Contacts of the helix formed by residues 520 - 542 (chain C) in PDB entry 5YD6
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 GLU 520 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C LEU* 4.7 1.0 - - - +
431C PRO* 3.8 17.9 - - + +
434C ASP* 2.9 17.4 + - - +
519C LYS* 1.3 77.1 - - - +
521C PRO* 1.4 64.5 - - - +
522C LYS* 3.2 5.4 + - + -
523C ARG* 2.9 48.4 + - + +
524C VAL* 3.7 13.0 + - - +
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Residues in contact with PRO 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C ARG 5.8 0.2 - - - +
518C LEU* 3.9 37.0 - - + +
519C LYS 3.3 13.0 - - - +
520C GLU* 1.4 82.2 - - - +
522C LYS* 1.3 65.5 + - + +
524C VAL* 3.5 3.6 + - + +
525C GLU* 3.0 28.1 + - - +
401D GLN* 6.1 3.6 - - - +
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Residues in contact with LYS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C GLU* 3.2 3.1 - - + -
521C PRO* 1.3 84.8 - - + +
523C ARG* 1.3 60.4 + - + +
525C GLU* 3.2 11.1 + - - +
526C GLU* 2.8 44.5 + - - +
404D GLN* 6.6 0.2 - - + -
408D ASP* 5.9 2.8 + - - +
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Residues in contact with ARG 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C GLY 4.8 2.0 + - - -
429C ASP* 3.4 36.8 + - - +
430C LEU* 4.0 23.8 - - + +
431C PRO* 4.0 8.9 - - - +
520C GLU* 2.9 38.2 + - + +
522C LYS* 1.3 77.8 - - + +
524C VAL* 1.3 59.0 + - - +
526C GLU* 3.9 19.7 - - + +
527C LEU* 3.2 26.0 + - - +
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Residues in contact with VAL 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LEU* 3.8 27.8 - - + -
434C ASP* 4.8 2.7 - - + +
438C LEU* 4.2 8.5 - - + -
512C VAL* 3.5 12.3 - - + +
513C THR* 3.7 37.7 - - - +
514C GLU* 4.8 1.1 - - - +
518C LEU* 3.9 29.4 - - + -
520C GLU 3.7 11.1 + - - +
521C PRO 3.5 7.6 + - - +
522C LYS 3.3 0.4 - - - -
523C ARG* 1.3 75.0 - - - +
525C GLU* 1.3 59.2 + - - +
527C LEU* 3.3 1.6 + - - -
528C GLN* 2.9 28.9 + - + +
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Residues in contact with GLU 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C GLU* 3.7 25.1 - - + +
521C PRO 3.0 14.4 + - - +
522C LYS* 3.2 13.5 + - - +
524C VAL* 1.3 77.1 - - - +
526C GLU* 1.3 58.5 + - + +
528C GLN* 3.3 11.8 - - - +
529C ASN* 3.0 57.5 + - - +
386D ARG* 4.9 5.8 + - - -
401D GLN* 5.0 13.5 + - - +
405D GLN* 3.7 24.3 + - - -
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Residues in contact with GLU 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C LYS* 2.8 34.0 + - - +
523C ARG* 4.0 21.4 - - + +
524C VAL 3.3 0.2 - - - -
525C GLU* 1.3 72.0 - - + +
527C LEU* 1.3 63.0 + - - +
529C ASN* 3.9 6.7 + - - +
530C LYS* 3.3 28.3 + - - +
386D ARG* 6.1 5.2 - - - -
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Residues in contact with LEU 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C LEU* 5.4 6.7 - - + -
424C ILE* 4.4 11.4 - - + -
425C PRO 3.3 27.8 - - - +
426C GLY* 4.1 9.6 - - - +
427C PHE* 3.9 19.1 - - - +
430C LEU* 4.9 7.6 - - + -
512C VAL* 4.1 16.4 - - + -
523C ARG 3.2 18.6 + - - +
524C VAL* 3.8 3.6 - - - +
