Contacts of the strand formed by residues 896 - 906 (chain C) in PDB entry 5Z58
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 896 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ASN* 5.5 7.6 - - - +
331A TRP* 4.1 16.4 - + - -
332A TYR 6.0 0.2 - - - -
333A HIS* 5.7 6.3 - - - -
336A ASN* 5.2 4.7 - - - +
137C HIS* 5.8 4.5 - + - -
138C LEU* 3.3 33.2 - - + -
139C HIS* 6.3 0.7 - + - -
236C MET* 6.5 0.4 - - + -
835C GLU 3.6 1.9 - - - +
836C VAL* 3.3 4.7 - - - -
837C GLN* 3.0 43.3 + - + +
884C GLU* 3.6 22.4 - - - -
887C LEU* 4.9 0.7 - - - -
888C ARG* 4.1 26.9 - - - +
894C GLN 3.9 2.0 + - - +
895C ALA* 1.3 77.7 - - - +
897C SER* 1.3 66.5 + - - +
898C LEU* 3.8 30.1 - - + -
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Residues in contact with SER 897 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834C VAL* 3.4 10.9 - - - +
835C GLU 3.6 3.6 - - - -
836C VAL* 4.0 3.1 - - - -
883C PHE* 3.2 25.7 - - - -
884C GLU* 3.9 28.9 - - - +
887C LEU* 3.8 24.4 - - - +
888C ARG* 5.2 0.6 - - - +
896C PHE* 1.3 84.3 - - - +
898C LEU* 1.3 76.3 + - - +
899C SER* 4.4 2.9 + - - -
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Residues in contact with LEU 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C HIS* 4.3 24.2 - - + +
138C LEU* 4.8 11.2 - - + -
207C GLY 5.3 2.5 - - - +
208C HIS* 3.5 37.7 - - + +
209C VAL* 4.3 15.9 - - + +
237C LEU* 3.9 25.1 - - + +
238C ASN* 5.5 2.7 - - + -
833C PHE 3.8 0.6 - - - +
834C VAL* 3.2 4.7 - - - -
835C GLU* 3.0 36.7 + - + +
884C GLU* 5.6 0.9 - - - +
896C PHE* 3.8 23.3 + - + -
897C SER* 1.3 83.5 + - - +
899C SER* 1.3 63.6 + - - +
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Residues in contact with SER 899 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C VAL* 3.5 7.1 - - - +
210C ASN* 3.5 20.4 - - - +
237C LEU* 4.6 0.2 - - - +
832C TYR* 3.1 34.2 - - - +
833C PHE 3.3 5.4 - - - -
834C VAL* 3.8 12.4 - - - +
875C ILE* 4.9 1.4 - - - +
880C SER* 5.3 3.5 - - - -
883C PHE* 5.6 4.2 - - - -
897C SER* 4.7 5.2 - - - -
898C LEU* 1.3 80.4 - - - +
900C VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C VAL* 3.7 20.4 - - + +
210C ASN* 5.2 1.1 - - - +
237C LEU* 4.1 26.2 - - + -
241C ARG* 3.5 38.8 - - - +
584C THR* 4.0 13.2 - - + -
832C TYR* 3.3 7.0 - - - -
833C PHE* 2.8 42.8 + - + +
899C SER* 1.3 79.0 + - - +
901C PHE* 1.3 71.9 + - - +
902C HIS* 3.8 1.3 - - + +
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Residues in contact with PHE 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ARG* 4.3 10.2 + - - -
584C THR* 5.5 3.7 - - - +
585C THR* 3.9 43.7 - - - +
587C VAL* 3.9 19.5 - - + -
632C THR 5.6 0.6 + - - +
830C PRO* 3.5 26.2 - - + -
831C TYR 3.4 10.5 - - - -
832C TYR* 3.4 18.8 - + + -
900C VAL* 1.3 88.3 - - + +
902C HIS* 1.3 64.9 + - - +
903C HIS 3.6 24.0 - - - -
904C TRP* 3.4 34.8 - + - -
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Residues in contact with HIS 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ARG* 5.5 8.1 - - - +
831C TYR 3.0 6.9 + - - +
832C TYR 4.4 0.7 - - - -
833C PHE* 3.6 40.8 - + + +
874C PHE* 3.4 24.8 - + - -
900C VAL* 3.8 2.0 - - + +
901C PHE* 1.3 86.5 - - - +
903C HIS* 1.3 77.5 + + + +
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Residues in contact with HIS 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694C LYS* 4.1 26.4 + - - -
830C PRO 3.6 0.2 - - - -
831C TYR* 2.7 54.0 + + + +
874C PHE* 4.5 12.1 - + + -
901C PHE* 3.6 9.6 - - - -
902C HIS* 1.3 103.2 + + + +
904C TRP* 1.3 73.5 + - - +
905C GLN* 2.9 31.0 + - + +
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Residues in contact with TRP 904 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585C THR* 5.0 15.0 + - + +
587C VAL* 5.3 3.1 - - + -
661C THR* 4.0 20.4 - - - -
662C PHE 4.6 0.2 - - - -
663C CYS* 3.2 35.0 - - - -
694C LYS* 5.5 2.9 - - - -
785C ARG* 3.6 38.3 - - - +
828C MET* 3.8 37.0 - - + +
829C GLU 3.7 5.4 - - - -
830C PRO* 3.6 39.9 - - + -
901C PHE* 3.4 26.1 - + - -
903C HIS* 1.3 89.2 + - - +
905C GLN* 1.3 65.9 + - - +
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Residues in contact with GLN 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828C MET* 3.6 9.2 - - - +
829C GLU* 2.9 33.7 + - - +
831C TYR* 3.6 36.6 + - + -
903C HIS* 2.9 24.8 + - + +
904C TRP* 1.3 79.6 - - - +
906C ILE* 1.3 72.8 + - + +
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Residues in contact with ILE 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665C THR* 4.4 7.4 - - + -
667C VAL* 4.3 19.3 - - + -
826C ARG* 4.0 20.2 - - + -
827C LEU 3.3 10.3 - - - +
828C MET* 3.4 23.1 - - + -
831C TYR* 5.1 3.6 + - - -
905C GLN* 1.3 86.2 + - + +
907C VAL* 1.3 76.0 + - - +
908C PRO* 3.5 7.5 - - + +
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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