Contacts of the strand formed by residues 779 - 784 (chain A) in PDB entry 5A7R
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 GLU 779 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A ALA* 4.1 3.6 - - - +
618A ALA* 2.8 24.5 + - - -
699A ARG* 2.7 43.9 + - - +
700A GLN 3.2 6.7 - - - +
701A SER* 3.5 24.0 + - - +
774A VAL 4.0 0.5 - - - +
775A LEU* 4.2 12.4 - - + +
776A ASP* 2.9 35.0 + - - +
777A HIS 3.5 1.0 + - - -
778A ASN* 1.3 89.0 - - - +
780A CYS* 1.3 65.2 + - - +
847A LYS* 2.9 27.1 + - - +
850A CYS* 4.0 3.8 - - - -
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Residues in contact with CYS 780 (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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699A ARG* 3.6 9.0 - - - +
700A GLN* 3.0 36.7 + - - +
775A LEU* 4.0 9.9 - - - -
779A GLU* 1.3 75.8 - - - +
781A LEU* 1.3 59.8 + - - +
782A ILE* 3.8 24.2 - - - -
822A VAL* 3.8 8.1 - - + -
823A ALA 3.5 15.9 - - - +
824A ILE* 3.8 15.5 - - + -
850A CYS* 3.7 32.1 - - + -
851A GLY* 3.9 0.4 - - - -
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Residues in contact with LEU 781 (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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615A LEU* 4.2 10.3 - - + -
697A PHE* 4.6 5.2 - - + -
698A THR 3.4 28.5 - - - +
699A ARG* 4.2 4.7 - - + +
743A VAL* 4.4 17.3 - - + -
759A PHE* 6.0 0.9 - - + -
768A SER* 3.7 30.7 - - - +
772A THR* 4.0 24.0 - - + +
775A LEU* 4.3 5.8 - - + +
780A CYS* 1.3 74.8 - - - +
782A ILE* 1.3 62.9 + - - +
783A ILE* 3.8 24.6 - - + +
822A VAL* 3.4 3.3 - - - +
823A ALA* 2.9 42.7 + - + -
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Residues in contact with ILE 782 (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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696A THR* 3.7 1.2 - - - +
697A PHE* 3.6 1.9 - - - -
698A THR* 2.8 54.1 + - + +
700A GLN* 4.3 20.0 - - + +
780A CYS* 3.8 21.8 - - - -
781A LEU* 1.3 77.2 - - - +
783A ILE* 1.3 61.9 + - - +
784A THR* 4.2 6.5 - - - +
820A GLU* 3.5 34.5 - - + +
821A ILE 3.5 5.6 - - - +
822A VAL* 4.0 4.3 - - + -
854A ARG* 3.7 34.5 - - - +
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Residues in contact with ILE 783 (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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695A VAL* 3.8 3.8 - - + -
696A THR 3.3 9.9 - - - +
697A PHE* 3.7 26.7 - - + -
759A PHE* 5.8 4.5 - - + -
765A LEU* 4.0 22.2 - - + -
768A SER* 5.2 1.6 - - - -
781A LEU* 3.8 36.3 - - + +
782A ILE* 1.3 77.0 - - - +
784A THR* 1.3 64.4 + - - +
785A GLY 4.2 0.2 + - - -
786A THR* 3.6 29.1 + - + +
819A THR 3.7 2.1 - - - +
820A GLU* 3.6 1.3 - - - -
821A ILE* 2.8 55.7 + - + +
823A ALA* 4.7 8.3 - - + +
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Residues in contact with THR 784 (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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695A VAL* 3.4 5.5 - - - +
696A THR* 2.9 39.8 + - - +
782A ILE* 4.2 7.0 + - - +
783A ILE* 1.3 73.7 + - - +
785A GLY* 1.3 61.8 + - - +
786A THR 3.7 0.9 - - - -
812A ASP* 4.7 2.5 - - - +
816A ARG* 3.8 41.3 + - + +
817A ARG 4.2 7.9 - - - +
818A CYS* 5.7 1.3 - - - -
819A THR 3.4 11.7 - - - +
820A GLU* 3.8 19.7 - - + +
1986A PPI 5.1 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