Contacts of the helix formed by residues 605 - 616 (chain B) in PDB entry 5ZR1
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 605 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B MET* 4.3 1.1 - - - -
545B PRO* 4.6 17.6 - - + +
546B LYS 3.7 12.8 - - - -
547B ARG* 3.5 45.5 - - + +
604B TYR* 1.3 78.3 - - - +
606B TYR* 1.3 59.8 + - - +
607B ALA* 3.7 5.1 + - - +
608B GLU* 3.2 33.7 + - - +
609B LEU* 3.0 27.8 + - - +
20G T 5.1 0.9 - - - +
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Residues in contact with TYR 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B MET* 3.6 45.7 + - + +
536B MET* 3.7 39.6 - - + +
537B GLY* 4.3 11.4 - - - -
542B ASN 5.7 4.0 - - - +
543B THR* 4.8 18.6 - - + +
544B GLY 5.5 4.0 - - - +
545B PRO* 5.4 1.7 - - + +
546B LYS 3.8 8.2 + - - +
605B THR* 1.3 75.0 - - - +
607B ALA* 1.3 64.9 + - + +
609B LEU* 3.3 6.6 + - + +
610B GLU* 3.1 32.9 + - + +
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Residues in contact with ALA 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B PRO* 5.6 10.5 - - + +
605B THR* 3.4 4.8 + - - +
606B TYR* 1.3 81.3 - - + +
608B GLU* 1.3 63.2 + - + +
610B GLU* 3.5 16.5 - - - +
611B LYS* 3.2 24.6 + - - +
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Residues in contact with GLU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B ASP* 5.3 1.9 - - - +
505B SER* 2.6 35.5 + - - +
507B ALA* 3.5 26.7 - - + +
547B ARG* 4.5 6.6 + - - -
604B TYR* 4.1 5.4 - - + +
605B THR* 3.2 36.7 + - - +
607B ALA* 1.3 77.2 - - + +
609B LEU* 1.3 59.4 + - - +
610B GLU 3.5 0.2 - - - -
611B LYS* 4.1 8.7 - - - +
612B LEU* 3.3 28.6 + - - +
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Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B ILE* 3.7 51.6 - - + +
532B GLN* 4.5 9.4 - - + +
533B MET* 3.4 24.7 - - + +
536B MET* 3.9 27.1 - - - -
602B VAL* 3.8 10.3 - - + +
604B TYR* 3.8 29.6 - - + +
605B THR 3.0 12.0 + - - +
606B TYR* 3.6 6.1 - - - +
607B ALA 3.2 0.4 - - - -
608B GLU* 1.3 78.0 - - - +
610B GLU* 1.3 60.0 + - - +
612B LEU* 3.8 5.0 + - + +
613B LEU* 3.3 19.6 + - - +
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Residues in contact with GLU 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B MET* 3.7 22.0 - - + +
606B TYR* 3.1 28.3 + - + +
607B ALA* 3.5 20.5 - - - +
609B LEU* 1.3 76.2 - - - +
611B LYS* 1.3 67.0 + - - +
612B LEU 3.4 0.2 - - - -
613B LEU* 3.8 3.2 - - - +
614B LYS* 3.2 59.8 + - - +
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Residues in contact with LYS 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ARG* 5.4 9.2 - - - +
497B LYS* 5.9 5.1 - - - +
508B GLU* 4.9 14.7 + - - +
511B LYS* 5.9 6.1 - - - +
607B ALA 3.2 19.9 + - - +
608B GLU* 4.3 7.4 - - - +
610B GLU* 1.3 84.3 - - - +
612B LEU* 1.3 63.4 + - + +
614B LYS* 3.4 9.2 + - - +
615B THR* 3.2 47.9 + - + +
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Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B ALA* 3.8 23.6 - - + +
510B ALA* 4.2 16.8 - - + -
511B LYS* 4.5 12.3 - - + +
514B LEU* 4.1 10.3 - - + -
525B TYR* 3.9 19.1 - - + +
529B ILE* 4.8 7.4 - - + -
604B TYR* 4.4 15.5 - - + -
608B GLU 3.3 18.9 + - - +
609B LEU* 4.1 5.2 - - + +
610B GLU 3.4 0.2 - - - -
611B LYS* 1.3 80.4 - - + +
613B LEU* 1.3 64.9 + - - +
614B LYS 3.5 0.2 + - - -
615B THR* 4.1 8.0 - - + +
616B VAL* 3.8 17.6 + - + +
617B LEU* 3.7 26.6 + - + +
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Residues in contact with LEU 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B LYS* 3.7 39.0 - - + +
529B ILE* 3.9 13.5 - - + -
530B GLU* 3.8 26.2 - - + +
533B MET* 3.8 27.1 - - + -
609B LEU 3.3 17.8 + - - +
610B GLU* 3.8 7.0 - - + +
611B LYS 3.2 0.8 - - - -
612B LEU* 1.3 78.8 - - - +
614B LYS* 1.3 60.1 + - + +
617B LEU* 3.4 12.8 - - + +
618B ASN* 3.1 32.3 + - + +
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Residues in contact with LYS 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B GLU* 3.2 41.9 + - - +
611B LYS* 3.4 7.9 + - - +
612B LEU 3.3 0.4 - - - -
613B LEU* 1.3 85.9 - - + +
615B THR* 1.3 63.0 + - - +
616B VAL 3.5 0.2 - - - -
617B LEU 4.6 0.4 - - - -
618B ASN* 4.4 19.6 + - - +
619B THR* 5.0 3.6 + - - -
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Residues in contact with THR 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B LYS* 4.3 13.2 - - + +
611B LYS* 3.2 38.7 + - - +
612B LEU* 4.1 10.1 - - - -
614B LYS* 1.3 80.3 - - - +
616B VAL* 1.3 75.8 + - + +
619B THR* 5.3 5.9 - - - +
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Residues in contact with VAL 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B LYS* 3.7 39.3 - - + +
514B LEU* 3.7 39.9 - - + +
515B GLN* 4.5 12.8 - - + +
522B LYS* 4.8 13.7 + - + +
612B LEU* 3.8 6.8 + - + +
615B THR* 1.3 88.6 - - + +
617B LEU* 1.3 68.4 + - + +
618B ASN 3.7 1.1 - - - -
619B THR* 3.4 20.6 - - - +
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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