Contacts of the strand formed by residues 871 - 875 (chain D) in PDB entry 1ZYR
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 871 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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867D ARG* 3.8 6.8 - - - +
868D TYR* 3.0 25.2 + - - +
869D MET 2.7 14.7 + - - +
870D GLY* 1.3 77.8 - - - +
872D ARG* 1.3 64.6 + - - +
873D LEU* 3.2 35.0 + - + +
897D TRP* 3.8 25.6 - - - -
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Residues in contact with ARG 872 (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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74B ASP* 5.1 7.3 - - - +
76B VAL* 4.1 9.1 + - - +
77B GLU* 3.0 54.0 + - - +
80B LEU* 5.2 7.4 - - + +
842D VAL* 5.9 6.5 - - + +
865D THR* 4.7 14.6 - - + -
866D VAL 3.7 7.4 - - - +
867D ARG* 4.8 14.8 - - + +
871D LYS* 1.3 74.6 - - - +
873D LEU* 1.3 65.1 + - - +
874D GLU* 3.8 7.6 + - - +
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Residues in contact with LEU 873 (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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865D THR* 3.5 3.1 - - - +
866D VAL* 3.0 37.4 + - + +
868D TYR* 3.5 37.9 - - + -
871D LYS* 3.2 40.5 + - + +
872D ARG* 1.3 75.2 - - - +
874D GLU* 1.3 61.5 + - - +
875D THR* 3.8 14.6 + - + +
880D ILE* 5.9 4.5 - - + -
897D TRP* 3.9 19.1 - - + -
902D LEU* 4.2 12.3 - - + -
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Residues in contact with GLU 874 (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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833D GLU* 4.1 6.3 - - - +
834D THR* 4.1 12.6 - - - +
838D ARG* 2.8 44.0 + - - -
864D VAL 3.6 6.1 - - - -
865D THR* 4.1 15.3 + - + +
872D ARG 3.8 6.5 + - - +
873D LEU* 1.3 74.3 - - - +
875D THR* 1.3 69.3 + - - +
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Residues in contact with THR 875 (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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795D VAL* 6.0 1.3 - - - -
862D ASP 4.3 0.2 - - - -
863D VAL* 4.9 4.7 - - - -
864D VAL* 2.5 40.5 + - - +
865D THR* 4.8 0.2 - - - +
866D VAL* 5.3 6.5 + - - +
873D LEU* 3.8 21.4 + - + +
874D GLU* 1.3 83.6 - - - +
876D SER* 1.3 67.5 + - - +
879D ARG* 3.6 17.3 - - + +
880D ILE* 5.5 5.5 - - - +
902D LEU* 3.5 30.8 - - + +
903D ASP* 4.6 7.4 - - - +
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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