Contacts of the helix formed by residues 850 - 858 (chain A) in PDB entry 5M9O
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 ASP 850 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A THR* 4.5 13.5 - - - +
842A LEU 3.5 11.5 + - - +
843A GLN* 4.5 8.7 - - + +
844A PHE* 4.8 2.3 - - - -
848A LYS 3.7 2.0 + - - +
849A GLY* 1.3 69.3 - - - -
851A VAL* 1.3 66.9 + - - +
852A GLY* 3.1 4.2 + - - -
853A LEU* 3.0 29.1 + - + +
854A GLY* 3.1 17.8 + - - -
874A VAL* 4.5 4.5 - - - +
878A TYR* 2.8 38.7 + - - -
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Residues in contact with VAL 851 (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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798A PHE* 3.9 20.2 - - + -
817A VAL* 5.1 6.3 - - + -
820A ASP* 4.9 10.7 - - + +
821A ILE* 3.9 33.4 - - + -
826A CYS* 4.8 0.9 - - - -
842A LEU* 2.9 38.6 + - + +
843A GLN 4.4 0.7 - - - -
844A PHE* 3.9 35.4 - - + +
850A ASP* 1.3 70.1 - - - +
852A GLY* 1.3 65.5 + - - +
854A GLY* 3.0 13.2 + - - -
855A LEU* 3.2 12.3 + - + +
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Residues in contact with GLY 852 (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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798A PHE* 4.1 16.5 - - - -
801A ILE* 3.3 34.6 - - - +
842A LEU 4.6 1.0 + - - +
850A ASP* 3.1 6.2 + - - -
851A VAL* 1.3 80.3 - - - +
853A LEU* 1.3 59.9 + - - +
855A LEU* 3.1 15.2 + - - +
856A VAL* 3.1 11.1 + - - +
878A TYR* 4.0 4.5 - - - -
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Residues in contact with LEU 853 (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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850A ASP* 3.0 38.2 + - + +
852A GLY* 1.3 74.4 - - - +
854A GLY* 1.3 57.6 + - - +
856A VAL* 3.1 4.5 + - + +
857A LYS* 2.8 53.4 + - + +
877A GLU* 3.7 24.7 - - + +
878A TYR* 3.5 34.5 + - + -
881A ALA* 3.7 29.4 - - + -
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Residues in contact with GLY 854 (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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820A ASP* 6.0 1.1 - - - -
844A PHE* 6.4 1.1 - - - -
850A ASP 3.1 10.2 + - - -
851A VAL* 3.0 10.2 + - - -
853A LEU* 1.3 76.9 - - - +
855A LEU* 1.3 61.4 + - - +
857A LYS* 3.4 11.1 + - - +
858A GLU* 3.1 25.3 + - - +
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Residues in contact with LEU 855 (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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694A LEU* 4.6 5.2 - - + -
798A PHE* 4.3 19.1 - - + -
801A ILE* 4.5 5.2 - - + -
813A ALA* 4.2 5.4 - - - +
816A SER* 3.9 10.3 - - - +
817A VAL* 3.5 34.8 - - + -
820A ASP* 4.4 6.7 - - - +
851A VAL* 3.2 9.9 + - + +
852A GLY* 3.1 17.3 + - - +
854A GLY* 1.3 73.6 - - - +
856A VAL* 1.3 64.1 + - - +
858A GLU 3.4 1.2 + - - -
859A GLY 3.3 2.9 + - - -
860A LEU* 2.9 54.7 + - + +
861A VAL* 3.6 24.7 + - + -
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Residues in contact with VAL 856 (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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801A ILE* 4.0 5.6 - - + -
852A GLY 3.1 11.8 + - - +
853A LEU* 3.1 10.1 + - + +
855A LEU* 1.3 76.7 - - - +
857A LYS* 1.3 59.0 + - - +
859A GLY* 2.9 18.2 + - - -
861A VAL* 3.7 28.2 - - + +
862A MET 4.8 0.7 - - - +
863A VAL* 3.9 13.9 - - + -
878A TYR* 3.5 47.1 - - + +
881A ALA* 3.8 4.2 - - + +
882A GLN* 3.5 18.6 - - + +
885A ALA* 3.4 10.9 - - - +
893A TRP* 5.1 0.3 + - - -
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Residues in contact with LYS 857 (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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853A LEU* 2.8 48.7 + - + +
854A GLY* 3.8 10.1 - - - +
855A LEU 3.3 0.2 - - - -
856A VAL* 1.3 74.8 - - - +
858A GLU* 1.3 60.4 + - - +
859A GLY 3.2 0.2 - - - -
881A ALA* 3.4 28.7 - - + +
884A SER* 4.9 7.7 + - - +
885A ALA* 3.4 15.4 + - - +
890A LEU* 3.5 10.6 - - - +
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Residues in contact with GLU 858 (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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816A SER* 5.6 0.2 - - - +
854A GLY 3.1 16.7 + - - +
855A LEU 3.4 0.9 + - - +
856A VAL 3.2 0.2 - - - -
857A LYS* 1.3 76.1 - - - +
859A GLY* 1.3 58.5 + - - +
860A LEU* 3.2 23.6 - - + -
890A LEU* 3.2 28.7 - - - +
891A ASN* 2.8 45.8 + - - +
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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