Contacts of the strand formed by residues 775 - 780 (chain A) in PDB entry 6RUT
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 775 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A ASP* 5.0 0.4 - - - +
717A SER* 3.3 32.8 + - - +
733A MET* 4.1 18.8 - - - +
734A GLY 4.4 3.9 + - - +
773A THR 4.0 0.2 + - - -
774A GLN* 1.3 72.1 + - - +
776A LEU* 1.3 71.5 + - - +
791A ALA* 3.3 2.7 - - - -
792A LYS* 2.9 48.0 + - + +
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Residues in contact with LEU 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A LYS* 4.1 20.4 + - + +
713A ILE* 3.4 32.5 - - + -
715A ASP* 3.8 24.2 + - + +
735A PHE* 3.5 33.0 - - + -
774A GLN 3.9 3.0 + - - -
775A THR* 1.3 79.7 - - - +
777A THR* 1.4 59.0 + - - +
778A GLY* 3.7 21.8 - - - +
779A VAL* 3.8 9.4 - - + -
789A VAL* 3.8 19.3 - - + -
790A ILE 3.6 17.7 - - - +
791A ALA* 4.1 3.6 - - - -
792A LYS* 5.1 1.8 + - - -
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Residues in contact with THR 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.8 22.5 - - + +
31A LYS* 3.9 19.2 + - - +
32A GLU* 4.1 18.4 - - - +
699A LYS* 2.8 22.4 + - - +
776A LEU* 1.4 72.1 - - - +
778A GLY* 1.3 55.2 + - - +
790A ILE* 2.8 36.3 + - + +
792A LYS* 2.9 42.8 + - - +
797A ASN* 5.1 0.7 - - - +
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Residues in contact with GLY 778 (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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30A VAL* 4.6 11.4 - - - -
699A LYS* 4.5 3.1 - - - -
713A ILE* 6.2 0.7 - - - -
776A LEU* 3.7 8.6 - - - +
777A THR* 1.3 80.5 - - - +
779A VAL* 1.4 66.3 + - - +
790A ILE* 3.0 35.9 + - - +
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Residues in contact with VAL 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 5.7 0.2 - - - +
702A THR* 5.9 2.8 - - - +
711A SER* 6.4 0.7 - - - -
713A ILE* 4.5 27.0 - - + +
737A VAL* 4.8 10.1 - - + -
769A ILE* 4.9 9.9 - - + -
776A LEU* 3.8 19.7 - - + -
778A GLY* 1.4 76.7 - - - +
780A LEU* 1.3 71.5 + - - +
781A PRO* 3.7 9.7 - - + +
787A SER* 4.6 11.2 - - - +
788A ALA 3.4 11.2 - - - +
789A VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.7 28.0 - - + -
29A LEU 5.3 0.7 - - - +
30A VAL* 3.6 30.7 - - + -
40A TYR* 3.9 27.8 - - + -
44A ALA* 3.9 17.7 - - + -
779A VAL* 1.3 76.3 - - - +
781A PRO* 1.4 64.5 - - + +
782A LEU* 2.9 29.3 + - + -
787A SER* 3.4 2.8 + - - -
788A ALA* 2.8 42.8 + - + +
790A ILE* 3.8 15.9 - - + -
799A ILE* 6.1 0.2 - - + -
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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