Contacts of the helix formed by residues 538 - 552 (chain C) in PDB entry 1JLH
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 538 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537C HIS* 1.3 83.6 - - - +
539C ALA* 1.3 63.2 + - - +
540C SER* 2.8 34.7 + - - -
541C THR* 2.8 27.2 + - - -
542C ASN* 3.1 15.6 + - - -
29D PHE* 4.0 15.6 - - + -
56D LYS* 4.3 1.2 - - - -
433D GLU* 3.8 10.1 + - - +
436D MET* 3.2 34.5 - - + +
437D ARG* 4.9 6.5 - - - +
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Residues in contact with ALA 539 (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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537C HIS 3.8 0.2 + - - -
538C ASP* 1.3 73.6 - - - +
540C SER* 1.3 56.3 + - - +
542C ASN* 3.5 8.5 + - - +
543C GLY* 2.9 24.3 + - - -
29D PHE* 4.0 13.7 - - + +
32D ASN 4.7 1.6 - - - +
33D LYS* 3.6 28.7 - - - +
35D ARG 4.7 0.7 - - - +
36D PHE* 3.4 30.4 - - + +
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Residues in contact with SER 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C ASP* 2.8 15.7 + - - -
539C ALA* 1.3 71.3 - - - +
541C THR* 1.3 60.5 + - - -
543C GLY* 3.2 1.6 + - - -
544C LEU* 2.9 34.4 + - - +
29D PHE* 3.6 10.9 - - - -
36D PHE* 3.7 11.0 - - - -
53D ASP* 2.7 18.7 + - - +
55D SER* 3.2 18.9 + - - -
56D LYS* 2.7 34.7 + - - +
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Residues in contact with THR 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C ILE* 4.3 14.8 - - + -
537C HIS* 3.6 31.9 - - + +
538C ASP* 2.8 28.0 + - - -
540C SER* 1.3 75.2 + - - +
542C ASN* 1.3 62.6 + - - +
544C LEU* 3.8 9.3 - - - +
545C ILE* 3.0 43.3 + - + +
56D LYS* 4.1 6.9 + - - -
429D LEU* 4.8 9.3 + - + -
433D GLU* 3.7 17.2 - - + +
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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
----------------------------------------------------------
534C VAL* 3.4 24.2 + - - +
535C THR* 3.3 14.9 - - - +
536C SER 3.8 2.4 - - - +
537C HIS* 2.8 54.4 - - - +
538C ASP 3.1 12.1 + - - +
539C ALA* 3.6 6.9 - - - +
541C THR* 1.3 74.3 - - - +
543C GLY* 1.3 65.8 + - - +
545C ILE* 3.1 6.4 + - - +
546C ASN* 2.9 32.5 + - - +
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Residues in contact with GLY 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C ALA 2.9 13.7 + - - -
540C SER 3.6 1.3 - - - -
542C ASN* 1.3 77.5 - - - +
544C LEU* 1.3 60.9 + - - +
546C ASN* 3.4 7.7 + - - +
547C PHE* 3.0 23.6 + - - +
36D PHE* 3.4 37.1 - - - -
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Residues in contact with LEU 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C SER 2.9 21.5 + - - +
541C THR* 3.8 2.9 - - - +
543C GLY* 1.3 75.0 - - - +
545C ILE* 1.3 63.8 + - - +
547C PHE* 3.2 4.0 + - - +
548C ILE* 3.0 29.7 + - + +
36D PHE* 4.1 0.4 - - + -
51D LEU* 3.9 16.6 - - + -
53D ASP* 3.5 17.5 - - + +
56D LYS* 3.5 25.6 - - - +
428D PHE* 4.7 1.8 - - + -
429D LEU* 3.5 24.2 - - + -
432D THR* 4.8 1.8 - - - +
475D SER* 3.8 24.5 - - - +
477D VAL* 3.6 29.8 - - + -
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Residues in contact with ILE 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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524C ILE* 4.3 12.6 - - + -
527C GLU* 4.3 8.5 - - + +
528C LEU* 4.3 11.7 - - + -
534C VAL* 3.5 45.3 - - + -
537C HIS* 4.1 6.7 - - + +
541C THR* 3.0 38.9 + - + +
542C ASN 3.5 3.8 - - - +
544C LEU* 1.3 76.2 - - - +
546C ASN* 1.3 57.8 + - - +
548C ILE* 3.1 10.8 + - - +
549C LYS* 3.0 40.8 + - - +
429D LEU* 3.6 20.9 - - + -
