Contacts of the strand formed by residues 821 - 826 (chain A) in PDB entry 3KSS
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 THR 821 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684A LYS* 4.4 8.3 - - + +
685A VAL 3.5 12.1 - - - -
686A SER* 3.1 30.1 - - - +
693A ILE* 4.1 2.2 - - - +
814A LYS* 3.5 18.4 + - - +
815A THR* 4.0 0.4 - - - +
816A GLU* 3.2 33.1 + - + +
819A ARG* 3.7 8.0 + - + +
820A PRO* 1.3 81.5 - - - +
822A SER* 1.3 55.6 + - - +
823A TRP* 2.7 33.3 + - - -
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Residues in contact with SER 822 (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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683A ILE 3.3 4.3 - - - +
684A LYS* 3.5 0.3 - - - -
685A VAL* 3.1 44.5 + - - +
693A ILE* 3.5 18.8 + - - +
694A ASP* 5.4 3.1 - - - -
697A ALA* 4.2 11.4 - - - +
715A ALA 5.0 10.8 - - - -
716A GLU* 6.3 0.9 - - - -
718A LEU* 6.2 5.2 - - - -
814A LYS* 6.5 0.7 - - - +
821A THR* 1.3 70.7 - - - +
823A TRP* 1.3 64.8 + - - +
824A ILE* 3.9 3.2 + - - +
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Residues in contact with TRP 823 (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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83A ARG* 3.2 50.3 - - + -
85A PHE* 5.2 8.5 - + - -
675A THR* 4.7 3.8 - - - -
676A GLY* 4.4 14.1 - - - -
677A ILE* 4.3 12.6 - - + -
682A GLY* 6.1 1.1 - - - -
683A ILE 3.0 10.1 - - - +
684A LYS* 4.3 19.1 - - + -
714A LEU 3.8 4.5 - - - +
715A ALA 4.5 5.3 + - - +
814A LYS* 4.9 29.4 + - + +
815A THR 4.8 5.8 - - - -
816A GLU* 3.5 18.1 - - + +
821A THR* 2.7 40.0 + - - -
822A SER* 1.3 74.9 - - - +
824A ILE* 1.3 61.7 + - - +
825A TYR* 2.9 46.5 - - + -
859A SER* 6.0 0.2 - - - -
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Residues in contact with ILE 824 (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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682A GLY* 3.0 23.9 - - - -
683A ILE* 3.1 22.5 + - + +
685A VAL* 5.7 3.6 - - + +
697A ALA* 4.1 24.5 - - + +
700A ILE* 3.4 49.8 - - + -
701A GLU* 5.6 0.7 - - - -
713A ALA* 4.1 21.1 - - + -
714A LEU 3.4 22.7 - - - +
715A ALA* 4.1 8.5 - - + +
822A SER 4.4 6.3 - - - +
823A TRP* 1.3 73.6 - - - +
825A TYR* 1.3 62.0 + - - +
826A ILE* 3.6 5.6 + - + +
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Residues in contact with TYR 825 (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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676A GLY 4.2 4.8 + - - -
677A ILE* 2.3 44.5 - - + +
678A LYS 5.2 0.2 - - - -
679A SER* 3.2 30.3 - - - +
681A ILE 3.9 4.0 - - - -
682A GLY* 4.3 0.9 - - - -
712A SER 2.9 22.3 - - - +
713A ALA* 3.4 1.1 - - - -
714A LEU* 3.3 38.2 + - + +
814A LYS* 3.7 21.9 + - - -
823A TRP* 2.9 37.7 - - + -
824A ILE* 1.3 73.4 - - - +
826A ILE* 1.3 61.1 + - - +
827A ASP* 4.1 0.9 + - - +
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Residues in contact with ILE 826 (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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679A SER* 5.1 0.7 - - - -
681A ILE* 2.8 84.5 + - + +
682A GLY* 3.3 6.3 - - - +
683A ILE* 4.7 13.9 - - + -
704A ALA* 3.5 33.4 - - + +
711A ALA* 4.2 15.7 - - + -
712A SER 4.5 0.4 - - - -
713A ALA* 3.9 16.6 - - + -
824A ILE* 4.2 9.6 - - + +
825A TYR* 1.3 72.3 - - - +
827A ASP* 1.3 59.3 + - - +
828A ALA 4.1 1.0 + - - -
840A LEU* 5.8 8.3 - - + -
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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