Contacts of the helix formed by residues 551 - 566 (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 LYS 551 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548Z THR* 4.3 21.8 + - - +
549Z GLU* 3.2 11.6 - - - +
550Z LEU* 1.3 87.0 - - + +
552Z ASP* 1.3 64.1 + - - +
553Z THR* 3.5 5.8 - - - +
554Z TYR* 4.0 34.9 - - + +
555Z ALA* 3.6 17.3 + - - +
587Z PHE* 5.0 0.2 - - - -
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Residues in contact with ASP 552 (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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550Z LEU 4.7 5.1 - - - +
551Z LYS* 1.3 75.4 - - - +
553Z THR* 1.3 65.6 + - + +
554Z TYR 3.3 0.7 - - - -
555Z ALA* 3.9 3.7 + - - +
556Z ARG* 3.1 48.9 + - - +
587Z PHE* 5.2 3.3 - - - -
625Z LYS* 2.9 32.5 + - - +
788Z MET* 6.5 1.1 - - + -
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Residues in contact with THR 553 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551Z LYS* 4.8 6.1 - - - +
552Z ASP* 1.3 77.0 - - + +
554Z TYR* 1.3 62.6 + - - +
556Z ARG* 3.5 10.3 + - - +
557Z TRP* 2.9 70.5 + - + -
788Z MET* 3.9 27.6 - - - -
793Z VAL* 5.1 6.1 - - + -
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Residues in contact with TYR 554 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505Z MET* 3.5 11.8 - - + +
508Z SER* 3.3 30.1 + - - -
515Z ALA* 3.6 11.0 - - + +
516Z GLY* 3.1 33.4 - - - -
544Z GLU* 3.8 19.8 - - + +
548Z THR 5.1 2.7 - - - -
549Z GLU* 3.5 21.5 - - - +
551Z LYS* 3.9 36.7 + - + +
552Z ASP 3.3 0.4 - - - -
553Z THR* 1.3 81.8 + - - +
555Z ALA* 1.3 58.1 + - - +
556Z ARG 3.1 0.5 + - - -
557Z TRP* 3.1 6.4 + - - -
558Z LEU* 3.0 58.7 + - + +
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Residues in contact with ALA 555 (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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545Z LYS* 4.9 1.2 + - - -
549Z GLU* 3.3 32.5 + - - +
551Z LYS 3.6 10.5 + - - +
552Z ASP* 4.5 4.7 - - - +
553Z THR 3.5 0.2 - - - -
554Z TYR* 1.3 77.8 - - - +
556Z ARG* 1.3 58.5 + - + +
559Z PRO* 2.9 26.6 - - - +
587Z PHE* 3.6 27.8 - - + +
590Z PHE* 3.9 9.4 - - + +
625Z LYS* 5.8 2.0 - - - +
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Residues in contact with ARG 556 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552Z ASP* 3.1 29.5 + - - +
553Z THR* 3.5 9.6 + - - +
554Z TYR 3.1 0.6 - - - -
555Z ALA* 1.3 79.3 - - + +
557Z TRP* 1.3 69.4 + - + +
559Z PRO* 3.7 2.6 - - - +
560Z LEU* 3.2 25.7 + - + +
590Z PHE* 3.7 32.3 - - + -
625Z LYS* 3.7 36.6 - - + +
670Z MET* 5.7 9.3 - - - +
673Z ARG* 5.2 3.6 - - - +
786Z GLN* 3.2 49.7 + - + +
787Z LEU 5.8 1.4 + - - -
788Z MET* 5.1 16.0 - - - +
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Residues in contact with TRP 557 (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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515Z ALA 5.6 0.2 - - - -
516Z GLY* 3.5 22.9 - - - +
517Z VAL* 3.3 44.6 - - + +
519Z ALA* 4.6 1.1 - - - -
520Z LEU* 3.8 34.9 + - + +
553Z THR* 2.9 57.1 + - + +
554Z TYR* 3.1 2.2 + - - +
556Z ARG* 1.3 81.9 - - + +
558Z LEU* 1.3 64.3 + - - +
560Z LEU* 3.1 11.8 + - + +
561Z GLY* 3.0 21.7 + - - -
786Z GLN* 5.1 14.7 + - + +
793Z VAL* 4.8 22.9 - - + -
796Z LEU* 5.6 7.2 - - + -
797Z LEU* 6.2 3.6 - - + +
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Residues in contact with LEU 558 (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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505Z MET* 3.6 21.1 - - + -
516Z GLY 3.5 21.3 - - - +
519Z ALA* 3.8 18.2 - - + +
537Z THR* 5.2 2.3 - - - +
540Z GLN* 4.0 12.3 - - - +
541Z THR* 3.6 29.0 - - - +
544Z GLU* 5.0 4.7 - - + -
545Z LYS 5.8 0.9 - - - +
549Z GLU* 4.7 7.6 - - - +
554Z TYR* 3.0 50.6 + - + +
557Z TRP* 1.3 76.6 - - - +
559Z PRO* 1.3 71.7 - - + +
560Z LEU 3.1 0.5 + - - -
561Z GLY* 3.3 1.7 + - - -
562Z LEU* 2.9 22.2 + - - +
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Residues in contact with PRO 559 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541Z THR* 4.9 1.8 - - - +
545Z LYS* 3.6 26.5 - - - +
555Z ALA* 2.9 31.0 - - - +
556Z ARG 3.7 2.0 - - - +
558Z LEU* 1.3 93.0 - - + +
