Contacts of the helix formed by residues 587 - 598 (chain Z) in PDB entry 5L4K
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 PHE 587 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545Z LYS* 2.8 43.3 + - + -
549Z GLU* 3.0 45.3 - - + -
550Z LEU* 5.2 1.6 - - + -
551Z LYS 5.0 1.1 - - - -
552Z ASP* 5.2 2.2 - - - -
555Z ALA* 3.6 25.9 - - + +
559Z PRO* 4.9 0.2 - - - +
585Z GLU* 3.2 10.5 - - + -
586Z PRO* 1.3 97.6 - - + +
588Z ARG* 1.3 57.4 + - - +
589Z SER 3.2 2.2 - - - -
590Z PHE* 3.6 19.9 - - - +
591Z ALA 4.1 0.2 + - - -
625Z LYS* 4.5 19.1 - - - -
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Residues in contact with ARG 588 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541Z THR* 4.4 0.6 + - - +
542Z ILE* 3.6 50.5 + - - +
545Z LYS* 3.9 22.8 - - - +
546Z SER* 4.2 6.1 - - - +
580Z LEU* 3.4 38.0 + - + +
581Z GLU* 5.1 0.2 - - - -
583Z VAL* 3.0 52.9 + - - +
584Z SER* 4.4 1.8 - - - -
585Z GLU* 3.4 34.9 + - + +
586Z PRO 3.4 1.2 - - - -
587Z PHE* 1.3 76.0 - - - +
589Z SER* 1.3 54.5 + - - +
590Z PHE 3.4 0.9 - - - -
591Z ALA* 4.1 2.5 - - - +
592Z ASN* 2.6 50.2 + - - +
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Residues in contact with SER 589 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585Z GLU 3.7 12.1 + - - -
586Z PRO* 4.0 11.0 + - - +
587Z PHE 3.2 0.6 - - - -
588Z ARG* 1.3 77.3 - - - +
590Z PHE* 1.3 63.1 + - - +
591Z ALA 3.2 1.0 + - - -
592Z ASN* 4.3 7.6 + - - +
593Z THR* 3.4 28.0 + - - +
626Z GLU* 3.0 34.0 + - - +
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Residues in contact with PHE 590 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555Z ALA* 3.9 16.6 - - + +
556Z ARG* 3.7 43.5 - - + -
559Z PRO* 4.2 11.9 - - + -
586Z PRO 4.6 2.3 + - - +
587Z PHE* 3.6 18.7 + - + +
588Z ARG 3.4 0.4 - - - -
589Z SER* 1.3 79.4 - - - +
591Z ALA* 1.3 56.5 + - - +
593Z THR* 3.2 15.9 + - - -
594Z LEU 3.8 2.3 + - - -
625Z LYS* 3.4 47.6 - - + -
626Z GLU* 4.2 9.5 + - + +
629Z LYS* 3.7 42.9 - - + +
786Z GLN* 5.1 11.4 - - + -
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Residues in contact with ALA 591 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545Z LYS* 4.2 14.1 - - - +
559Z PRO* 3.8 25.6 - - + +
562Z LEU* 5.1 7.4 - - + -
580Z LEU* 4.1 18.8 - - + -
587Z PHE 4.1 0.2 + - - -
588Z ARG* 3.8 4.5 + - - +
590Z PHE* 1.3 77.2 - - - +
592Z ASN* 1.3 67.4 + - - +
593Z THR 3.1 2.5 - - - -
594Z LEU* 2.9 19.4 + - + +
595Z VAL* 2.9 20.1 + - + +
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Residues in contact with ASN 592 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577Z LEU* 3.0 28.6 - - + +
580Z LEU* 3.4 14.2 - - - +
581Z GLU* 3.3 31.9 + - - +
584Z SER* 5.8 1.4 + - - -
588Z ARG* 2.6 35.0 + - - +
589Z SER* 4.3 7.7 + - - +
590Z PHE 3.7 0.2 - - - -
591Z ALA* 1.3 75.7 - - - +
593Z THR* 1.3 59.4 + - + +
596Z ASP* 2.8 30.7 + - - +
607Z LEU* 5.8 1.1 - - - -
