Contacts of the helix formed by residues 723 - 728 (chain E) in PDB entry 6M04
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 723 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697E THR* 6.1 0.7 - - - +
698E ILE* 5.1 6.4 - - + +
700E PRO* 5.3 9.9 - - + -
721E LEU 3.9 10.1 - - - +
722E PRO* 1.3 73.3 - - + +
724E ALA* 1.3 65.7 + - + +
725E VAL* 3.2 5.6 + - - +
726E PHE* 3.2 19.2 - - + -
747E GLU* 2.9 19.6 - - - +
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Residues in contact with ALA 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698E ILE* 5.1 2.8 - - + +
700E PRO* 3.8 24.0 - - + +
702E ILE* 3.7 22.2 - - + +
703E THR* 3.7 24.0 - - + +
723E VAL* 1.3 76.3 - - + +
725E VAL* 1.3 63.8 + - - +
726E PHE* 3.2 8.3 - - - -
727E SER* 3.0 22.6 + - - -
728E LEU* 4.5 0.7 + - - +
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Residues in contact with VAL 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698E ILE* 4.8 3.1 - - + -
702E ILE* 3.8 20.0 - - + -
711E LEU* 6.1 3.1 - - + -
722E PRO* 3.7 35.7 - - + +
723E VAL 3.2 3.0 + - - +
724E ALA* 1.3 76.6 - - - +
726E PHE* 1.3 57.7 + - - +
727E SER 3.0 6.2 + - - -
728E LEU* 3.3 17.2 + - + +
731E LEU* 5.5 2.7 - - + -
734E LEU* 4.5 22.0 - - + -
735E ASP* 5.2 10.5 - - - +
747E GLU* 3.4 15.3 - - + +
750E LEU* 3.2 16.0 - - + +
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Residues in contact with PHE 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723E VAL* 3.2 31.2 - - + -
724E ALA* 3.1 5.1 + - - -
725E VAL* 1.3 76.8 - - - +
727E SER* 1.3 58.4 + - - -
728E LEU 3.6 0.4 - - - -
746E ILE 5.7 0.2 - - - -
747E GLU* 3.2 40.4 + - + +
750E LEU* 3.2 33.5 - - + +
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Residues in contact with SER 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703E THR* 3.6 33.9 + - - +
706E LYS* 6.1 0.5 - - - +
724E ALA 3.0 14.6 + - - -
725E VAL 3.0 0.8 + - - -
726E PHE* 1.3 80.7 - - - +
728E LEU* 1.3 62.1 + - - +
729E GLN* 2.9 14.6 + - - +
750E LEU* 4.0 0.9 - - - -
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Residues in contact with LEU 728 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702E ILE* 3.3 44.4 - - + +
703E THR* 5.0 2.2 - - - +
705E VAL 3.3 21.5 - - - +
706E LYS* 5.3 3.6 - - - +
708E LEU* 3.7 22.9 - - + +
711E LEU* 3.7 29.4 - - + -
724E ALA 5.2 0.7 - - - +
725E VAL* 3.3 18.1 + - + +
726E PHE 3.6 0.4 - - - -
727E SER* 1.3 72.8 - - - +
729E GLN* 1.3 64.1 + - - +
730E LYS 3.2 3.1 + - - -
731E LEU* 3.4 19.1 + - + +
750E LEU* 3.3 17.8 - - + +
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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
------------------------------------------------------------
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