560Z LEU* 1.3 56.0 + - - +
562Z LEU* 3.5 11.7 - - + +
563Z GLY 2.9 20.6 + - - -
587Z PHE 4.9 0.2 - - - +
590Z PHE* 4.2 16.8 - - + -
591Z ALA* 3.8 22.7 - - + -
594Z LEU* 3.0 17.2 - - + +
629Z LYS* 5.8 0.7 - - - +
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Residues in contact with LEU 560 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520Z LEU* 3.4 29.2 - - + -
556Z ARG* 3.2 20.4 + - + +
557Z TRP* 3.1 13.9 + - + +
558Z LEU 3.1 1.2 + - - -
559Z PRO* 1.3 73.9 - - - +
561Z GLY* 1.3 64.7 + - - +
562Z LEU 3.1 0.9 - - - -
563Z GLY* 3.0 12.9 + - - -
564Z LEU* 3.0 17.4 + - + +
594Z LEU* 4.5 4.9 - - + -
629Z LYS* 4.3 19.5 - - - +
632Z LYS* 4.7 4.0 - - - +
782Z HIS* 4.0 46.7 - - + +
785Z ARG* 5.9 1.6 - - + -
786Z GLN* 5.5 12.1 - - + -
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Residues in contact with GLY 561 (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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519Z ALA 3.2 24.0 - - - -
520Z LEU* 3.9 7.8 - - - +
523Z GLY* 3.4 10.4 - - - -
537Z THR* 4.8 1.3 - - - -
557Z TRP 3.0 11.9 + - - -
558Z LEU 3.8 1.8 - - - -
560Z LEU* 1.3 75.5 - - - +
562Z LEU* 1.3 52.8 + - - +
564Z LEU* 4.3 1.6 - - - -
565Z ASN* 2.4 43.1 + - - -
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Residues in contact with LEU 562 (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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537Z THR* 3.7 37.8 - - + +
538Z ILE* 4.2 6.1 - - + -
541Z THR* 4.4 15.5 - - + -
558Z LEU 2.9 17.0 + - - +
559Z PRO* 3.5 13.7 - - + +
560Z LEU 3.1 0.2 - - - -
561Z GLY* 1.3 75.2 - - - +
563Z GLY* 1.3 64.9 + - - +
564Z LEU 3.4 0.5 + - - -
565Z ASN* 4.0 2.6 - - - +
566Z HIS* 3.4 56.3 + - + +
576Z ILE* 5.6 3.1 - - + -
580Z LEU* 4.5 23.1 - - + -
591Z ALA* 5.1 5.4 - - + -
595Z VAL* 5.0 12.5 - - + +
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Residues in contact with GLY 563 (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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559Z PRO 2.9 12.3 + - - -
560Z LEU 3.0 4.7 + - - -
562Z LEU* 1.3 76.7 - - - +
564Z LEU* 1.3 62.7 + - - +
566Z HIS* 3.9 2.8 - - - +
567Z LEU* 3.3 25.9 + - - +
573Z ILE* 6.1 0.3 - - - +
594Z LEU* 3.8 24.4 - - - +
595Z VAL* 5.5 4.7 - - - -
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Residues in contact with LEU 564 (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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520Z LEU* 4.0 25.4 - - + +
523Z GLY* 3.1 36.1 - - - +
524Z MET* 3.8 12.8 - - + +
527Z VAL* 3.5 16.8 - - + +
531Z ASN* 3.5 7.3 + - - -
560Z LEU* 3.0 14.1 + - + +
561Z GLY 3.3 0.6 + - - +
562Z LEU 3.2 0.2 - - - -
563Z GLY* 1.3 77.5 - - - +
565Z ASN* 1.3 65.9 + - - +
567Z LEU* 3.0 37.6 + - + +
778Z LEU* 5.6 2.2 - - + -
779Z CYS* 4.6 9.2 - - - -
782Z HIS* 3.7 30.1 - - + +
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Residues in contact with ASN 565 (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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498Z LEU* 4.2 2.3 - - - +
519Z ALA 4.5 0.8 + - - -
522Z CYS* 3.6 5.2 + - - +
523Z GLY* 3.4 12.7 - - - +
526Z ALA* 3.0 28.4 - - + +
531Z ASN* 2.6 31.0 + - - +
533Z ASP* 4.3 3.9 + - - +
534Z VAL* 3.3 23.2 + - + +
537Z THR* 3.6 27.2 + - - +
561Z GLY 2.4 38.9 + - - +
562Z LEU* 4.0 3.8 - - - +
563Z GLY 3.5 0.4 - - - -
564Z LEU* 1.3 75.5 - - - +
566Z HIS* 1.3 74.8 + - + +
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Residues in contact with HIS 566 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531Z ASN* 5.1 0.2 - - - -
533Z ASP* 3.7 36.9 - - + +
534Z VAL 4.0 2.6 + - - -
537Z THR* 5.6 0.2 - - - -
538Z ILE* 3.3 27.7 - - + +
562Z LEU* 3.4 42.0 + - + +
563Z GLY* 3.9 4.0 - - - +
564Z LEU 3.3 0.6 - - - -
565Z ASN* 1.3 81.0 - - + +
567Z LEU* 1.3 58.7 - - - +
568Z GLY 3.9 1.0 + - - -
569Z LYS* 4.0 10.0 + - - +
573Z ILE* 3.8 37.5 - - + +
576Z ILE* 3.6 35.0 - - + +
595Z VAL* 5.4 6.8 - - + +
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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
------------------------------------------------------------
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