Contacts of the helix formed by residues 598 - 614 (chain B) in PDB entry 5M64
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 HIS 598 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B PRO 4.0 16.4 - - - -
582B SER* 4.2 14.1 + - - +
584B CYS* 3.4 30.9 - - - -
596B VAL 3.7 1.2 + - - -
597B SER* 1.3 72.4 + - - +
599B GLU* 1.3 71.9 + - - +
601B GLY* 3.2 1.7 + - - -
602B LYS* 3.0 19.6 + - - +
628B TYR* 3.1 24.2 + + - -
629B VAL 3.8 13.4 + - - -
631B PRO* 3.2 45.1 - - + +
638B PRO* 4.1 4.3 - - + +
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Residues in contact with GLU 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B SER* 2.7 19.3 + - - +
598B HIS* 1.3 78.9 + - - +
600B GLN* 1.3 70.5 + - - +
602B LYS* 3.1 7.7 + - - +
603B ILE* 3.1 36.2 + - + +
90N MET* 6.2 1.8 - - + -
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Residues in contact with GLN 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B GLY 5.2 8.7 - - - +
596B VAL* 3.8 17.0 - - + -
597B SER* 3.1 31.9 + - - +
599B GLU* 1.3 82.1 - - - +
601B GLY* 1.3 56.6 - - - +
603B ILE* 3.3 6.7 + - - +
604B ILE* 2.8 43.2 + - + +
90N MET* 3.2 54.7 - - - +
140N SER* 4.3 12.2 + - - -
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Residues in contact with GLY 601 (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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584B CYS* 4.2 17.9 - - - -
596B VAL* 4.5 3.0 - - - +
597B SER 3.1 12.7 + - - -
598B HIS 3.2 5.0 + - - -
600B GLN* 1.3 76.5 - - - +
602B LYS* 1.3 55.3 + - - +
604B ILE* 3.8 7.9 - - - +
605B ALA* 2.8 30.3 + - - +
628B TYR* 3.5 12.0 - - - -
640B LEU* 4.6 8.0 - - - +
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Residues in contact with LYS 602 (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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598B HIS 3.0 14.0 + - - +
599B GLU* 3.1 12.1 + - - +
601B GLY* 1.3 74.8 - - - +
603B ILE* 1.3 76.9 + - + +
605B ALA* 3.3 15.6 + - + +
606B ASP* 3.7 20.5 + - - +
628B TYR* 3.9 22.0 - - + +
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Residues in contact with ILE 603 (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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568B LEU* 5.4 3.6 - - + -
599B GLU* 3.1 34.4 + - + +
600B GLN* 4.0 7.6 - - - +
602B LYS* 1.3 89.8 - - + +
604B ILE* 1.3 56.6 + - + +
606B ASP* 3.2 5.5 + - - +
607B THR* 2.6 51.0 + - + +
90N MET* 5.5 8.7 - - + -
140N SER* 5.9 0.7 - - - +
142N THR* 4.2 30.5 - - + -
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Residues in contact with ILE 604 (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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565B LEU* 4.9 5.2 - - + -
568B LEU* 3.7 27.6 - - + -
569B GLY 5.7 1.6 - - - -
570B VAL* 3.7 30.7 - - + +
586B VAL* 5.7 3.4 - - + -
596B VAL* 4.9 4.3 - - + -
600B GLN* 2.8 33.9 + - + +
601B GLY* 4.0 4.3 - - - +
603B ILE* 1.3 76.9 - - + +
605B ALA* 1.3 63.5 + - - +
607B THR* 3.9 6.3 - - - -
608B LEU* 3.0 53.1 + - + +
640B LEU* 4.4 16.6 - - + -
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Residues in contact with ALA 605 (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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601B GLY 2.8 19.4 + - - +
602B LYS* 3.4 9.9 - - + +
603B ILE 3.2 0.4 - - - -
604B ILE* 1.3 76.6 - - - +
606B ASP* 1.3 62.5 + - - +
608B LEU* 5.3 0.2 - - - -
609B ARG* 3.2 24.3 + - - +
626B ILE* 5.0 6.4 - - - +
628B TYR* 3.7 34.5 - - + -
640B LEU* 4.7 8.5 - - - -
672B MET* 6.1 0.2 - - - +
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Residues in contact with ASP 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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602B LYS* 3.7 22.0 + - - +
603B ILE* 3.2 4.9 + - - +
605B ALA* 1.3 86.4 - - - +
607B THR* 1.3 63.8 + - - +
608B LEU 3.4 1.6 - - - -
609B ARG* 3.2 13.4 + - + +
610B TYR* 3.1 21.3 + - - +
655B TYR* 4.7 7.4 + - - +
672B MET* 5.6 2.4 - - - +
687B THR* 4.9 11.0 + - - +
145N ILE* 4.9 18.8 - - + +
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Residues in contact with THR 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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568B LEU* 3.8 25.4 - - + -
