Contacts of the strand formed by residues 778 - 782 (chain A) in PDB entry 3KTQ
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 ARG 778 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A THR* 3.9 24.7 - - + +
559A ARG* 3.9 11.9 - - - +
601A GLU* 4.4 9.7 + - - +
604A TRP* 3.4 42.1 - - + +
769A PHE* 6.1 1.8 - - - -
772A LEU* 4.3 5.1 - - - +
776A GLY 4.6 0.7 - - - +
777A ALA* 1.3 79.5 - - - +
779A MET* 1.3 59.8 + - - +
780A LEU* 4.1 9.9 - - + -
789A LEU* 3.0 10.0 - - - +
790A GLU* 2.7 73.5 + - - +
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Residues in contact with MET 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A VAL* 3.9 10.3 - - - -
443A HIS 5.0 0.3 - - - -
444A MET* 3.2 49.0 + - + +
447A THR* 4.7 3.8 + - - -
765A MET* 3.6 44.6 - - - +
768A LEU* 4.0 8.5 - - + -
769A PHE* 3.7 31.9 - - + +
772A LEU* 3.9 17.1 - - + +
778A ARG* 1.3 71.6 - - - +
780A LEU* 1.3 64.6 + - - +
787A LEU* 4.0 16.2 - - + -
788A VAL 4.9 0.7 - - - +
789A LEU* 3.3 20.4 - - + -
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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
----------------------------------------------------------
444A MET* 3.5 23.7 - - - +
447A THR* 3.5 21.8 - - + -
448A GLY* 3.2 25.6 - - - +
449A VAL* 4.0 18.4 - - + -
559A ARG* 3.9 7.2 - - - +
564A PHE* 3.7 7.6 - - - -
606A LEU* 3.9 20.6 - - + -
778A ARG* 4.1 4.3 - - + -
779A MET* 1.3 77.2 - - - +
781A LEU* 1.3 75.3 + - + +
788A VAL* 2.9 16.6 + - + +
789A LEU 4.2 3.8 - - - -
790A GLU* 3.6 37.0 - - + +
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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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444A MET* 3.7 7.3 - - - +
448A GLY 6.1 1.1 - - - -
449A VAL* 4.6 20.4 - - + -
562A THR* 5.1 0.9 - - - -
564A PHE* 3.8 17.3 - - + -
581A LEU* 3.6 36.3 - - + +
598A PHE* 5.0 0.9 - - + -
779A MET* 5.1 0.5 - - - +
780A LEU* 1.3 89.6 + - + +
782A GLN* 1.3 62.8 + - - +
783A VAL* 4.2 5.4 - - + -
787A LEU* 3.3 9.9 - - - +
788A VAL* 2.9 46.8 + - + +
827A TRP* 3.6 35.2 - - + -
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Residues in contact with GLN 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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444A MET* 3.7 14.5 - - + +
564A PHE* 3.8 11.0 - - + -
574A LEU* 3.7 27.3 + - + +
582A GLN* 3.0 36.6 - - - +
758A ALA* 5.3 1.2 + - - +
761A MET* 3.3 27.1 - - + +
762A LYS* 4.9 5.1 - - - +
765A MET* 3.5 27.1 - - + -
781A LEU* 1.3 75.0 - - - +
783A VAL* 1.3 63.7 + - - +
784A HIS* 3.0 30.4 + - - +
786A GLU 3.3 6.3 - - - +
787A LEU* 3.7 10.8 - - + -
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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