Contacts of the helix formed by residues 537 - 554 (chain V) in PDB entry 5IY8
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 ASN 537 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161 MET* 5.0 0.6 - - - +
512V CYS 4.3 1.2 + - - -
513V PRO 2.8 16.8 + - - +
514V MET* 2.8 37.6 - - - +
515V SER* 3.7 3.3 + - - -
518V PHE* 4.1 4.6 - - + +
533V LEU 3.2 17.4 + - - +
534V TYR 4.0 2.0 - - - +
535V THR 3.4 0.8 - - - -
536V MET* 1.4 72.8 - - - +
538V PRO* 1.3 71.4 - - - +
539V ASN* 2.8 29.7 + - - -
540V LYS* 3.1 20.1 + - + +
541V PHE 3.0 17.0 + - - -
664V SER* 3.2 17.5 + - - +
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Residues in contact with PRO 538 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515V SER* 3.0 28.9 - - - +
518V PHE* 3.7 22.9 - - + -
536V MET 3.6 9.2 - - - +
537V ASN* 1.3 84.7 - - - +
539V ASN* 1.3 59.7 + - - +
541V PHE* 3.5 8.0 - - + +
542V ARG* 2.9 30.0 + - - +
703V PHE* 3.6 36.8 - - + -
709V GLN* 3.8 19.7 - - + -
712V LEU* 5.2 0.4 - - + -
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Residues in contact with ASN 539 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512V CYS* 4.7 3.1 - - - +
513V PRO* 3.4 32.8 - - + +
514V MET 3.7 0.8 - - - -
515V SER* 2.7 51.5 + - - +
537V ASN* 2.8 15.4 + - - -
538V PRO* 1.3 75.6 - - - +
540V LYS* 1.4 54.9 + - - +
542V ARG* 3.6 12.6 - - - +
543V ALA* 3.1 22.7 + - - +
696V MET* 3.7 14.9 - - + +
709V GLN* 5.6 2.1 + - - -
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Residues in contact with LYS 540 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512V CYS* 3.9 25.1 - - + +
534V TYR 2.9 24.2 + - - +
535V THR* 3.6 10.8 - - - +
537V ASN* 3.1 20.4 + - - +
539V ASN* 1.4 75.7 - - - +
541V PHE* 1.3 57.0 + - - +
543V ALA* 3.2 4.2 + - - +
544V CYS* 3.0 27.2 + - - +
571V TYR* 4.5 4.0 - - - +
626V ILE* 2.8 32.0 + - - +
662V LEU* 3.5 22.7 + - + +
663V VAL 4.5 0.7 - - - -
664V SER* 3.3 13.5 - - - +
669V GLU* 2.6 35.1 + - - +
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Residues in contact with PHE 541 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536V MET* 4.4 15.9 - - + +
537V ASN 3.0 11.5 + - - +
538V PRO* 3.5 15.0 - - + +
540V LYS* 1.3 75.2 - - - +
542V ARG* 1.3 52.1 + - - +
544V CYS* 3.1 6.2 + - - +
545V GLN* 2.7 35.1 + - - +
571V TYR* 3.5 57.7 + + - +
574V ARG* 3.8 36.3 - - + -
575V LEU* 3.9 30.5 - - + -
702V ALA* 4.3 12.8 - - + -
703V PHE* 4.0 23.8 - + - -
712V LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 542 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538V PRO* 2.9 22.7 + - - +
539V ASN* 3.6 11.7 - - - +
541V PHE* 1.3 74.7 - - - +
543V ALA* 1.4 56.7 + - - +
545V GLN* 3.4 8.6 + - - +
546V PHE* 2.9 31.5 + - - +
696V MET* 3.4 45.4 + - - +
697V GLU* 4.7 7.3 + - - -
699V GLU 4.4 4.8 + - - -
701V LEU* 3.4 36.6 + - + +
702V ALA* 2.8 48.5 + - + +
703V PHE* 4.6 8.9 - - + -
704V SER* 4.5 11.3 - - - +
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Residues in contact with ALA 543 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510V VAL* 5.0 3.4 - - + -
512V CYS* 4.2 19.5 - - - -
539V ASN 3.1 14.9 + - - +
540V LYS 3.2 8.3 + - - +
542V ARG* 1.4 74.6 - - - +
544V CYS* 1.4 55.3 + - - +
546V PHE* 3.4 3.2 + - - +
547V LEU* 2.9 43.8 + - + +
662V LEU* 5.2 2.5 - - + -
693V LEU* 4.1 19.7 - - + -
696V MET* 3.4 10.6 - - + -
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Residues in contact with CYS 544 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540V LYS 3.0 15.3 + - - +
541V PHE 3.3 8.7 - - - +
543V ALA* 1.4 67.3 - - - +
545V GLN* 1.3 65.1 + - - +
547V LEU* 3.4 7.6 + - - +
548V ILE* 3.0 41.4 + - - +
560V VAL* 4.6 3.4 - - - -
571V TYR* 3.8 27.8 - - + -
575V LEU* 5.2 0.4 - - + -
606V PHE* 5.4 0.2 - - - -
624V ILE* 3.8 26.0 - - - +
626V ILE* 3.9 11.7 - - - -
662V LEU* 3.6 14.0 - - + +
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Residues in contact with GLN 545 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541V PHE* 2.7 21.8 + - + +
542V ARG* 3.5 6.2 - - - +
