Contacts of the strand formed by residues 824 - 832 (chain A) in PDB entry 5M9O
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 824 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A PHE* 3.6 6.7 - - - -
687A VAL* 3.1 25.7 + - - +
819A ARG 5.9 0.4 - - - +
820A ASP 4.1 8.6 + - - +
821A ILE* 2.6 32.0 + - - +
822A GLN 3.5 11.2 - - - +
823A ASN* 1.3 85.7 - - - +
825A GLN* 1.3 64.7 + - - +
826A CYS* 3.6 13.0 + - - -
844A PHE* 5.5 3.0 - - + -
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Residues in contact with GLN 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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684A PRO* 3.8 21.0 - - - +
685A VAL 3.3 12.1 - - - +
686A PHE* 3.9 10.0 - - + -
701A VAL* 3.9 18.1 - - + +
824A THR* 1.3 76.7 + - - +
826A CYS* 1.3 68.6 + - - +
827A LEU* 5.3 2.4 - - - +
844A PHE* 4.6 0.5 - - - -
845A ALA* 3.1 35.8 + - + +
111B 2MR 3.6 19.8 + - - +
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Residues in contact with CYS 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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684A PRO* 3.5 4.2 - - - +
685A VAL* 2.8 44.4 + - + +
687A VAL* 3.9 14.8 - - + -
821A ILE* 3.9 21.5 - - - -
824A THR* 3.6 22.4 + - - -
825A GLN* 1.3 76.0 - - - +
827A LEU* 1.3 64.3 - - - +
842A LEU* 4.4 15.3 - - + -
843A GLN 3.2 15.7 - - - +
844A PHE* 4.6 7.2 - - - -
845A ALA* 4.1 2.2 - - - +
851A VAL* 4.8 1.1 - - - -
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Residues in contact with LEU 827 (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 TYR* 3.6 27.9 - - + -
683A LYS 3.4 3.1 - - - -
684A PRO* 4.0 25.8 - - + -
825A GLN* 5.3 2.0 - - - +
826A CYS* 1.3 79.8 - - - +
828A LEU* 1.3 60.6 + - - +
842A LEU* 3.2 6.4 - - - -
843A GLN* 2.7 61.7 + - + +
845A ALA* 4.4 16.4 - - + +
848A LYS* 4.6 23.1 - - + -
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Residues in contact with LEU 828 (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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681A SER 3.9 1.4 - - - +
682A TYR* 3.4 5.0 - - - -
683A LYS* 2.8 52.2 + - + +
685A VAL* 4.0 11.0 - - + -
696A PHE* 4.5 0.2 - - + -
698A VAL* 4.2 13.7 - - + -
796A TYR* 3.7 37.2 - - + -
827A LEU* 1.3 75.0 - - - +
829A ASN* 1.3 63.9 + - - +
830A VAL* 4.0 26.9 - - + +
840A VAL* 4.0 15.7 - - + -
841A THR 3.4 3.4 - - - -
842A LEU* 3.7 22.9 - - + -
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Residues in contact with ASN 829 (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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681A SER 3.4 28.6 + - - +
682A TYR* 3.5 37.1 - - + -
828A LEU* 1.3 73.6 - - - +
830A VAL* 1.3 72.2 + - - +
831A GLU* 2.9 30.7 + - - +
840A VAL* 3.2 6.1 - - - -
841A THR* 2.9 34.2 + - - +
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Residues in contact with VAL 830 (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 LYS* 6.0 0.9 - - - +
796A TYR* 4.2 14.8 - - + +
828A LEU* 4.0 18.5 - - + +
829A ASN* 1.3 84.1 + - - +
831A GLU* 1.3 62.4 + - - +
832A HIS* 4.1 13.0 - - - +
833A LEU* 4.7 7.6 - - + -
838A PRO* 4.2 19.7 - - + -
839A HIS 4.2 1.1 - - - +
840A VAL* 4.0 10.8 - - + -
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Residues in contact with GLU 831 (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 TYR* 4.1 2.3 + - - -
799A ALA* 3.7 26.2 - - + -
800A PHE* 3.9 16.6 - - + -
829A ASN* 2.9 24.4 + - - +
830A VAL* 1.3 76.2 - - - +
832A HIS* 1.3 64.6 + - + +
839A HIS 2.9 13.4 + - - +
841A THR* 2.7 40.5 + - + +
871A PHE* 3.5 33.6 - - + -
874A VAL* 5.7 1.0 - - - +
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Residues in contact with HIS 832 (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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799A ALA* 4.3 10.6 - - + +
800A PHE* 4.6 9.3 + + - -
830A VAL* 3.9 3.2 - - - +
831A GLU* 1.3 89.3 - - + +
833A LEU* 1.3 86.4 + - - +
834A SER* 4.9 2.0 - - - -
838A PRO* 3.7 3.6 - - - +
839A HIS* 2.8 68.1 + + + +
866A ARG* 3.2 49.7 + - - +
871A PHE* 4.4 5.2 - + + -
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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