - + -
743J LEU 3.4 14.8 + - - +
744J ALA* 3.1 20.6 + - - +
746J ARG* 1.3 81.1 - - - +
748J MET* 1.3 75.1 + - - +
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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