Contacts of the helix formed by residues 850 - 863 (chain A) in PDB entry 3E0D
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
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Residue Dist Surf HB Arom Phob DC
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847A GLU* 3.2 17.3 + - - +
848A ARG 3.3 0.9 - - - -
849A HIS* 1.3 77.1 - - - +
851A SER* 1.3 57.8 + - - +
852A ASP* 3.0 14.6 + - - +
853A LYS* 3.0 37.4 + - + +
854A VAL* 2.9 34.4 + - - +
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Residues in contact with SER 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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848A ARG 5.7 0.4 - - - -
849A HIS 3.8 3.7 + - - -
850A ASP* 1.3 71.8 + - - +
852A ASP* 1.3 60.9 + - - +
854A VAL* 3.9 5.4 - - - +
855A ALA* 3.0 28.9 + - - +
895A LYS* 1.8 55.4 + - - +
1006A LEU 4.1 2.8 + - - +
1007A GLY* 3.5 19.1 + - - +
1008A ILE* 3.5 5.4 - - - +
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Residues in contact with ASP 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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850A ASP* 3.0 10.6 + - - +
851A SER* 1.3 77.0 - - - +
853A LYS* 1.3 61.5 + - + +
855A ALA* 3.5 6.9 - - - +
856A GLU* 3.0 26.6 + - - +
859A ARG* 4.3 2.9 + - - -
1007A GLY 5.4 2.6 - - - +
1095A GLU* 5.6 3.1 - - - +
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Residues in contact with LYS 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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671A GLU* 2.1 37.4 + - - +
847A GLU* 3.4 31.1 + - + +
850A ASP* 3.0 32.2 + - + +
852A ASP* 1.3 74.0 - - + +
854A VAL* 1.3 56.7 + - - +
856A GLU* 2.9 23.9 + - - +
857A TYR* 2.7 58.1 + - + +
7C G 5.5 13.9 + - - -
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Residues in contact with VAL 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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844A LEU* 3.7 14.3 - - + +
847A GLU 3.4 17.0 - - - +
848A ARG* 3.7 22.2 - - + +
850A ASP 2.9 22.3 + - - +
851A SER* 3.9 4.3 - - - +
853A LYS* 1.3 75.4 - - - +
855A ALA* 1.3 64.4 + - - +
857A TYR* 4.5 1.5 - - + -
858A ILE* 3.0 30.4 + - + +
880A PHE* 4.2 6.5 - - + -
889A PHE* 3.4 35.2 - - + -
893A ALA* 5.4 4.7 - - + -
1006A LEU 4.4 12.6 - - - +
1008A ILE* 4.5 0.9 - - + -
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Residues in contact with ALA 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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851A SER 3.0 11.9 + - - +
852A ASP* 3.5 7.9 - - - +
854A VAL* 1.3 74.2 - - - +
856A GLU* 1.3 62.7 + - - +
858A ILE* 3.3 3.3 + - - +
859A ARG* 3.1 37.9 + - - +
1007A GLY 4.5 2.0 - - - +
1008A ILE* 1.7 47.5 - - + +
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Residues in contact with GLU 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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665A LYS* 3.1 26.1 - - - +
671A GLU* 4.7 3.0 - - - +
852A ASP 3.0 13.9 + - - +
853A LYS* 2.9 36.0 + - - +
855A ALA* 1.3 75.6 - - - +
857A TYR* 1.3 60.0 + - - +
859A ARG* 3.1 35.9 + - + +
860A ASP* 2.9 41.6 + - - +
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Residues in contact with TYR 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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665A LYS* 3.3 24.7 - - + -
666A GLY* 3.3 11.7 - - - -
671A GLU* 3.7 15.4 + - - -
840A MET* 4.0 7.1 - - - +
843A LEU* 3.5 53.1 - - + +
844A LEU* 3.6 24.5 - - + -
847A GLU* 3.6 32.7 + - + -
853A LYS* 2.7 42.3 + - + +
854A VAL* 4.5 1.1 - - - -
856A GLU* 1.3 75.5 - - - +
858A ILE* 1.3 57.3 + - - +
860A ASP* 3.3 12.9 + - + +
861A ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 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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844A LEU* 3.9 12.1 - - + -
854A VAL* 3.0 19.4 + - + +
855A ALA 3.6 4.7 - - - +
857A TYR* 1.3 75.1 - - - +
859A ARG* 1.3 58.2 + - - +
861A ALA* 3.1 6.1 + - - +
862A ARG* 2.9 68.3 + - + +
868A VAL* 4.0 9.4 - - + -
880A PHE* 4.3 2.9 - - + -
889A PHE* 2.0 54.7 - - + -
1008A ILE* 2.8 28.3 - - + -
1009A TYR 5.1 1.1 - - - +
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Residues in contact with ARG 859 (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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852A ASP 4.3 2.2 + - - -
855A ALA* 3.1 22.8 + - - +
856A GLU* 3.1 59.1 + - - +
858A ILE* 1.3 77.8 - - - +
860A ASP* 1.3 67.1 + - - +
862A ARG* 4.3 6.7 - - - +
863A ALA* 3.3 25.5 + - - +
1052A GLU* 3.9 20.4 + - - -
1069A THR* 6.1 1.6 - - - +
1071A SER* 6.0 3.8 - - - -
1075A GLY* 5.4 5.8 - - - -
1076A ALA* 4.8 25.4 - - - +
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Residues in contact with ASP 860 (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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665A LYS* 1.9 65.7 + - + +
840A MET* 4.4 8.5 - - - -
856A GLU* 2.9 27.3 + - - +
857A TYR* 3.5 14.1 - - - +
858A ILE 3.2 0.2 - - - -
859A ARG* 1.3 82.8 - - - +
861A ALA* 1.3 63.0 + - - +
863A ALA* 3.5 9.9 - - - +
864A LEU* 3.2 21.8 - - - +
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Residues in contact with ALA 861 (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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840A MET* 3.5 28.2 - - + -
844A LEU* 5.4 3.4 - - + -
857A TYR 2.9 17.3 + - - +
858A ILE* 3.6 5.6 - - - +
860A ASP* 1.3 73.9 - - - +
862A ARG* 1.3 63.4 + - - +
864A LEU* 3.2 20.6 + - - +
865A GLY 3.5 6.2 + - - -
866A ILE* 4.0 9.9 + - - +
868A VAL* 4.4 16.6 - - + -
887A ILE* 4.6 8.5 - - + -
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Residues in contact with ARG 862 (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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858A ILE* 2.9 32.4 + - + +
859A ARG* 4.3 6.2 - - - +
861A ALA* 1.3 75.7 - - - +
863A ALA* 1.3 57.2 + - - +
864A LEU 3.1 4.6 + - - -
865A GLY* 3.7 7.4 + - - -
866A ILE 4.3 14.5 - - - +
867A PRO* 5.2 0.2 - - - -
868A VAL* 2.9 50.0 + - + +
1009A TYR 4.6 3.4 + - - -
1010A VAL* 2.8 45.3 - - - +
1011A SER* 3.6 13.6 - - - +
1012A GLY 5.8 0.2 - - - +
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Residues in contact with ALA 863 (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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665A LYS* 5.5 0.5 + - - -
859A ARG 3.3 18.8 + - - +
860A ASP* 3.5 4.9 - - - +
861A ALA 3.3 0.2 - - - -
862A ARG* 1.3 75.5 - - - +
864A LEU* 1.3 64.4 + - - +
1074A THR 5.7 4.7 - - - +
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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