Contacts of the helix formed by residues 898 - 912 (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 GLY 898 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892A SER* 5.5 2.3 - - - -
896A ASN 3.3 5.9 + - - -
897A VAL* 1.3 92.3 - - - +
899A GLU* 1.3 62.2 + - - -
900A MET 3.5 1.6 - - - -
901A ALA* 4.0 13.8 - - - +
902A ALA* 3.7 5.5 + - - +
934A ALA* 5.3 1.2 - - - +
14D A 4.7 14.1 - - - -
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Residues in contact with GLU 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A ARG* 5.3 1.6 + - - -
849A HIS* 3.9 23.4 + - + -
878A PHE* 3.7 22.1 - - + -
892A SER* 6.2 0.9 - - - +
898A GLY* 1.3 71.4 - - - -
900A MET* 1.3 66.0 + - + +
901A ALA 3.2 1.3 - - - -
902A ALA* 3.4 4.9 + - - +
903A ARG* 3.0 46.6 + - - +
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Residues in contact with MET 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A GLY* 5.8 0.4 - - - -
899A GLU* 1.3 79.0 - - + +
901A ALA* 1.3 55.5 + - - +
903A ARG* 3.6 4.4 + - - +
904A ALA* 2.9 30.3 + - - +
929A VAL* 5.4 1.8 - - + +
13D C 6.1 5.2 - - - +
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Residues in contact with ALA 901 (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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897A VAL* 4.0 17.5 - - + -
898A GLY* 4.0 12.4 - - - +
899A GLU 3.2 0.4 - - - -
900A MET* 1.3 77.2 - - - +
902A ALA* 1.3 59.3 + - - +
904A ALA* 3.2 7.0 + - - +
905A ILE* 2.8 38.0 + - + +
929A VAL* 3.9 24.0 - - - +
930A VAL* 4.6 12.1 - - + -
934A ALA* 5.6 2.9 - - + -
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Residues in contact with ALA 902 (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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878A PHE* 3.7 26.0 - - + -
891A LEU* 4.2 7.9 - - + +
892A SER* 4.3 15.5 - - - +
897A VAL* 3.9 12.0 - - + +
898A GLY 3.7 13.4 + - - +
899A GLU 3.4 4.2 + - - +
900A MET 3.4 0.2 - - - -
901A ALA* 1.3 78.8 - - - +
903A ARG* 1.3 61.6 + - - +
905A ILE* 3.4 8.4 + - - +
906A LEU* 3.2 29.1 + - - +
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Residues in contact with ARG 903 (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* 5.6 1.2 - - - +
878A PHE* 3.2 51.1 - - + +
899A GLU* 3.0 41.3 + - - +
900A MET* 4.0 4.7 - - - +
902A ALA* 1.3 75.1 - - - +
904A ALA* 1.3 55.4 + - - +
906A LEU* 3.2 9.8 + - + +
907A GLU* 2.8 55.3 + - + +
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Residues in contact with ALA 904 (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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900A MET 2.9 19.8 + - - +
901A ALA 3.2 5.6 + - - +
903A ARG* 1.3 75.6 - - - +
905A ILE* 1.3 57.7 + - - +
907A GLU* 3.1 6.3 + - - +
908A GLU* 2.8 32.6 + - - +
925A LEU* 4.2 6.7 - - + -
929A VAL* 3.5 28.9 - - + -
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Residues in contact with ILE 905 (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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873A VAL* 4.3 9.2 - - + +
891A LEU* 3.9 21.8 - - + -
897A VAL* 4.8 7.9 - - + -
901A ALA 2.8 29.1 + - - +
902A ALA* 3.7 9.2 - - - +
904A ALA* 1.3 72.6 - - - +
906A LEU* 1.3 59.6 + - - +
908A GLU* 3.3 2.6 + - - +
909A ARG* 2.9 27.2 + - - +
915A PHE* 3.8 10.8 - - + -
921A PHE* 4.1 19.1 - - + -
925A LEU* 3.8 24.0 - - + -
930A VAL* 4.0 16.6 - - + -
938A LEU* 4.0 27.8 - - + -
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Residues in contact with LEU 906 (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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876A SER 3.1 26.9 - - - +
877A GLY* 4.0 5.6 - - - -
878A PHE* 3.7 37.0 - - + +
891A LEU* 3.8 17.5 - - + -
902A ALA 3.2 20.4 + - - +
903A ARG* 3.2 9.5 + - + +
905A ILE* 1.3 77.4 - - + +
907A GLU* 1.3 71.0 + - - +
909A ARG* 3.2 28.4 + - - +
910A GLU* 3.1 28.7 + - + +
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Residues in contact with GLU 907 (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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903A ARG* 2.8 43.3 + - + +
904A ALA* 3.8 4.0 - - - +
906A LEU* 1.3 75.9 - - - +
908A GLU* 1.3 65.3 + - - +
910A GLU* 3.1 23.0 + - - +
911A ARG* 3.2 16.7 + - - +
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Residues in contact with GLU 908 (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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904A ALA 2.8 15.7 + - - +
905A ILE 3.7 4.0 - - - +
907A GLU* 1.3 76.0 - - - +
909A ARG* 1.3 61.8 + - - +
911A ARG* 3.5 35.9 + - - +
912A GLY* 3.1 24.9 + - - -
915A PHE* 4.3 4.7 - - + -
924A ARG* 3.2 66.5 + - + +
925A LEU* 3.9 22.1 - - + +
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Residues in contact with ARG 909 (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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873A VAL 2.8 37.0 + - - -
874A ASN* 3.4 30.8 + - - +
875A ARG 3.7 3.0 + - - +
876A SER 2.9 29.5 + - - +
877A GLY* 5.0 1.0 - - - -
881A LYS* 5.0 7.1 - - - +
905A ILE 2.9 17.4 + - - +
906A LEU* 3.2 25.9 + - - +
908A GLU* 1.3 76.2 - - - +
910A GLU* 1.3 79.5 + - - +
912A GLY 2.6 16.8 - - - +
913A GLY* 3.2 19.9 - - - +
914A PRO* 4.1 9.4 - - + -
915A PHE* 3.6 17.9 - - + -
924A ARG* 4.4 0.2 - - - +
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Residues in contact with GLU 910 (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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906A LEU* 3.1 19.4 + - + +
907A GLU* 3.1 18.3 + - - +
909A ARG* 1.3 108.4 + - - +
911A ARG* 1.3 61.7 + - - +
912A GLY 3.5 1.8 - - - +
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Residues in contact with ARG 911 (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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907A GLU 3.2 16.9 + - - +
908A GLU* 3.5 30.4 + - - +
910A GLU* 1.3 77.4 - - - +
912A GLY* 1.3 65.0 - - - +
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Residues in contact with GLY 912 (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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908A GLU* 3.1 10.4 + - - -
909A ARG 2.6 27.0 - - - +
910A GLU 3.5 2.9 - - - +
911A ARG* 1.3 83.1 - - - +
913A GLY* 1.3 58.5 + - - -
924A ARG* 3.3 15.5 - - - -
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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