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Residues in contact with ASN 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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532C ALA 4.6 0.3 - - - +
533C GLN* 3.3 39.2 - - - +
534C VAL* 2.9 42.6 + - - +
535C THR* 5.8 0.2 - - - +
542C ASN* 2.9 26.7 + - - +
543C GLY* 3.9 6.8 - - - +
545C ILE* 1.3 74.3 - - - +
547C PHE* 1.3 65.8 + - - +
549C LYS* 3.5 6.9 + - - +
550C GLN* 3.1 23.4 + - - +
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Residues in contact with PHE 547 (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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543C GLY 3.0 17.0 + - - +
544C LEU 3.5 4.7 - - - +
546C ASN* 1.3 77.1 - - - +
548C ILE* 1.3 59.5 + - - +
550C GLN* 3.2 20.4 + - - +
551C GLN* 2.9 55.2 + - + +
36D PHE* 5.8 0.2 - - + -
42D THR* 5.1 12.3 - - + -
49D HIS* 3.8 29.4 - - + -
50D ILE 5.1 0.2 - - - -
51D LEU* 3.5 38.4 - - + -
409D VAL* 4.3 4.0 - - + -
477D VAL* 3.5 46.0 - - + -
478D PHE* 4.6 0.7 - - - -
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Residues in contact with ILE 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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528C LEU* 5.0 9.9 - - + -
544C LEU* 3.0 20.0 + - + +
545C ILE* 3.1 8.0 + - - +
547C PHE* 1.3 77.4 - - - +
549C LYS* 1.3 58.4 + - + +
552C ARG* 2.9 38.2 + - - +
409D VAL* 3.4 24.0 - - + +
425D LEU* 3.6 40.4 - - + -
428D PHE* 5.3 3.4 - - + -
429D LEU* 4.0 31.6 - - + -
477D VAL* 4.3 21.5 - - + -
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Residues in contact with LYS 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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527C GLU 2.8 29.3 + - - -
528C LEU* 3.7 8.1 - - + -
529C ASP 3.6 4.8 + - - -
530C GLY 2.8 25.6 + - - +
531C SER* 4.0 13.7 - - - +
532C ALA* 2.6 32.9 + - - +
533C GLN* 5.2 3.1 - - - +
534C VAL* 4.0 3.2 - - - +
545C ILE* 3.0 35.1 + - + +
546C ASN* 3.8 10.3 - - - +
547C PHE 3.3 0.2 - - - -
548C ILE* 1.3 77.5 - - + +
550C GLN* 1.3 62.7 + - - +
552C ARG* 3.4 36.2 + - - +
553C GLU* 3.6 12.1 - - - +
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Residues in contact with GLN 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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546C ASN 3.1 17.7 + - - +
547C PHE* 3.6 24.0 - - - +
549C LYS* 1.3 80.0 - - - +
551C GLN* 1.3 85.5 + - - +
552C ARG 3.4 0.3 + - - -
553C GLU* 3.8 11.0 + - - +
554C ALA* 4.2 5.5 + - - +
49D HIS* 5.0 5.5 + - - -
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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 PHE* 2.9 42.4 + - + +
550C GLN* 1.3 102.2 + - - +
552C ARG* 1.3 64.9 + - - +
553C GLU 3.1 3.8 + - - -
554C ALA* 3.3 26.6 + - - +
556C VAL* 5.7 0.2 - - - +
48D GLY* 5.2 0.2 - - - -
49D HIS* 3.7 30.3 + - - -
409D VAL* 3.9 21.1 - - + -
410D GLN* 3.0 19.4 - - - +
479D THR* 2.8 27.5 + - + +
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Residues in contact with ARG 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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528C LEU* 2.6 30.3 + - - +
529C ASP* 4.8 0.6 - - - +
530C GLY 2.9 36.7 + - - +
531C SER* 4.3 2.6 - - - +
548C ILE* 2.9 27.1 + - - +
549C LYS* 3.4 31.3 + - - +
550C GLN 3.2 0.4 - - - -
551C GLN* 1.3 77.3 - - - +
553C GLU* 1.3 72.0 + - - +
555C ARG* 4.9 3.5 + - - -
409D VAL* 3.9 11.0 - - + +
410D GLN* 3.6 13.7 - - - +
425D LEU* 6.1 2.2 - - - +
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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