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Residues in contact with THR 593 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589Z SER* 3.4 14.4 + - - +
590Z PHE* 3.2 13.9 + - - -
592Z ASN* 1.3 78.6 - - + +
594Z LEU* 1.3 65.4 + - - +
596Z ASP* 3.6 5.1 - - - -
597Z VAL* 2.9 22.3 + - - +
607Z LEU* 4.2 19.5 - - + -
611Z GLN* 5.3 4.9 - - + +
626Z GLU* 5.0 14.3 + - + +
629Z LYS* 3.7 9.5 - - - +
630Z ASP* 4.1 16.6 - - - +
633Z GLU* 3.0 25.0 + - - +
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Residues in contact with LEU 594 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559Z PRO* 3.0 33.0 - - + +
560Z LEU* 4.5 5.4 - - + +
563Z GLY* 3.8 21.1 - - - +
590Z PHE 4.1 3.4 - - - +
591Z ALA* 2.9 10.1 + - + +
593Z THR* 1.3 82.2 + - - +
595Z VAL* 1.3 65.2 + - + +
597Z VAL* 4.0 2.1 - - - +
598Z CYS* 3.3 24.2 + - + +
629Z LYS* 3.7 33.0 - - - +
632Z LYS* 4.3 12.3 - - - +
633Z GLU* 3.0 21.8 + - + +
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Residues in contact with VAL 595 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562Z LEU* 5.0 17.9 - - + -
563Z GLY* 5.5 5.6 - - - -
566Z HIS* 5.4 8.3 - - + +
573Z ILE* 3.0 41.8 - - + +
576Z ILE* 4.8 9.0 - - + -
577Z LEU* 4.2 24.0 - - + +
580Z LEU* 5.1 5.6 - - + -
591Z ALA* 2.9 17.2 + - + +
592Z ASN 3.8 2.0 - - - +
594Z LEU* 1.3 85.5 - - + +
596Z ASP* 1.3 57.0 + - - +
597Z VAL 3.5 0.2 - - - -
598Z CYS* 4.4 2.2 - - - +
599Z ALA* 3.3 22.5 + - - +
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Residues in contact with ASP 596 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577Z LEU* 3.4 21.6 - - + +
592Z ASN 2.8 22.3 + - - +
593Z THR* 3.6 7.6 - - - +
594Z LEU 3.2 0.6 - - - -
595Z VAL* 1.3 77.9 - - - +
597Z VAL* 1.3 61.9 - - + +
599Z ALA* 4.2 4.0 - - - -
600Z TYR* 3.3 36.1 + - - -
605Z ASN* 3.9 6.2 - - - +
606Z VAL* 5.7 1.9 + - - +
607Z LEU* 4.0 33.2 + - + +
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Residues in contact with VAL 597 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593Z THR* 2.9 11.0 + - - +
594Z LEU 3.3 2.9 + - - +
596Z ASP* 1.3 82.3 - - + +
598Z CYS* 1.3 60.9 + - - +
599Z ALA 3.2 1.6 - - - -
600Z TYR 3.5 1.2 - - - -
601Z ALA* 3.0 29.0 + - - +
605Z ASN* 4.1 19.0 - - - +
607Z LEU* 6.6 0.2 - - + -
608Z LYS* 3.8 16.6 - - + +
633Z GLU* 3.1 56.5 - - + +
636Z ASP* 4.4 13.9 - - + +
637Z LYS* 5.2 2.9 - - + +
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Residues in contact with CYS 598 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563Z GLY 5.9 0.7 - - - -
567Z LEU* 3.8 24.2 - - - -
569Z LYS 3.5 21.5 - - - -
570Z GLY* 3.2 27.4 - - - +
573Z ILE* 3.9 18.2 - - + -
594Z LEU* 3.3 16.5 + - + +
595Z VAL* 5.1 0.4 - - - -
597Z VAL* 1.3 79.0 - - - +
599Z ALA* 1.3 58.5 + - - +
600Z TYR 3.4 0.2 - - - -
601Z ALA* 3.6 13.1 - - - +
636Z ASP* 5.9 1.1 - - - -
640Z LYS* 6.1 1.1 - - - -
773Z LYS* 4.2 6.1 - - - -
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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