Contacts of the strand formed by residues 820 - 825 (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 ILE 820 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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810D ILE* 5.4 3.8 - - + +
811D LEU* 4.1 23.8 - - + -
814D CYS* 3.6 36.3 - - + +
817D ASN* 3.5 28.2 + - + +
818D ASP 3.7 0.8 - - - -
819D GLY* 1.3 74.9 - - - +
821D VAL* 1.3 55.8 + - - +
822D HIS 4.2 2.2 - - - +
823D ILE* 3.6 31.2 - - + -
836D VAL* 4.1 11.0 - - + -
837D LYS 3.7 5.6 - - - +
838D CYS* 3.9 13.7 - - - +
847D ALA* 4.6 2.7 - - + -
884D PRO* 3.2 2.8 - - - +
885D LEU* 2.5 39.7 + - + +
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Residues in contact with VAL 821 (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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819D GLY 3.3 14.1 - - - +
820D ILE* 1.3 72.7 - - - +
822D HIS* 1.3 66.4 + - - +
837D LYS* 3.0 28.9 + - + +
838D CYS 4.4 5.4 - - - +
839D LEU* 3.6 14.1 - - + -
881D SER* 3.4 36.4 - - - +
882D ASN* 3.6 14.4 - - - +
883D THR 3.3 32.7 - - - +
884D PRO* 3.8 2.7 - - + -
885D LEU* 3.8 16.3 - - - +
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Residues in contact with HIS 822 (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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820D ILE* 3.7 1.6 - - - +
821D VAL* 1.3 81.7 - - + +
823D ILE* 1.3 73.3 + - - +
824D ALA* 3.7 27.7 - - + +
837D LYS* 2.8 42.6 + - + +
871D TYR* 3.0 26.3 + - - +
875D PHE* 4.2 13.2 - - + -
877D GLN* 4.3 16.5 + - + +
878D ALA* 3.7 18.8 - - + +
881D SER* 4.0 20.2 - - - -
885D LEU* 4.4 6.0 - - + +
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Residues in contact with ILE 823 (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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807D GLN* 3.3 66.9 + - + +
810D ILE* 4.5 9.9 - - + -
811D LEU* 3.9 20.6 - - + -
820D ILE* 3.6 19.3 - - + -
822D HIS* 1.3 88.5 + - - +
824D ALA* 1.3 61.3 + - - +
834D VAL* 5.0 5.6 - - + -
835D TYR 3.3 7.2 - - - +
836D VAL* 3.5 24.9 - - + -
885D LEU* 4.7 9.9 - - + +
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Residues in contact with ALA 824 (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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807D GLN* 4.7 2.9 - - - +
822D HIS* 3.7 16.4 - - + +
823D ILE* 1.3 75.5 - - - +
825D VAL* 1.3 63.9 + - - +
834D VAL* 3.5 1.0 - - - +
835D TYR* 2.8 42.3 + - - +
871D TYR* 4.1 1.0 + - - +
875D PHE* 3.7 36.1 - - + -
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Residues in contact with VAL 825 (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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792D PHE* 4.1 6.1 - - + -
802D TRP* 4.5 10.3 - - + -
803D HIS* 3.5 30.7 - - + +
806D ILE* 3.8 15.7 - - + -
807D GLN* 4.2 21.2 - - + +
824D ALA* 1.3 76.0 - - - +
826D ASP* 1.3 58.4 + - - +
827D LYS* 3.3 19.6 + - + +
833D CYS 3.9 3.8 - - - -
834D VAL* 3.6 32.8 - - + -
875D PHE* 4.9 4.7 - - - -
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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