Contacts of the helix formed by residues 603 - 616 (chain N) in PDB entry 6LTJ
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 603 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602N THR* 1.3 80.2 + - - +
604N GLN* 1.3 67.3 + - - +
606N THR* 2.5 25.5 + - + +
607N LEU* 2.9 22.3 + - + +
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Residues in contact with GLN 604 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602N THR* 2.8 33.3 + - + +
603N GLU* 1.3 85.4 - - - +
605N GLU* 1.3 60.2 + - - +
607N LEU* 3.3 23.0 - - + +
608N LEU* 2.9 32.1 + - - +
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Residues in contact with GLU 605 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602N THR* 3.1 42.8 + - + +
604N GLN* 1.3 77.8 - - - +
606N THR* 1.3 70.7 + - - +
608N LEU* 3.5 8.9 + - - +
609N LEU* 2.9 28.8 + - - +
627N VAL* 3.2 36.8 - - - +
629N SER* 3.8 21.8 - - - -
630N ARG* 3.8 27.3 + - - +
638N HIS* 3.6 15.2 + - - -
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Residues in contact with THR 606 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602N THR 3.4 5.8 - - - +
603N GLU* 2.5 34.9 + - + +
605N GLU* 1.3 95.7 - - - +
607N LEU* 1.3 58.5 + - - +
608N LEU 3.1 0.2 - - - -
609N LEU* 3.2 11.2 - - + +
610N LEU* 2.9 38.2 + - - +
638N HIS* 3.3 27.8 - - + +
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Residues in contact with LEU 607 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603N GLU* 2.9 22.1 + - + +
604N GLN* 3.3 33.2 - - + +
606N THR* 1.3 77.1 + - - +
608N LEU* 1.3 61.1 + - + +
610N LEU* 3.6 17.8 - - + +
611N GLU* 2.9 45.7 + - - +
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Residues in contact with LEU 608 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604N GLN 2.9 19.7 + - - +
605N GLU* 3.6 4.9 - - - +
607N LEU* 1.3 78.5 - - + +
609N LEU* 1.3 65.3 + - - +
611N GLU* 3.1 24.5 - - + +
612N ALA* 2.9 27.3 + - - +
626N HIS* 3.1 63.0 - - + +
627N VAL 3.8 11.2 - - - +
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Residues in contact with LEU 609 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605N GLU* 2.9 18.1 + - - +
606N THR* 3.2 17.9 - - + +
608N LEU* 1.3 76.9 - - - +
610N LEU* 1.3 61.3 + - + +
612N ALA* 3.3 4.0 + - - +
613N LEU* 2.9 42.7 + - + +
620N TRP* 6.3 0.2 - - + -
623N VAL* 3.4 27.5 - - + +
627N VAL* 3.6 23.8 - - + +
635N CYS* 4.0 24.2 - - + +
638N HIS* 4.2 32.3 - - + +
639N PHE* 4.5 9.2 - - + +
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Residues in contact with LEU 610 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606N THR* 2.9 30.6 + - - +
607N LEU* 3.6 18.8 - - + +
609N LEU* 1.3 76.4 - - + +
611N GLU* 1.3 62.1 + - + +
613N LEU* 3.6 12.5 - - + +
614N GLU* 2.8 29.9 + - + +
639N PHE* 5.3 9.2 - - + -
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Residues in contact with GLU 611 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607N LEU* 2.9 33.0 + - - +
608N LEU* 3.1 30.6 - - + +
610N LEU* 1.3 78.3 - - + +
612N ALA* 1.3 70.6 + - - +
613N LEU 3.0 1.3 - - - -
614N GLU* 3.1 18.4 + - - +
615N MET* 3.0 39.4 + - + +
626N HIS* 5.5 1.4 - - - -
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Residues in contact with ALA 612 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608N LEU 2.9 17.8 + - - +
609N LEU 3.7 3.4 - - - +
611N GLU* 1.3 76.5 - - - +
613N LEU* 1.3 55.1 + - - +
615N MET* 3.7 11.4 - - + -
616N TYR* 2.7 39.3 + - + +
623N VAL* 3.9 17.2 - - - +
626N HIS* 3.4 36.8 - - + -
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Residues in contact with LEU 613 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609N LEU* 2.9 38.0 + - + +
610N LEU* 3.6 6.7 - - - +
611N GLU 3.0 0.2 - - - -
612N ALA* 1.3 76.6 - - - +
614N GLU* 1.3 65.4 + - - +
615N MET 3.1 1.8 - - - -
616N TYR 4.1 1.1 - - - +
617N LYS* 3.0 45.8 + - + +
620N TRP* 4.4 11.7 - - + -
623N VAL* 3.7 22.0 - - + -
639N PHE* 3.4 43.1 - - + -
686N PRO* 4.4 20.6 - - + -
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Residues in contact with GLU 614 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610N LEU* 2.8 19.3 + - + +
611N GLU* 3.4 19.5 - - - +
613N LEU* 1.3 76.7 - - - +
615N MET* 1.3 63.9 + - + +
617N LYS* 4.0 15.6 + - - +
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Residues in contact with MET 615 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611N GLU* 3.0 24.0 + - + +
612N ALA* 3.7 20.0 - - - +
614N GLU* 1.3 80.4 - - + +
616N TYR* 1.3 102.2 + - + +
617N LYS* 3.8 2.2 + - - -
618N ASP* 4.5 1.9 - - - +
626N HIS* 3.9 19.7 - - + +
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Residues in contact with TYR 616 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612N ALA* 2.7 23.6 + - + +
613N LEU* 3.6 1.1 - - - -
615N MET* 1.3 126.1 - - + +
617N LYS* 1.3 63.7 + - - +
618N ASP* 3.1 11.9 - - - -
619N ASP* 3.2 37.0 - - - +
622N LYS* 3.6 42.0 + - + -
623N VAL* 3.8 6.7 - - + +
626N HIS* 4.8 3.8 - + - -
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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