Contacts of the helix formed by residues 895 - 900 (chain O) in PDB entry 6IY3
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 GLU 895 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824O PRO* 3.7 31.0 - - + +
827O THR* 5.7 2.6 - - - +
873O PHE* 4.0 11.9 - - + -
894O ASP* 1.3 91.2 - - - +
896O GLY* 1.3 65.1 + - - +
897O HIS* 2.3 43.7 + - + +
898O ARG* 3.4 14.1 + - + +
899O MET* 4.0 4.7 + - - +
922O LEU 3.2 9.1 + - - -
923O THR* 5.4 0.9 - - - +
1167O GLY 5.6 1.4 - - - +
1168O LEU* 4.0 22.5 - - - +
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Residues in contact with GLY 896 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894O ASP 3.7 0.4 - - - -
895O GLU* 1.3 75.2 - - - +
897O HIS* 1.3 57.1 + - - +
898O ARG 3.1 1.3 - - - -
899O MET* 2.9 19.4 + - - +
900O LYS* 3.0 13.7 + - - +
921O ILE* 3.7 32.0 - - - +
922O LEU 4.0 7.1 + - - -
923O THR* 4.1 13.3 - - - -
935O TRP* 4.9 4.4 + - - -
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Residues in contact with HIS 897 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J C 3.3 12.6 + - - +
895O GLU* 2.3 39.6 + - + -
896O GLY* 1.3 75.8 - - - +
898O ARG* 1.3 58.8 + - + +
900O LYS* 3.3 34.0 + - + +
923O THR* 4.8 3.7 + - - -
925O THR* 4.3 23.8 + - + +
928O GLN* 5.3 6.1 - - - +
1168O LEU* 5.0 2.4 - - + +
1188O HIS* 6.1 4.0 - + + +
1192O GLN* 4.1 22.3 + - - -
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Residues in contact with ARG 898 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J C 3.9 10.3 + - - -
95J C 3.3 47.8 + - - +
96J C 3.4 13.7 + - - -
873O PHE* 3.5 48.5 - - + +
874O GLU* 5.4 6.5 - - - +
895O GLU* 3.4 12.7 + - + +
896O GLY 3.1 0.4 - - - -
897O HIS* 1.3 80.1 - - + +
899O MET* 1.3 60.3 + - - +
900O LYS 3.1 6.0 + - - -
901O ASN* 4.1 4.0 + - - +
904O SER* 4.7 10.6 + - - -
906O LEU* 3.4 39.9 - - - +
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Residues in contact with MET 899 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893O ILE* 4.6 10.5 - - + -
895O GLU 4.0 2.6 + - - +
896O GLY* 2.9 13.5 + - - +
898O ARG* 1.3 74.5 - - - +
900O LYS* 1.3 55.8 + - - +
901O ASN 3.0 20.9 + - - +
904O SER* 6.2 0.7 - - - -
906O LEU* 3.7 24.7 - - - -
907O SER* 3.7 31.9 - - - -
910O LEU* 3.9 9.0 - - + -
921O ILE* 3.7 27.6 - - + -
935O TRP* 4.2 13.0 - - + +
936O ALA* 5.2 4.3 - - + -
940O PHE* 3.6 47.8 - - + -
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Residues in contact with LYS 900 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J C 3.9 16.8 - - - +
97J C 2.7 43.4 + - - -
896O GLY 3.0 10.0 + - - +
897O HIS* 3.3 38.0 + - + +
898O ARG 3.1 0.4 - - - -
899O MET* 1.3 73.4 - - - +
901O ASN* 1.3 58.3 + - + +
928O GLN* 4.2 24.5 + - + +
930O ASN* 4.1 16.0 + - + +
935O TRP* 3.3 46.8 - - + +
1186O ASN* 5.3 0.4 - - - -
1188O HIS* 6.4 0.2 - - - +
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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