Contacts of the strand formed by residues 859 - 865 (chain D) in PDB entry 5ZOJ
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 LYS 859 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A ASN* 4.5 2.9 - - + -
790D ASN* 3.4 42.0 + - - +
791D MET 5.8 0.2 - - - -
792D PHE* 4.3 7.4 + - - +
793D ASP* 3.3 39.8 + - - +
855D TRP* 3.4 8.2 - - - -
856D PHE 2.9 32.7 + - - +
857D ASP* 3.8 16.0 + - + +
858D GLY* 1.3 82.4 - - - +
860D LEU* 1.3 62.3 + - - +
861D VAL* 3.7 1.7 + - - +
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Residues in contact with LEU 860 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A TYR* 5.1 11.1 + - + +
368A TRP* 3.7 31.0 - - + -
374A CYS* 4.1 7.0 - - - -
381A ASN 4.6 2.0 + - - +
382A LEU* 3.6 26.5 - - + -
769D ALA* 3.8 16.4 - - + -
770D PHE* 5.5 0.2 - - + -
789D ARG* 5.7 0.2 - - - -
790D ASN* 3.0 27.1 + - - +
853D GLY* 3.8 11.7 - - - +
854D SER 3.7 9.4 - - - +
855D TRP* 3.5 35.9 - - + -
859D LYS* 1.3 72.0 - - - +
861D VAL* 1.3 69.3 + - - +
862D THR* 3.9 8.3 + - + +
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Residues in contact with VAL 861 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765D TRP* 4.4 5.8 - - + -
788D ILE* 3.5 31.2 - - + -
789D ARG 3.7 5.2 - - - +
790D ASN 3.8 15.7 - - - +
791D MET* 3.7 23.1 - - - -
851D LEU* 3.6 17.5 - - + +
853D GLY* 2.8 35.5 + - - -
854D SER 2.8 21.3 + - - +
856D PHE* 4.0 15.5 - - + -
859D LYS 4.1 1.8 - - - +
860D LEU* 1.3 74.0 - - - +
862D THR* 1.3 60.0 + - - +
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Residues in contact with THR 862 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A TYR* 4.1 23.3 - - + -
368A TRP* 4.0 24.0 - - + +
787D LYS 3.9 0.3 - - - +
788D ILE* 3.7 0.7 - - - -
789D ARG* 3.2 51.4 + - - +
852D HIS* 3.6 18.8 - - + -
853D GLY* 5.0 1.1 - - - +
860D LEU* 3.9 12.0 + - + +
861D VAL* 1.3 77.7 - - - +
863D VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 863 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778D PRO* 5.7 1.2 - - - +
786D LEU* 4.0 22.9 - - + -
787D LYS 3.2 9.9 - - - +
788D ILE* 3.7 20.6 - - + -
848D PHE* 3.5 42.1 - - + -
851D LEU* 3.9 11.7 - - + +
852D HIS* 3.1 37.2 + - + +
861D VAL* 4.6 0.2 - - + -
862D THR* 1.3 81.9 - - - +
864D LYS* 1.3 69.9 + - - +
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Residues in contact with LYS 864 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D LEU* 3.6 2.4 - - - -
787D LYS* 2.6 55.9 + - + +
863D VAL* 1.3 77.1 - - - +
865D TYR* 1.3 76.1 + - - +
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Residues in contact with TYR 865 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778D PRO* 4.2 25.8 - - + -
780D ASN 4.8 0.4 - - - -
781D SER* 3.2 41.1 + - - -
782D LEU* 4.0 15.7 - - + -
783D THR* 3.3 36.8 - - - +
785D CYS 3.6 2.7 - - - +
786D LEU* 3.5 21.5 - - + +
844D ALA 4.3 2.5 - - - -
845D GLY* 3.7 4.3 - - - -
848D PHE* 3.5 46.5 - + - +
864D LYS* 1.3 98.6 - - - +
866D LEU* 1.3 60.8 + - - +
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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