Contacts of the helix formed by residues 890 - 899 (chain A) in PDB entry 6A5T
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 SER 890 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889A GLY* 1.3 75.2 - - - +
891A ASP* 1.3 67.0 + - - +
892A LYS* 3.0 13.4 + - - +
893A ALA* 3.1 14.0 + - - +
894A PHE* 3.0 19.1 + - - +
941A ARG* 4.1 0.2 - - - -
1298A SER* 3.0 31.9 - - - -
1300A GLU* 3.4 26.9 + - - +
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Residues in contact with ASP 891 (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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890A SER 1.3 66.1 - - - -
892A LYS* 1.3 63.0 + - + +
894A PHE* 3.2 9.3 - - + +
895A HIS* 2.9 25.5 + - - +
941A ARG* 3.3 16.6 + - - -
945A ARG* 4.1 3.6 + - - -
1297A GLU 3.7 9.2 - - - +
1298A SER* 2.1 41.4 + - - +
1299A GLY* 3.5 10.0 + - - -
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Residues in contact with LYS 892 (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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890A SER* 3.0 9.3 + - - +
891A ASP* 1.3 76.5 - - + +
893A ALA* 1.3 67.3 + - - +
895A HIS* 2.8 24.1 + - + +
896A LYS* 2.8 15.6 + - - +
1298A SER* 4.1 4.4 + - - -
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Residues in contact with ALA 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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889A GLY* 5.2 4.0 - - - -
890A SER* 3.1 19.8 + - - +
892A LYS* 1.3 78.2 - - - +
894A PHE* 1.3 65.7 + - - +
896A LYS* 3.5 11.0 - - - +
897A ARG* 2.9 23.7 + - - +
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Residues in contact with PHE 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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886A THR* 4.3 17.5 - - + -
888A PRO 5.5 1.6 - - - -
889A GLY 5.2 0.8 - - - +
890A SER 3.0 8.2 + - - +
891A ASP* 3.2 9.9 - - + +
892A LYS 2.9 0.4 + - - -
893A ALA* 1.3 78.7 - - - +
895A HIS* 1.3 60.8 + - + +
896A LYS 2.8 6.6 + - - -
898A TYR* 3.1 53.2 + + - +
934A TYR* 3.2 36.1 - + - -
937A LEU* 4.2 28.7 - - + -
938A VAL* 4.9 4.5 - - + -
941A ARG* 3.0 51.1 - - + +
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Residues in contact with HIS 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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891A ASP 2.9 11.8 + - - +
892A LYS* 2.8 16.5 + - + +
894A PHE* 1.3 81.4 - - + +
896A LYS* 1.3 56.7 + - - +
899A TYR* 3.0 75.6 + + + +
907A ASN* 5.9 2.9 - - - -
934A TYR* 3.8 18.4 - + - +
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Residues in contact with LYS 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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892A LYS* 2.8 13.1 + - - +
893A ALA* 3.5 15.3 - - - +
894A PHE 2.8 2.2 + - - -
895A HIS* 1.3 79.4 - - - +
897A ARG* 1.3 63.1 + - - +
898A TYR 3.3 0.2 - - - -
1031A ARG* 2.8 32.4 + - - +
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Residues in contact with ARG 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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885A ASP* 4.0 17.5 + - - +
893A ALA 2.9 14.2 + - - +
894A PHE 4.2 1.3 - - - +
896A LYS* 1.3 78.7 - - - +
898A TYR* 1.3 77.4 + - + +
1031A ARG* 2.8 28.0 + - - +
1032A ARG* 2.8 66.8 - - + +
1035A GLU* 4.1 3.5 - - - +
1036A GLU* 5.8 2.9 - - - +
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Residues in contact with TYR 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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885A ASP* 3.5 20.7 - - - +
886A THR* 3.5 14.3 + - + +
894A PHE* 3.1 51.8 + + + +
897A ARG* 1.3 101.1 + - + +
899A TYR* 1.3 65.3 + - - +
900A VAL* 3.2 11.1 + - - +
934A TYR* 4.5 15.0 - - + -
937A LEU* 3.5 31.4 - - + +
1026A ALA 3.3 26.0 + - - -
1029A ALA* 4.0 15.4 - - + +
1031A ARG* 3.2 13.3 + - - +
1032A ARG* 4.0 13.0 - - + -
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Residues in contact with TYR 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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895A HIS* 3.0 60.2 + + + +
898A TYR* 1.3 74.4 - - - +
900A VAL* 1.3 85.6 + - - +
901A ASP* 4.5 12.3 - - + -
907A ASN* 4.7 11.3 - - + +
927A GLN* 4.2 14.8 + - - -
930A LEU 6.5 0.2 - - - -
931A ASN* 4.8 8.6 + - - -
934A TYR* 3.9 35.2 - + + -
1031A ARG* 3.2 20.6 + - - +
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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