526C GLU* 1.3 74.1 - - - +
528C GLN* 1.3 66.2 + - - +
530C LYS* 3.2 19.9 + - + +
531C ILE* 3.1 37.7 + - + +
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Residues in contact with GLN 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C LEU* 3.6 14.9 + - + +
512C VAL* 3.2 33.5 + - + +
513C THR* 3.5 12.2 + - - +
514C GLU* 3.0 40.1 + - - +
524C VAL* 2.9 14.9 + - - +
525C GLU* 3.3 16.3 - - - +
527C LEU* 1.3 74.1 - - - +
529C ASN* 1.3 63.3 + - - +
531C ILE* 3.0 11.8 + - - +
532C VAL* 2.9 33.8 + - + +
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Residues in contact with ASN 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C GLU* 3.0 40.9 + - - +
526C GLU* 4.2 7.0 - - - +
527C LEU 3.4 0.2 - - - -
528C GLN* 1.3 86.4 - - - +
530C LYS* 1.3 54.0 + - - +
532C VAL* 3.3 13.6 + - - +
533C ASN* 2.7 40.5 + - - +
385D SER* 3.8 15.9 - - - +
386D ARG* 4.0 28.6 - - + +
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Residues in contact with LYS 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C LEU* 3.9 26.7 - - + +
526C GLU 3.3 16.0 + - - +
527C LEU* 3.2 22.1 + - + +
529C ASN* 1.3 77.9 - - - +
531C ILE* 1.3 61.7 + - - +
533C ASN* 3.5 10.8 + - - +
534C CYS* 3.3 24.8 + - - +
385D SER* 6.2 2.2 - - - -
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Residues in contact with ILE 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C LEU* 4.7 11.9 - - + -
368C LEU* 3.8 25.8 - - + -
424C ILE* 4.7 7.4 - - + -
505C CYS* 3.7 27.5 - - + +
508C ALA* 4.1 11.2 - - + -
509C LEU* 3.8 10.8 - - + -
512C VAL* 4.0 30.1 - - + -
527C LEU* 3.1 26.2 + - + +
528C GLN* 3.0 7.7 + - - +
530C LYS* 1.3 74.3 - - - +
532C VAL* 1.3 65.9 + - - +
534C CYS* 3.4 7.8 + - - -
535C LEU* 3.0 22.3 + - - +
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Residues in contact with VAL 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C LEU* 3.7 24.0 - - + -
528C GLN* 2.9 27.0 + - + +
529C ASN* 3.5 17.0 - - - +
531C ILE* 1.3 74.3 - - - +
533C ASN* 1.3 55.9 + - - +
535C LEU* 3.4 10.1 + - + +
536C LYS* 2.8 40.0 + - + +
552C LEU* 6.2 1.1 - - + -
556C LEU* 5.2 15.0 - - + -
388D GLN* 4.1 20.2 - - - +
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Residues in contact with ASN 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C ASN 2.7 26.0 + - - +
530C LYS* 3.5 9.8 - - - +
531C ILE 3.2 0.2 - - - -
532C VAL* 1.3 77.1 - - - +
534C CYS* 1.3 60.6 + - - +
536C LYS* 3.1 18.5 - - - +
537C ASP* 2.8 36.2 + - - +
384D TYR 4.2 4.5 - - - +
385D SER* 2.9 48.9 + - - +
387D PHE 5.5 1.2 - - - +
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Residues in contact with CYS 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C LEU* 4.0 27.6 - - + -
365C ILE* 3.5 33.9 - - + +
368C LEU* 5.1 1.3 - - - -
505C CYS* 4.8 4.5 - - - -
530C LYS 3.3 14.7 + - - +
531C ILE* 3.8 9.9 - - - -
533C ASN* 1.3 75.6 - - - +
535C LEU* 1.3 59.7 + - - +
537C ASP* 3.9 10.1 - - + +
538C HIS* 3.2 28.2 + - - +
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Residues in contact with LEU 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502C ALA* 4.1 32.1 - - + +