603B ILE* 2.6 44.2 + - - +
604B ILE* 3.9 7.9 - - - -
606B ASP* 1.3 72.2 - - - +
608B LEU* 1.3 62.6 + - - +
610B TYR* 3.2 5.3 + - - +
611B TRP* 3.0 52.6 + - + +
141N GLU 4.5 7.9 - - - +
143N ALA* 4.6 16.9 + - + -
145N ILE* 6.3 1.3 - - - -
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Residues in contact with LEU 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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564B ILE* 4.3 23.8 - - + -
565B LEU* 4.6 13.2 - - + -
568B LEU* 4.5 16.6 - - + -
604B ILE* 3.0 37.0 + - + +
605B ALA 5.3 0.2 - - - +
607B THR* 1.3 76.2 - - - +
609B ARG* 1.3 58.7 + - - +
611B TRP* 4.0 4.8 - - + +
612B LYS* 3.0 30.0 + - - +
620B LEU* 5.2 10.2 - - + +
624B LEU* 6.2 0.7 - - + -
626B ILE* 3.9 30.5 - - + +
640B LEU* 4.2 9.0 - - + -
642B LEU* 4.3 11.2 - - + -
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Residues in contact with ARG 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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605B ALA 3.2 24.6 + - - +
606B ASP* 3.4 13.0 - - - +
607B THR 3.1 0.8 - - - -
608B LEU* 1.3 76.7 - - - +
610B TYR* 1.3 64.5 + - - +
612B LYS* 3.3 9.4 + - - +
613B VAL* 3.0 31.7 + - + +
626B ILE* 3.2 52.6 + - + +
627B GLY* 4.9 2.4 - - - -
628B TYR 5.7 0.6 - - - +
655B TYR* 4.0 23.3 - - + +
662B ASP* 4.5 6.6 + - - -
663B ILE 5.1 1.2 + - - -
664B VAL* 4.2 12.3 - - - +
668B GLU* 3.3 15.8 - - - +
672B MET* 2.9 39.0 - - + +
687B THR* 5.6 1.1 - - + -
688B HIS* 4.3 16.4 + - + -
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Residues in contact with TYR 610 (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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606B ASP 3.1 9.5 + - - +
607B THR* 3.2 7.8 + - - +
609B ARG* 1.3 77.2 - - - +
611B TRP* 1.3 80.8 + + - +
613B VAL* 3.3 8.8 - - + +
614B GLU* 3.0 58.2 + - + +
616B LYS* 5.1 10.0 - - - -
655B TYR* 4.7 1.5 + + - -
658B LEU* 3.7 24.9 - - + +
143N ALA* 4.8 12.3 - - + +
144N LYS 5.0 5.6 - - - -
145N ILE* 3.8 22.9 - - + -
146N PRO* 3.5 35.2 - - + +
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Residues in contact with TRP 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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564B ILE* 6.5 1.1 - - + -
568B LEU* 5.3 7.3 - - + +
607B THR* 3.0 43.0 + - + +
608B LEU* 4.4 6.1 - - + +
610B TYR* 1.3 89.3 - + - +
612B LYS* 1.3 60.2 + - - +
614B GLU* 3.4 6.1 - - + +
616B LYS* 3.8 23.1 - - - -
617B THR* 3.0 51.7 + - + +
620B LEU* 3.4 18.4 - - + +
84N LYS* 5.7 10.8 - - + -
86N ASP* 4.1 19.5 - - - -
141N GLU* 5.7 4.4 + - + -
143N ALA* 3.4 23.5 - - + +
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Residues in contact with LYS 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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608B LEU 3.0 21.1 + - - +
609B ARG* 3.6 11.7 - - - +
610B TYR 3.1 0.2 - - - -
611B TRP* 1.3 80.0 - - - +
613B VAL* 1.3 63.3 + - + +
614B GLU 3.4 4.5 + - - +
617B THR* 4.8 1.6 + - - -
620B LEU* 4.2 13.7 - - + +
621B PRO 3.5 7.1 + - - +
622B ILE* 2.4 52.8 + - + +
624B LEU* 3.1 41.1 + - + +
626B ILE* 4.4 16.4 - - + -
662B ASP* 3.7 23.3 - - - +
663B ILE 4.2 12.3 - - - -
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Residues in contact with VAL 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B ARG* 3.0 15.2 + - + +
610B TYR* 3.3 20.9 - - + +
612B LYS* 1.3 73.5 - - + +
614B GLU* 1.3 62.9 + - - +
615B GLY* 3.6 1.2 + - - -
622B ILE* 5.7 3.8 - - - +
655B TYR* 4.2 35.0 - - + -
658B LEU* 4.7 16.4 - - + +
660B LYS* 3.3 36.9 - - + +
661B GLU 5.0 4.3 - - - +
662B ASP* 3.3 31.4 - - + +
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Residues in contact with GLU 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 TYR* 3.0 37.4 + - + +
611B TRP* 3.4 9.5 - - - +
612B LYS 3.7 3.7 - - - +
613B VAL* 1.3 77.9 - - - +
615B GLY* 1.3 64.5 + - - +
616B LYS* 3.3 42.6 + - + +
617B THR* 3.3 24.0 + - + -
622B ILE* 5.7 1.3 - - - +
658B LEU* 3.3 26.5 - - - +
660B LYS* 5.2 2.8 - - - +
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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
------------------------------------------------------------
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