Contacts of the helix formed by residues 892 - 902 (chain A) in PDB entry 1T65
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 892 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702A SER 5.6 0.4 - - - +
705A ASN* 3.8 33.2 - - + +
706A GLU* 3.8 24.5 - - + +
709A GLU* 3.3 27.6 - - + +
890A ASP* 3.9 3.4 - - + +
891A PHE* 1.3 87.1 - - + +
893A GLU* 1.3 67.0 + - - +
894A MET 3.5 0.4 - - - -
895A MET* 3.3 8.5 + - + -
896A ALA* 3.0 20.5 + - - +
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Residues in contact with GLU 893 (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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709A GLU* 3.8 4.8 + - - +
892A PRO* 1.3 73.2 - - - +
894A MET* 1.3 66.4 + - + +
896A ALA* 3.4 4.9 + - - +
897A GLU* 3.1 26.1 + - + +
920B HIS* 2.7 43.6 + - - +
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Residues in contact with MET 894 (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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709A GLU* 3.1 48.3 + - + +
712A LEU* 3.7 32.1 - - + -
713A VAL* 4.1 16.8 - - + +
893A GLU* 1.3 79.4 - - + +
895A MET* 1.3 64.4 + - - +
897A GLU* 3.3 8.4 + - - +
898A ILE* 3.0 30.8 + - + +
922B ILE 5.0 4.3 - - - +
923B LEU* 4.3 33.9 - - + +
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Residues in contact with MET 895 (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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705A ASN* 3.8 26.2 - - - +
708A GLY* 4.0 17.7 - - - +
709A GLU* 3.0 23.6 + - + +
712A LEU* 5.4 8.3 - - - -
741A TRP* 4.1 25.6 - - + -
891A PHE* 4.6 4.7 - - + -
892A PRO* 3.3 16.1 + - + +
894A MET* 1.3 74.7 - - - +
896A ALA* 1.3 64.1 + - - +
898A ILE* 3.4 5.7 + - - +
899A ILE* 3.0 40.8 + - + +
931A DHT 3.7 44.9 - - + -
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Residues in contact with ALA 896 (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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881A LEU* 3.9 18.2 - - + +
891A PHE* 4.2 20.6 - - + +
892A PRO 3.0 17.8 + - - +
893A GLU* 3.7 6.1 - - - +
895A MET* 1.3 76.2 - - - +
897A GLU* 1.3 60.1 + - - +
899A ILE* 4.9 0.2 - - - -
900A SER* 2.9 30.2 + - - -
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Residues in contact with GLU 897 (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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738A GLN* 4.8 0.3 - - - +
893A GLU* 3.1 20.1 + - - +
894A MET* 3.6 8.5 - - - +
896A ALA* 1.3 77.8 - - - +
898A ILE* 1.3 60.7 + - + +
900A SER* 3.3 6.6 + - - -
901A VAL* 3.0 43.8 + - + +
902A GLN* 6.3 0.2 - - - +
920B HIS* 2.9 39.9 + - + -
922B ILE* 2.8 49.2 - - - +
923B LEU* 4.4 4.0 + - - +
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Residues in contact with ILE 898 (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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712A LEU* 3.8 34.8 - - + -
738A GLN* 4.0 34.8 - - + +
741A TRP* 3.2 42.4 - - + +
894A MET* 3.0 16.8 + - + +
895A MET* 4.0 6.1 - - - +
897A GLU* 1.3 79.3 - - + +
899A ILE* 1.3 59.0 + - - +
902A GLN* 2.9 34.3 + - + -
903A VAL* 3.0 12.8 + - + -
923B LEU* 4.5 13.5 - - + -
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Residues in contact with ILE 899 (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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741A TRP* 4.4 11.4 - - + -
877A THR* 3.3 35.7 - - + +
878A PHE* 3.9 30.2 - - - -
881A LEU* 3.8 18.6 - - + -
891A PHE* 3.8 19.5 - - + -
895A MET* 3.0 36.6 + - + +
898A ILE* 1.3 77.7 - - + +
900A SER* 1.3 57.7 + - - +
903A VAL* 3.5 19.3 - - + +
904A PRO* 3.3 19.2 - - - +
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Residues in contact with SER 900 (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* 5.7 2.2 - - - -
881A LEU* 4.0 14.1 - - - -
896A ALA 2.9 22.0 + - - -
897A GLU* 3.3 7.3 + - - -
899A ILE* 1.3 77.6 - - - +
901A VAL* 1.3 68.5 + - - +
904A PRO* 3.6 15.6 - - - +
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Residues in contact with VAL 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 GLU* 3.0 28.0 + - + +
900A SER* 1.3 90.3 - - - +
902A GLN* 1.3 80.4 + - - +
904A PRO* 3.8 5.7 - - - +
905A LYS* 2.6 38.0 + - - +
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Residues in contact with GLN 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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734A MET* 5.3 3.2 - - - +
738A GLN* 3.5 51.4 + - + +
739A TYR* 3.4 42.5 + - + -
897A GLU* 6.3 0.2 - - - +
898A ILE* 2.9 26.9 + - + +
901A VAL* 1.3 96.3 - - - +
903A VAL* 1.3 65.9 + - - +
904A PRO* 3.3 1.8 - - - -
905A LYS* 2.9 30.0 + - - +
906A ILE* 3.6 2.9 + - - +
922B ILE* 5.4 3.8 - - - +
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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