Contacts of the helix formed by residues 539 - 554 (chain C) in PDB entry 1JIQ
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 ASP 539 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538C HIS* 1.3 82.6 - - - +
540C ALA* 1.3 57.4 + - - +
541C SER* 2.9 31.4 + - - -
542C THR* 2.5 29.1 + - - -
543C ASN* 3.0 23.2 + - - -
30D PHE* 3.9 16.3 - - + -
57D LYS* 4.2 0.7 - - - -
434D GLU* 3.7 12.7 + - - +
437D MET* 3.6 30.8 - - + +
438D ARG* 4.9 8.0 - - - +
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Residues in contact with ALA 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C ASP* 1.3 74.6 - - - +
541C SER* 1.3 52.2 + - - +
543C ASN* 3.7 10.2 - - - +
544C GLY* 2.8 30.5 + - - -
30D PHE* 3.9 16.2 - - + +
33D ASN 5.2 0.4 - - - +
34D LYS* 4.0 24.0 - - + +
36D ARG 5.1 0.2 - - - +
37D PHE* 3.5 25.0 - - + +
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Residues in contact with SER 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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539C ASP* 2.9 10.1 + - - -
540C ALA* 1.3 73.4 - - - +
542C THR* 1.3 58.5 + - - +
544C GLY* 3.0 1.6 + - - -
545C LEU* 2.7 38.4 + - - +
30D PHE* 3.6 12.9 - - - -
37D PHE* 3.7 10.5 - - - -
54D ASP* 2.6 21.7 + - - +
56D SER* 3.2 20.2 + - - -
57D LYS* 2.7 27.9 + - - +
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Residues in contact with THR 542 (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 ILE* 4.2 14.8 - - + -
538C HIS* 3.6 33.2 - - + +
539C ASP* 2.5 30.3 + - - -
541C SER* 1.3 75.4 + - - +
543C ASN* 1.3 64.6 + - - +
545C LEU* 3.3 9.9 + - - +
546C ILE* 3.0 37.0 + - + +
57D LYS* 4.0 6.8 + - - +
430D LEU* 4.7 9.5 + - + +
434D GLU* 3.5 18.3 - - + +
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Residues in contact with ASN 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C VAL 3.5 19.0 - - - +
536C THR* 3.5 17.1 + - - +
537C SER 3.5 5.0 + - - -
538C HIS* 2.8 47.6 + - - +
539C ASP 3.0 17.6 + - - +
540C ALA* 3.7 8.3 - - - +
542C THR* 1.3 77.1 - - - +
544C GLY* 1.3 58.4 - - - +
546C ILE* 3.4 6.7 + - - +
547C ASN* 2.9 39.0 + - - +
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Residues in contact with GLY 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C ALA 2.8 20.0 + - - -
541C SER 3.0 3.8 + - - -
543C ASN* 1.3 70.9 - - - +
545C LEU* 1.3 60.0 + - - +
547C ASN* 3.4 6.4 + - - +
548C PHE* 3.0 28.9 + - - +
37D PHE* 3.6 29.9 - - - -
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Residues in contact with LEU 545 (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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541C SER 2.7 20.0 + - - +
542C THR* 3.7 2.0 - - - +
544C GLY* 1.3 70.6 - - - +
546C ILE* 1.3 65.3 + - - +
548C PHE* 3.2 3.6 + - - +
549C ILE* 3.0 30.5 + - + +
37D PHE* 4.2 0.2 - - - -
52D LEU* 3.8 16.6 - - + -
54D ASP* 3.4 24.2 - - + +
57D LYS* 3.5 24.7 - - - +
429D PHE* 4.8 0.9 - - + -
430D LEU* 3.4 24.5 - - + -
433D THR* 4.6 2.2 - - - +
476D SER* 3.7 25.6 - - - +
478D VAL* 3.7 27.4 - - + -
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Residues in contact with ILE 546 (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 ILE* 4.6 6.3 - - + -
528C GLU* 4.4 4.9 - - + +
529C LEU* 4.1 16.8 - - + -
535C VAL* 3.8 23.8 - - + -
538C HIS* 4.0 28.7 - - + +
542C THR* 3.0 28.8 + - + +
543C ASN* 3.6 3.6 - - - +
545C LEU* 1.3 76.5 - - - +
547C ASN* 1.3 59.2 + - - +
549C ILE* 3.2 11.2 + - - +
550C LYS* 2.9 51.9 + - - +
430D LEU* 3.7 23.8 - - + +
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Residues in contact with ASN 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C GLN* 3.2 34.8 + - + +
