Contacts of the strand formed by residues 894 - 899 (chain A) in PDB entry 4Z96
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 PHE 894 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892A ARG* 3.6 44.2 - - - +
893A SER* 1.3 74.2 + - - +
895A LYS* 1.3 66.1 + - - +
896A CYS* 3.6 15.8 + - + -
909A THR* 3.5 3.4 - - - +
910A LEU 2.9 40.5 + - - +
912A PRO* 4.0 15.5 - - + -
921A LEU* 3.6 34.5 - - + -
959A LEU* 4.6 5.2 - - + -
962A LEU* 4.1 21.1 - - + -
970A PHE* 4.2 33.4 - + + -
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Residues in contact with LYS 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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893A SER* 4.1 8.4 + - - +
894A PHE* 1.3 79.5 - - - +
896A CYS* 1.3 62.4 + - - +
907A GLU* 4.9 15.1 + - - +
908A ILE 3.8 5.8 - - - +
909A THR* 3.6 25.8 - - + +
970A PHE* 5.2 5.5 + - - +
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Residues in contact with CYS 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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894A PHE* 4.0 18.8 - - + -
895A LYS* 1.3 77.0 - - - +
897A ILE* 1.3 69.5 + - - +
907A GLU* 3.8 7.3 - - - +
908A ILE* 3.0 41.7 + - - +
910A LEU* 4.0 14.6 - - - -
921A LEU* 5.1 0.2 - - - -
969A THR* 6.2 0.2 - - - -
970A PHE* 3.3 28.5 - - + +
971A ARG* 5.0 0.7 - - - -
972A ILE* 3.9 27.6 - - + -
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Residues in contact with ILE 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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896A CYS* 1.3 81.6 - - - +
898A TRP* 1.3 64.4 + - - +
905A GLU* 3.8 39.3 - - + +
906A GLU 3.3 7.4 - - - +
907A GLU* 3.2 41.3 - - + +
908A ILE* 4.6 2.0 - - - -
969A THR* 3.9 26.0 - - + -
970A PHE 3.1 5.8 + - - +
971A ARG* 3.4 17.7 - - + +
972A ILE* 2.9 29.0 + - - +
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Residues in contact with TRP 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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896A CYS 4.1 0.6 + - - -
897A ILE* 1.3 72.8 - - - +
899A LEU* 1.3 62.4 + - - +
900A ASN* 3.5 33.5 + - - +
901A SER 5.0 0.2 - - - -
904A ARG 3.6 2.8 - - - +
905A GLU* 3.7 0.5 - - - -
906A GLU* 2.7 63.2 + - + +
908A ILE* 4.1 19.2 - - + +
925A CYS* 3.8 18.6 - - - -
929A VAL* 3.6 31.9 - - + +
930A GLU 4.3 7.9 + - - -
931A LEU* 3.5 31.2 - - + -
939A LEU* 4.2 5.2 - - + -
972A ILE* 3.1 36.3 - - + -
973A GLU* 3.8 13.9 - - - -
974A GLU* 4.1 14.6 - - - -
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Residues in contact with LEU 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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897A ILE 3.8 1.2 + - - -
898A TRP* 1.3 77.5 - - - +
900A ASN* 1.3 74.0 + - - +
903A PHE* 3.7 28.3 - - + +
904A ARG 3.3 34.1 - - - +
905A GLU* 3.9 15.7 - - + -
971A ARG* 3.7 36.8 - - - +
972A ILE 2.8 15.2 + - - +
973A GLU* 3.7 33.0 - - + +
974A GLU 4.2 1.6 + - - -
1005A ILE* 4.6 5.2 - - + -
1007A PHE* 6.0 0.4 - - + -
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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