505C CYS* 3.8 14.7 - - + -
506C ILE* 3.8 17.0 - - + -
509C LEU* 3.7 25.8 - - + -
531C ILE 3.0 13.6 + - - +
532C VAL* 3.4 10.1 - - + +
534C CYS* 1.3 75.0 - - - +
536C LYS* 1.3 64.7 + - - +
538C HIS* 3.4 3.2 + - - +
539C VAL* 3.0 46.1 + - + +
552C LEU* 5.4 8.1 - - + -
555C LEU* 4.2 11.4 - - + -
556C LEU* 3.9 15.7 - - + -
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Residues in contact with LYS 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C VAL* 2.8 24.6 + - + +
533C ASN* 3.1 24.2 + - - +
535C LEU* 1.3 74.2 - - - +
537C ASP* 1.3 66.3 + - - +
539C VAL* 3.5 2.8 + - - +
540C THR* 3.1 27.4 + - - -
552C LEU* 3.6 32.0 - - + +
384D TYR 5.6 1.4 + - - -
387D PHE* 3.4 34.2 + - - -
388D GLN* 4.0 26.6 - - - +
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Residues in contact with ASP 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A PHE 5.5 2.0 - - - +
533C ASN* 2.8 25.3 + - - +
534C CYS* 4.1 8.9 - - + +
536C LYS* 1.3 77.5 - - - +
538C HIS* 1.3 58.4 + - - +
540C THR* 3.4 8.7 + - - +
541C PHE* 3.0 27.0 + - - +
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Residues in contact with HIS 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ILE* 6.4 0.2 - - - +
365C ILE* 3.6 17.3 - - + -
499C ASP* 2.9 39.5 + - - -
501C SER* 3.4 23.7 + - - -
502C ALA* 4.1 11.6 + - + +
534C CYS 3.2 20.7 + - - +
535C LEU* 3.9 3.6 + - - +
537C ASP* 1.3 75.2 - - - +
539C VAL* 1.3 66.2 + - - +
541C PHE* 3.4 15.0 + + - +
542C ASN* 3.2 40.4 + - - -
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Residues in contact with VAL 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ALA* 5.1 4.3 - - + -
535C LEU* 3.0 29.3 + - + +
536C LYS 3.9 3.6 - - - +
538C HIS* 1.3 78.4 - - - +
540C THR* 1.3 58.8 + - - +
542C ASN* 3.1 12.1 + - + +
543C ASN* 3.0 25.2 + - - -
549C PRO* 4.3 22.6 - - + +
551C TYR* 4.3 22.0 - - + -
552C LEU* 4.6 15.3 - - + -
555C LEU* 4.1 25.1 - - + -
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Residues in contact with THR 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C LYS 3.1 19.0 + - - -
537C ASP* 3.5 8.7 - - - +
539C VAL* 1.3 76.5 - - - +
541C PHE* 1.3 58.1 + - - +
543C ASN* 3.1 33.9 + - - +
549C PRO* 5.6 9.0 - - - +
552C LEU* 5.9 0.7 - - - +
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Residues in contact with PHE 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ILE* 6.2 3.8 - - + -
537A ASP* 3.4 47.3 - - + -
538A HIS* 4.8 7.2 - + + -
540A THR* 6.1 0.9 - - - -
541A PHE* 3.6 27.6 - - - +
537C ASP 3.0 14.3 + - - +
538C HIS* 3.5 18.8 - + + +
539C VAL 3.3 0.2 - - - -
540C THR* 1.3 76.6 - - - +
542C ASN* 1.3 68.3 + - - +
543C ASN* 3.2 10.0 + - - +
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Residues in contact with ASN 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A SER* 5.7 6.2 + - - -
499C ASP* 3.2 26.7 + - - -
538C HIS* 3.2 27.6 + - - +
539C VAL* 3.1 13.3 + - - +
541C PHE* 1.3 83.0 - - - +
543C ASN* 1.3 67.9 + - - +
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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