Contacts of the helix formed by residues 894 - 905 (chain E) in PDB entry 2X36
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 894 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770E TRP* 3.6 31.8 - - - -
893E GLY* 1.3 73.0 - - - -
895E ILE* 1.3 58.4 + - - +
896E LYS 3.4 2.7 - - - -
897E GLU* 3.4 17.4 + - - +
898E LYS* 2.9 33.8 + - - +
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Residues in contact with ILE 895 (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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880E THR* 4.8 2.7 - - + -
892E VAL* 3.8 22.2 - - + +
893E GLY* 4.5 1.3 - - - +
894E GLY* 1.3 74.3 - - - +
896E LYS* 1.3 57.8 + - - +
897E GLU* 4.0 0.2 + - - -
898E LYS* 4.0 4.8 - - + +
899E THR* 2.3 46.5 + - - +
912E LEU* 4.5 23.3 - - + -
913E PRO* 5.0 0.4 - - + -
916E ASN* 3.4 44.9 - - + +
919E ASP* 3.8 16.8 - - + +
920E PHE* 4.0 33.0 - - + +
923E LEU* 4.6 2.7 - - + -
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Residues in contact with LYS 896 (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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895E ILE* 1.3 77.9 - - - +
897E GLU* 1.3 70.4 + - - +
899E THR* 2.9 18.0 + - - -
900E ILE* 3.0 36.7 + - + +
923E LEU* 4.1 27.7 - - + +
927E ILE* 4.2 20.6 - - + +
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Residues in contact with GLU 897 (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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770E TRP* 3.9 22.1 + - + +
774E GLY* 3.8 23.3 - - - +
775E GLY* 3.5 29.3 - - - +
894E GLY* 3.4 21.4 - - - +
896E LYS* 1.3 85.6 - - + +
898E LYS* 1.4 57.5 + - + +
900E ILE* 3.6 11.2 + - + +
901E ALA 3.1 21.1 + - - -
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Residues in contact with LYS 898 (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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768E LEU* 3.6 33.7 - - + +
769E ALA 4.1 11.4 - - - -
770E TRP* 3.8 17.7 - - + +
852E ASP* 2.9 18.1 + - - -
855E SER* 2.7 29.5 + - - -
880E THR* 3.1 23.9 + - + +
892E VAL* 3.3 9.0 - - + +
893E GLY 3.1 22.4 + - - +
894E GLY 2.9 17.4 + - - +
895E ILE* 4.0 5.8 - - + +
897E GLU* 1.4 74.2 - - - +
899E THR* 1.3 68.0 + - - +
901E ALA* 3.3 7.7 + - - +
902E ALA* 3.0 20.1 + - - +
912E LEU* 5.7 3.8 - - + -
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Residues in contact with THR 899 (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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768E LEU* 6.0 0.4 - - - -
895E ILE* 2.3 39.5 + - - +
896E LYS 2.9 4.2 + - - -
898E LYS* 1.3 73.6 - - - +
900E ILE* 1.3 62.8 + - - +
902E ALA* 3.3 8.0 + - - +
903E LYS* 3.1 21.3 + - - +
910E ILE* 5.1 6.0 - - + +
912E LEU* 4.9 6.1 - - - +
920E PHE* 3.8 17.8 - - + -
923E LEU* 3.7 13.0 - - + +
927E ILE* 3.7 18.8 - - + -
931E LEU* 3.3 32.9 - - + +
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Residues in contact with ILE 900 (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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775E GLY* 6.3 0.4 - - - -
896E LYS* 3.0 45.8 + - + +
897E GLU* 3.7 9.4 - - + +
899E THR* 1.3 76.2 - - - +
901E ALA* 1.3 52.1 + - - +
903E LYS* 3.1 9.6 + - - +
904E ARG* 2.9 47.8 + - + +
927E ILE* 4.6 23.1 - - + -
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Residues in contact with ALA 901 (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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768E LEU* 4.2 1.6 - - + -
775E GLY 4.0 4.3 - - - +
776E SER* 3.8 37.9 - - - +
777E THR* 3.7 7.0 + - - +
897E GLU 3.1 15.1 + - - +
898E LYS* 3.4 11.2 - - - +
899E THR 3.2 0.2 - - - -
900E ILE* 1.3 73.5 - - - +
902E ALA* 1.3 68.2 + - - +
904E ARG* 3.1 9.8 + - - +
905E ALA* 3.0 24.6 + - - +
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Residues in contact with ALA 902 (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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768E LEU* 3.8 16.7 - - + +
777E THR* 4.5 0.2 - - - -
898E LYS 3.0 12.2 + - - +
899E THR* 3.4 11.2 - - - +
901E ALA* 1.3 75.9 - - - +
903E LYS* 1.3 62.0 + - - +
905E ALA 3.1 5.9 + - - -
907E VAL* 2.9 46.4 + - + +
910E ILE* 3.9 28.0 - - + -
931E LEU* 5.1 1.8 - - + -
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Residues in contact with LYS 903 (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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899E THR 3.1 7.0 + - - +
900E ILE* 3.4 11.2 - - - +
901E ALA 3.1 0.6 - - - -
902E ALA* 1.3 78.3 - - - +
904E ARG* 1.3 64.1 + - + +
905E ALA 3.2 0.5 + - - -
906E GLY* 3.3 10.0 + - - -
907E VAL 4.3 10.7 + - - +
908E THR* 6.2 2.4 - - - +
926E PHE 4.2 7.4 - - - -
927E ILE* 3.2 40.3 + - + +
929E GLU 3.3 17.2 + - - -
930E GLY 4.9 1.4 - - - -
931E LEU* 4.0 23.0 - - + +
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Residues in contact with ARG 904 (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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900E ILE* 2.9 30.9 + - + +
901E ALA* 3.1 8.9 + - - +
903E LYS* 1.3 77.2 - - - +
905E ALA* 1.4 59.2 + - - +
906E GLY 3.4 0.6 + - - -
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Residues in contact with ALA 905 (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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766E MET* 4.4 7.4 - - + +
777E THR* 3.9 22.4 - - + +
901E ALA 3.0 16.4 + - - +
902E ALA 3.1 4.9 + - - +
904E ARG* 1.4 78.1 - - - +
906E GLY* 1.3 57.0 + - - +
907E VAL* 3.6 10.0 + - + +
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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