535C VAL* 2.8 42.4 + - - +
536C THR* 5.8 0.2 - - - +
543C ASN* 2.9 26.8 + - - +
544C GLY* 3.9 6.5 - - - +
545C LEU 3.2 0.2 - - - -
546C ILE* 1.3 81.3 - - - +
548C PHE* 1.3 55.0 + - - +
550C LYS* 3.4 7.1 + - - +
551C GLN* 3.0 27.7 + - - +
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Residues in contact with PHE 548 (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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544C GLY 3.0 17.9 + - - +
545C LEU 3.6 4.5 - - - +
547C ASN* 1.3 72.8 - - - +
549C ILE* 1.3 60.6 + - - +
551C GLN* 3.2 17.9 + - - +
552C GLN* 2.9 53.7 + - + +
37D PHE* 5.7 0.7 - - + -
43D THR* 5.1 12.1 - - + -
50D HIS* 3.7 29.6 - + + -
51D ILE 4.9 0.7 - - - -
52D LEU* 3.7 41.5 - - + -
410D VAL* 4.3 4.0 - - + -
478D VAL* 3.6 42.0 - - + -
479D PHE* 4.5 0.9 - - - -
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Residues in contact with ILE 549 (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 LEU* 5.0 7.9 - - + -
545C LEU* 3.0 23.1 + - + +
546C ILE* 3.3 8.3 - - - +
548C PHE* 1.3 75.3 - - - +
550C LYS* 1.3 63.0 + - + +
553C ARG* 2.9 38.6 + - - +
410D VAL* 3.5 32.2 - - + +
426D LEU* 3.9 38.8 - - + -
429D PHE* 5.4 1.6 - - + -
430D LEU* 3.9 31.2 - - + -
478D VAL* 4.3 13.7 - - + -
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Residues in contact with LYS 550 (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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528C GLU 2.9 28.3 + - - -
529C LEU* 3.4 6.2 + - + +
530C ASP 3.3 10.3 + - - -
531C GLY 2.7 24.0 + - - +
532C SER* 4.0 11.4 - - - +
533C ALA* 2.9 30.3 + - - +
534C GLN* 4.7 2.0 - - + -
535C VAL* 3.9 2.9 - - - +
546C ILE* 2.9 36.4 + - + +
547C ASN* 3.7 10.3 - - - +
549C ILE* 1.3 78.7 - - + +
551C GLN* 1.3 64.0 + - - +
553C ARG* 3.5 38.2 + - - +
554C GLU* 4.1 9.7 - - - +
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Residues in contact with GLN 551 (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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547C ASN 3.0 15.2 + - - +
548C PHE* 3.2 19.3 + - - +
550C LYS* 1.3 80.0 - - - +
552C GLN* 1.3 88.1 + - - +
554C GLU* 3.4 18.3 + - - +
555C ALA* 4.2 1.7 + - - +
50D HIS* 5.0 4.0 + - - -
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Residues in contact with GLN 552 (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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548C PHE* 2.9 42.7 + - + +
549C ILE 3.8 0.2 - - - -
551C GLN* 1.3 95.8 + - - +
553C ARG* 1.3 62.3 + - - +
554C GLU 3.0 2.5 - - - -
555C ALA* 3.1 21.6 + - - +
49D GLY* 5.2 0.2 - - - -
50D HIS* 3.6 31.9 + - - -
410D VAL* 3.9 21.1 - - + -
411D GLN* 2.9 24.3 + - - +
480D THR* 2.6 34.8 + - + +
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Residues in contact with ARG 553 (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 LEU* 2.7 32.5 + - - +
530C ASP* 4.8 1.3 - - - +
531C GLY* 2.7 39.2 + - - +
532C SER* 4.8 0.8 - - - +
549C ILE* 2.9 27.8 + - - +
550C LYS* 3.5 26.5 + - - +
552C GLN* 1.3 77.4 - - - +
554C GLU* 1.3 73.3 + - - +
555C ALA 3.5 1.4 + - - +
410D VAL* 3.8 11.6 - - + +
411D GLN* 3.7 14.5 + - + +
426D LEU* 6.0 2.2 - - - +
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Residues in contact with GLU 554 (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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550C LYS 4.1 8.3 - - - +
551C GLN* 3.7 12.6 - - - +
552C GLN 3.0 1.4 - - - -
553C ARG* 1.3 96.9 + - - +
555C ALA* 1.3 60.9 + - - +
556C ARG* 3.8 14.0 + - - +
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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