544V CYS* 1.3 73.6 - - - +
546V PHE* 1.3 55.3 + - - +
548V ILE* 3.3 12.2 + - + +
549V LYS* 3.0 42.8 + - + +
575V LEU* 3.9 30.5 - - + +
700V ASP* 5.0 3.6 + - - -
701V LEU* 3.7 22.7 - - + +
702V ALA* 2.9 40.2 + - - +
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Residues in contact with PHE 546 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542V ARG 2.9 21.1 + - - +
543V ALA* 3.6 4.0 - - - +
545V GLN* 1.3 71.2 - - - +
547V LEU* 1.4 68.0 + - + +
549V LYS* 3.3 6.5 + - - +
550V PHE* 2.9 50.3 + + + +
693V LEU* 3.9 41.5 - - + -
695V GLY* 4.4 14.4 - - - -
696V MET* 4.5 13.0 - - + -
699V GLU* 3.4 35.0 - - + -
701V LEU* 3.9 20.1 - - + +
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Residues in contact with LEU 547 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510V VAL* 4.5 10.8 - - + -
543V ALA* 2.9 30.0 + - + +
544V CYS* 3.6 7.2 - - - +
545V GLN 3.3 0.2 - - - -
546V PHE* 1.4 87.6 - - + +
548V ILE* 1.4 63.1 + - - +
550V PHE* 3.6 8.3 + - + +
551V HIS* 3.2 33.2 + - + +
624V ILE* 4.6 13.0 - - + +
660V TYR* 3.9 44.4 - - + +
662V LEU* 4.4 19.5 - - + -
690V ILE* 6.0 2.2 - - + -
693V LEU* 5.3 7.0 - - + -
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Residues in contact with ILE 548 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544V CYS* 3.0 34.6 + - - +
545V GLN* 3.7 5.6 - - + +
547V LEU* 1.4 71.6 - - - +
549V LYS* 1.3 61.7 + - + +
551V HIS 3.3 1.0 + - - -
552V GLU* 2.9 46.7 + - - +
558V ILE* 4.1 7.0 - - + +
560V VAL* 4.4 15.7 - - + -
575V LEU* 3.6 31.4 - - + -
577V LYS* 4.1 8.3 - - - -
604V THR* 3.5 29.2 - - + +
606V PHE* 4.5 5.6 - - + -
624V ILE* 4.0 19.1 - - + -
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Residues in contact with LYS 549 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545V GLN* 3.0 29.4 + - + +
546V PHE* 3.5 8.5 - - - +
548V ILE* 1.3 76.2 - - + +
550V PHE* 1.3 61.8 + - - +
552V GLU* 3.6 9.8 + - - +
553V ARG* 3.0 45.3 + - - +
699V GLU* 2.8 30.8 + - - +
700V ASP* 2.8 28.2 + - - +
701V LEU* 3.6 13.9 - - + +
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Residues in contact with PHE 550 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546V PHE* 2.9 36.4 + + + +
547V LEU* 3.8 11.7 - - + +
548V ILE 3.4 0.2 - - - -
549V LYS* 1.3 76.3 - - - +
551V HIS* 1.3 88.4 + + - +
553V ARG* 3.5 10.4 + - - +
554V ARG* 3.2 63.3 + - - +
658V PHE* 6.1 4.3 - + - -
660V TYR* 5.4 2.7 - - - -
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Residues in contact with HIS 551 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547V LEU* 3.2 25.4 + - + +
548V ILE 3.3 0.2 + - - -
550V PHE* 1.3 96.5 - + - +
552V GLU* 1.3 62.5 + - - +
554V ARG* 3.1 16.9 + - - +
556V ASP* 3.1 34.8 + - + -
558V ILE* 3.6 26.2 - - + -
622V VAL* 3.6 28.7 - - + +
624V ILE* 5.7 0.4 - - + -
658V PHE* 3.8 29.4 - + - -
660V TYR* 2.8 34.2 + + - -
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Residues in contact with GLU 552 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548V ILE* 2.9 31.0 + - - +
549V LYS* 4.1 8.8 - - - +
551V HIS* 1.3 71.0 - - - +
553V ARG* 1.3 56.0 + - - +
555V ASN* 3.1 24.7 + - - +
556V ASP 4.7 0.7 - - - -
558V ILE* 3.6 8.1 - - + -
577V LYS* 2.8 33.5 + - - +
603V ASN* 4.5 12.9 + - + +
604V THR* 2.7 33.5 + - - +
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Residues in contact with ARG 553 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549V LYS* 3.0 40.0 + - - +
550V PHE* 3.5 8.7 - - - +
551V HIS 3.3 0.2 - - - -
552V GLU* 1.3 74.7 - - - +
554V ARG* 1.4 70.5 + - + +
555V ASN* 3.4 1.5 + - - +
699V GLU* 5.1 11.8 + - - -
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Residues in contact with ARG 554 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550V PHE* 3.2 69.4 + - - +
551V HIS* 3.1 15.0 + - - +
553V ARG* 1.4 92.5 - - + +
555V ASN* 1.3 61.4 + - - +
556V ASP* 4.0 11.7 - - - +
647V LYS* 2.8 31.4 + - - +
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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