Contacts of the helix formed by residues 602 - 616 (chain O) 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 THR 602 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600O GLU 3.8 9.6 - - - +
601O TRP* 1.3 74.5 - - - +
603O GLU* 1.3 71.3 + - - +
604O GLN* 3.8 11.9 + - - +
605O GLU* 3.0 31.8 + - - +
606O THR* 2.8 29.0 + - - -
78R ARG* 3.8 18.8 - - - +
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Residues in contact with GLU 603 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398I THR* 4.6 16.8 - - - +
399I LYS* 5.5 13.1 - - + -
402I ILE* 4.1 20.0 - - + +
601O TRP 5.2 2.5 - - - +
602O THR* 1.3 82.8 - - - +
604O GLN* 1.3 71.9 + - - +
605O GLU 3.2 1.1 - - - -
606O THR* 3.3 7.4 + - - +
607O LEU* 2.9 27.1 + - - +
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Residues in contact with GLN 604 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398I THR* 5.3 15.6 + - + +
602O THR* 3.8 12.4 + - - +
603O GLU* 1.3 84.7 + - - +
605O GLU* 1.3 61.4 + - - +
607O LEU* 3.7 10.4 - - + +
608O LEU* 2.9 37.1 + - + +
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Residues in contact with GLU 605 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601O TRP* 3.4 23.0 - - + -
602O THR* 3.0 39.9 + - - +
603O GLU 3.2 0.2 - - - -
604O GLN* 1.3 78.4 - - - +
606O THR* 1.3 55.9 + - - +
608O LEU* 3.3 11.0 + - + +
609O LEU 2.9 22.9 + - - -
627O VAL* 4.2 13.9 - - + +
629O SER* 2.9 24.6 + - - -
630O ARG* 2.3 45.4 + - - +
78R ARG* 3.7 7.2 + - - -
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Residues in contact with THR 606 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402I ILE* 4.7 14.8 - - + -
601O TRP* 3.8 10.1 - - - +
602O THR 2.8 19.0 + - - -
603O GLU* 3.3 8.5 + - - -
605O GLU* 1.3 73.9 - - - +
607O LEU* 1.3 61.0 + - - +
609O LEU* 3.2 4.6 + - + +
610O LEU* 2.9 44.1 + - + +
638O HIS* 3.5 30.6 + - + -
642O LEU* 4.7 10.5 - - + -
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Residues in contact with LEU 607 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398I THR* 4.4 14.1 - - + +
401I THR* 3.6 31.0 - - + +
402I ILE* 3.6 19.0 - - + +
405I LYS* 4.6 18.8 - - + -
603O GLU 2.9 15.9 + - - +
604O GLN* 3.7 10.8 - - + +
605O GLU 3.3 0.2 - - - -
606O THR* 1.3 76.5 - - - +
608O LEU* 1.3 60.1 + - + +
610O LEU* 3.8 3.4 - - - +
611O GLU* 2.9 33.0 + - + +
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Residues in contact with LEU 608 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604O GLN* 2.9 24.0 + - + +
605O GLU* 3.5 9.2 - - + +
607O LEU* 1.3 77.0 - - + +
609O LEU* 1.3 65.2 + - - +
611O GLU* 4.8 0.4 - - + -
612O ALA* 2.9 27.0 + - - +
626O HIS* 3.5 41.6 + - + +
627O VAL* 3.8 31.4 - - - +
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Residues in contact with LEU 609 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601O TRP* 3.6 16.2 - - + -
605O GLU 2.9 14.2 + - - +
606O THR* 3.4 8.7 - - + +
608O LEU* 1.3 77.4 - - - +
610O LEU* 1.3 59.1 + - + +
612O ALA* 3.4 1.2 + - - +
613O LEU* 2.9 45.3 + - + +
620O TRP* 4.9 0.7 - - + -
623O VAL* 3.8 19.5 - - + -
627O VAL* 3.7 9.1 - - + +
635O CYS* 3.9 34.3 - - + +
638O HIS* 3.4 29.8 - - + +
639O PHE* 4.3 11.2 - - + +
642O LEU* 5.4 4.3 - - + -
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Residues in contact with LEU 610 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402I ILE* 3.2 40.2 - - + +
405I LYS* 3.9 16.8 - - + -
406I ALA* 3.9 20.0 - - + +
409I LEU* 4.0 17.2 - - + +
606O THR* 2.9 29.3 + - + +
607O LEU* 3.9 4.0 - - - +
608O LEU 3.2 0.2 - - - -
609O LEU* 1.3 75.5 - - + +
611O GLU* 1.3 61.7 + - - +
613O LEU* 3.3 7.1 + - + +
614O GLU* 2.9 33.1 + - - +
639O PHE* 4.6 9.4 - - + -
642O LEU* 4.0 22.4 - - + -
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Residues in contact with GLU 611 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405I LYS* 2.5 37.6 + - - +
607O LEU* 2.9 23.0 + - + +
608O LEU* 4.1 2.7 - - + +
610O LEU* 1.3 76.1 - - - +
612O ALA* 1.3 62.2 + - - +
614O GLU* 3.1 12.7 + - - +
615O MET* 3.0 46.3 + - + +
626O HIS* 4.1 12.3 - - + -
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Residues in contact with ALA 612 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608O LEU 2.9 19.9 + - - +
609O LEU* 3.6 4.5 - - - +
611O GLU* 1.3 77.6 - - - +
613O LEU* 1.3 55.7 + - - +
615O MET* 3.8 8.3 - - - -
616O TYR* 2.7 39.9 + - + +
623O VAL* 3.9 24.7 - - + +
626O HIS* 3.5 28.8 + - + -
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Residues in contact with LEU 613 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409I LEU* 3.5 20.0 - - + +
412I PHE* 3.6 18.9 - - + -
609O LEU* 2.9 42.7 + - + +
610O LEU* 3.7 3.4 - - + +
611O GLU 3.3 0.2 - - - -
612O ALA* 1.3 73.6 - - - +
614O GLU* 1.3 67.4 + - - +
616O TYR 3.5 3.8 - - - +
617O LYS* 3.2 51.7 - - - +
620O TRP* 3.7 20.4 - - + -
623O VAL* 4.4 5.8 - - + -
639O PHE* 3.7 35.2 - - + -
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Residues in contact with GLU 614 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405I LYS* 2.3 63.8 + - + +
408I ARG* 4.4 14.1 - - + +
409I LEU* 4.0 23.1 - - + -
610O LEU 2.9 17.3 + - - +
611O GLU* 3.1 15.4 + - - +
613O LEU* 1.3 78.9 - - - +
615O MET* 1.3 62.9 + - - +
617O LYS* 4.6 3.6 + - - +
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Residues in contact with MET 615 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611O GLU* 3.0 52.7 + - + +
612O ALA* 3.5 4.9 - - - +
614O GLU* 1.3 81.0 - - - +
616O TYR* 1.3 108.7 + - + +
617O LYS* 3.4 4.3 + - - +
626O HIS* 4.1 17.3 - - - +
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Residues in contact with TYR 616 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612O ALA* 2.7 26.6 + - - +
613O LEU* 3.4 2.2 - - - +
615O MET* 1.3 106.2 - - + +
617O LYS* 1.3 68.4 + - - +
618O ASP 3.6 1.6 - - - -
619O ASP* 4.2 11.2 - - + +
622O LYS* 3.4 64.8 - - + -
623O VAL* 3.3 13.1 - - + +
626O HIS* 4.2 15.1 - + + -
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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