Contacts of the helix formed by residues 791 - 797 (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 PRO 791 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767E LEU 5.3 5.6 - - - +
769E LYS* 3.5 23.6 - - + +
789E SER 4.1 4.7 - - - +
790E LEU* 1.3 92.2 - - + +
792E GLU* 1.3 66.2 + - - +
793E LYS* 3.1 35.1 + - + +
794E VAL* 3.3 17.2 + - - +
816E GLN* 3.8 6.9 - - - +
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Residues in contact with GLU 792 (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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769E LYS* 3.5 13.3 - - - +
791E PRO* 1.3 74.6 - - - +
793E LYS* 1.3 56.9 + - - +
794E VAL 3.2 0.4 - - - -
795E GLY* 2.9 28.5 + - - -
796E GLN 3.8 1.9 + - - -
816E GLN* 3.3 38.0 + - - +
819E GLN* 5.3 6.8 + - - -
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Residues in contact with LYS 793 (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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767E LEU* 3.5 16.2 - - - +
768E PRO 3.6 16.4 - - - +
769E LYS* 3.3 29.5 - - + +
771E LEU* 3.4 43.4 - - + +
772E PHE* 3.6 34.0 - - + +
780E LEU* 6.3 0.2 - - - +
790E LEU* 3.6 19.8 - - - +
791E PRO* 3.7 32.3 - - + -
792E GLU* 1.3 77.6 - - - +
794E VAL* 1.3 57.9 + - + +
796E GLN* 2.8 28.3 - - - +
797E LEU 4.1 0.7 + - - -
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Residues in contact with VAL 794 (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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771E LEU* 4.9 1.8 - - + -
780E LEU* 5.3 7.0 - - + -
790E LEU* 3.8 21.3 - - + -
791E PRO 3.3 18.4 - - - +
793E LYS* 1.3 76.0 - - - +
795E GLY* 1.3 58.8 + - - +
796E GLN 3.1 4.3 - - - -
797E LEU* 3.0 50.5 + - + +
803E LEU* 5.6 1.1 - - + -
816E GLN* 3.6 22.7 - - + +
817E LEU* 3.7 37.2 - - + -
820E CYS* 3.3 9.5 - - - -
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Residues in contact with GLY 795 (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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792E GLU* 2.9 16.3 + - - -
794E VAL* 1.3 80.0 - - - +
796E GLN* 1.3 62.7 + - - +
797E LEU 3.3 0.4 - - - -
798E SER* 4.3 6.4 + - - -
816E GLN* 3.4 17.6 + - - +
819E GLN* 3.5 28.9 - - - +
820E CYS* 4.3 1.3 - - - -
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Residues in contact with GLN 796 (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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771E LEU 4.8 0.4 - - - +
772E PHE* 2.5 47.0 + - + +
773E LYS 5.4 0.2 - - - -
774E CYS 3.4 22.2 - - - +
775E ILE* 3.7 31.9 - - - +
792E GLU 3.8 1.6 + - - -
793E LYS 2.8 20.7 + - - +
795E GLY* 1.3 78.3 - - - +
797E LEU* 1.3 57.2 + - + +
798E SER* 3.1 9.4 + - - -
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Residues in contact with LEU 797 (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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771E LEU* 3.8 24.5 - - + +
774E CYS 5.2 0.9 - - - +
775E ILE* 5.0 7.9 - - - +
777E LEU* 3.8 25.8 - - + +
780E LEU* 3.7 23.8 - - + -
793E LYS 4.5 1.3 - - - +
794E VAL* 3.0 38.4 + - + +
796E GLN* 1.3 75.7 - - + +
798E SER* 1.3 63.7 + - - +
799E GLN 3.4 2.7 - - - +
800E LEU* 3.3 42.8 + - + +
803E LEU* 6.0 2.0 - - + -
820E CYS* 3.2 19.0 - - + +
823E LEU* 5.8 1.8 - - + -
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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