Contacts of the helix formed by residues 643 - 652 (chain A) in PDB entry 3BK0
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 ASP 643 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641A GLY 4.6 0.7 - - - +
642A GLY* 1.3 75.7 - - - -
644A PHE* 1.3 57.9 + - - +
645A LEU* 2.9 18.5 + - - +
646A THR* 2.7 46.0 + - - -
647A PHE* 3.0 25.7 + - - +
687A ARG* 3.4 28.4 - - - +
689A CYS 3.2 7.2 - - - +
690A LEU* 3.9 7.2 - - + +
826A STU 3.9 23.0 + - + +
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Residues in contact with PHE 644 (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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642A GLY 3.8 0.6 + - - -
643A ASP* 1.3 70.4 - - - +
645A LEU* 1.3 61.1 + - - +
647A PHE* 4.0 5.6 - + - -
648A LEU* 2.8 54.3 + - + +
660A LEU* 5.5 0.4 - - + -
663A MET* 3.6 35.9 - - + -
664A VAL* 4.6 3.4 - - + -
686A ALA* 3.2 28.4 + - + +
689A CYS* 2.8 19.1 + - + +
691A VAL* 3.8 24.2 - - + -
697A LEU* 3.7 24.2 - - + -
749A LEU* 4.1 9.9 - - + -
753A THR* 3.4 31.6 - - + -
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Residues in contact with LEU 645 (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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4A EDO 4.4 13.5 - - - -
643A ASP* 2.9 10.3 + - - +
644A PHE* 1.3 79.0 - - - +
646A THR* 1.3 62.7 + - - +
648A LEU* 3.2 4.8 + - + +
649A ARG* 3.1 61.8 + - - +
686A ALA* 3.4 11.8 + - + -
687A ARG* 3.9 31.0 - - + +
726A TRP* 6.0 1.1 - - + -
752A GLU* 3.9 22.9 - - + +
757A GLY* 3.5 35.0 - - - +
758A ALA 4.9 1.1 - - - +
825A EDO 5.6 1.8 - - - +
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Residues in contact with THR 646 (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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643A ASP* 2.7 33.3 + - - -
645A LEU* 1.3 75.3 - - - +
647A PHE* 1.3 52.5 + - - +
649A ARG* 3.2 8.4 + - + +
650A THR* 2.8 52.7 + - - +
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Residues in contact with PHE 647 (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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641A GLY* 5.0 7.9 - - - +
643A ASP 3.0 14.1 + - - +
644A PHE* 3.5 26.9 - + - +
645A LEU 3.2 0.2 - - - -
646A THR* 1.3 76.5 - - - +
648A LEU* 1.3 58.1 + - - +
650A THR* 4.7 3.1 - - - -
651A GLU* 2.9 57.7 + - + +
655A LEU* 3.8 33.9 - - + -
663A MET* 3.6 24.9 - - + -
691A VAL* 4.1 18.2 - - + -
695A ASN* 3.5 36.3 - - - -
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Residues in contact with LEU 648 (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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644A PHE* 2.8 57.7 + - + +
645A LEU* 3.6 9.4 - - - +
647A PHE* 1.3 72.5 - - - +
649A ARG* 1.3 57.2 + - - +
652A GLY* 2.8 29.3 + - - -
655A LEU* 4.1 9.4 - - + -
660A LEU* 3.7 30.5 - - + -
686A ALA* 4.4 5.4 - - + -
752A GLU 3.6 21.5 - - - +
753A THR* 3.7 20.2 - - - +
756A LEU* 3.8 22.5 - - + +
757A GLY* 4.0 3.6 - - - +
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Residues in contact with ARG 649 (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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4A EDO 2.9 50.5 + - - -
645A LEU* 3.1 38.3 + - - +
646A THR* 3.7 7.4 - - + +
648A LEU* 1.3 77.6 - - - +
650A THR* 1.3 64.2 + - - +
652A GLY* 4.2 4.7 + - - -
756A LEU 3.9 11.2 - - - +
757A GLY* 2.7 30.4 + - - +
758A ALA 4.4 1.0 + - - -
759A SER* 3.2 14.6 + - - +
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Residues in contact with THR 650 (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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646A THR* 2.8 37.4 + - - +
647A PHE* 4.0 3.4 - - - -
649A ARG* 1.3 82.0 - - - +
651A GLU* 1.3 74.0 + - - +
652A GLY* 4.6 0.3 - - - -
654A ARG* 3.1 23.9 + - - +
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Residues in contact with GLU 651 (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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647A PHE* 2.9 48.4 + - + +
650A THR* 1.3 85.0 - - - +
652A GLY* 1.3 67.3 + - - +
653A ALA 3.0 0.9 + - - -
654A ARG* 2.8 57.8 + - + +
655A LEU* 4.0 21.3 - - + -
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Residues in contact with GLY 652 (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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648A LEU 2.8 22.4 + - - -
649A ARG 4.4 5.8 - - - -
650A THR 3.4 0.4 - - - -
651A GLU* 1.3 74.1 - - - +
653A ALA* 1.3 57.9 + - - -
655A LEU* 3.1 28.1 + - - +
756A LEU* 3.5 26.4 - - - +
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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