Contacts of the helix formed by residues 539 - 554 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A HIS* 1.3 82.6 - - - +
540A ALA* 1.3 65.0 + - - +
541A SER* 2.9 31.7 + - - -
542A THR* 2.7 28.3 + - - -
543A ASN* 3.1 18.2 + - - -
30B PHE* 4.0 14.8 - - + -
57B LYS* 4.1 1.8 - - - -
434B GLU* 3.8 11.5 + - - +
437B MET* 3.4 34.2 - - + +
438B ARG* 5.0 6.2 - - - +
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Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A HIS 3.8 0.6 + - - -
539A ASP* 1.3 74.0 - - - +
541A SER* 1.3 57.1 + - - +
543A ASN* 3.7 10.0 - - - +
544A GLY* 2.9 22.0 + - - -
30B PHE* 3.9 16.1 - - + +
33B ASN 5.0 1.1 - - - +
34B LYS* 3.8 24.9 - - - +
36B ARG 4.9 0.4 - - - +
37B PHE* 3.4 29.2 - - + +
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Residues in contact with SER 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ASP* 2.9 10.1 + - - -
540A ALA* 1.3 73.7 - - - +
542A THR* 1.3 62.3 + - - +
544A GLY* 3.0 1.6 + - - -
545A LEU* 2.8 34.8 + - - +
30B PHE* 3.6 12.6 - - - -
37B PHE* 3.8 10.3 - - - -
54B ASP* 2.5 21.0 + - - +
56B SER* 3.1 21.4 + - - -
57B LYS* 2.6 28.6 + - - +
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Residues in contact with THR 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 4.3 9.4 - - + -
538A HIS* 3.5 34.1 - - + +
539A ASP* 2.7 28.6 + - - -
541A SER* 1.3 75.4 + - - +
543A ASN* 1.3 61.1 + - - +
545A LEU* 3.7 10.7 - - - +
546A ILE* 3.0 38.0 + - + +
57B LYS* 3.9 7.3 + - - -
430B LEU* 4.5 8.4 + - + +
434B GLU* 3.6 24.6 - - + +
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Residues in contact with ASN 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A VAL* 3.4 19.6 - - - +
536A THR* 3.4 22.1 + - - +
537A SER 3.5 1.2 + - - -
538A HIS* 2.9 47.3 + - - +
539A ASP 3.1 17.3 + - - +
540A ALA* 3.7 9.1 - - - +
542A THR* 1.3 76.6 - - - +
544A GLY* 1.3 57.2 + - - +
546A ILE* 3.2 7.1 + - - +
547A ASN* 2.9 37.4 + - - +
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Residues in contact with GLY 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ALA 2.9 17.5 + - - -
541A SER 3.0 3.6 + - - -
543A ASN* 1.3 76.6 - - - +
545A LEU* 1.3 57.5 + - - +
547A ASN* 3.4 6.0 + - - +
548A PHE* 3.0 29.5 + - - +
37B PHE* 3.6 30.5 - - - -
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Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A SER 2.8 16.6 + - - +
542A THR* 3.7 2.9 - - - +
544A GLY* 1.3 74.3 - - - +
546A ILE* 1.3 64.9 + - - +
548A PHE* 3.3 2.8 + - - +
549A ILE* 2.9 31.4 + - + +
37B PHE* 4.3 0.4 - - + -
52B LEU* 3.8 24.2 - - + -
54B ASP* 3.5 20.0 - - + +
57B LYS* 3.4 29.4 - - - +
429B PHE* 4.9 1.6 - - + -
430B LEU* 3.4 24.5 - - + -
433B THR* 4.7 1.6 - - - +
476B SER* 3.8 28.0 - - - +
478B VAL* 3.8 15.2 - - + +
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Residues in contact with ILE 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 4.5 8.5 - - + -
528A GLU* 4.4 5.4 - - + +
529A LEU* 4.2 12.1 - - + -
535A VAL* 3.7 44.9 - - + -
538A HIS* 4.1 9.2 - - + +
542A THR* 3.0 34.9 + - + +
543A ASN 3.6 3.6 - - - +
545A LEU* 1.3 75.1 - - - +
547A ASN* 1.3 60.0 + - - +
549A ILE* 3.1 11.1 + - - +
550A LYS* 2.9 40.9 + - - +
430B LEU* 3.6 24.7 - - + -
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Residues in contact with ASN 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ALA 4.4 1.2 - - - +
534A GLN* 3.4 37.8 + - - +
535A VAL* 2.8 48.1 + - - +
536A THR* 5.6 0.4 - - - +
543A ASN* 2.9 21.9 + - - +
544A GLY* 4.0 5.9 - - - +
545A LEU 3.2 0.2 - - - -
546A ILE* 1.3 80.6 - - - +
548A PHE* 1.3 55.4 + - - +
550A LYS* 3.4 8.0 + - - +
551A GLN* 3.0 27.9 + - - +
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Residues in contact with PHE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A GLY 3.0 17.5 + - - +
545A LEU 3.6 4.0 - - - +
547A ASN* 1.3 73.2 - - - +
549A ILE* 1.3 63.3 + - - +
551A GLN* 3.2 18.1 + - - +
552A GLN* 2.9 53.8 + - + +
37B PHE* 5.7 0.2 - - + -
43B THR* 5.0 12.1 - - + -
50B HIS* 3.8 28.0 - + + -
51B ILE 5.0 0.2 - - - -
52B LEU* 3.7 41.1 - - + -
410B VAL* 4.3 3.8 - - + -
478B VAL* 3.7 40.2 - - + -
479B PHE* 4.8 0.4 - - - -
480B THR* 5.1 0.2 - - - -
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Residues in contact with ILE 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 5.0 8.7 - - + -
545A LEU* 2.9 20.7 + - + +
546A ILE* 3.3 8.5 - - - +
548A PHE* 1.3 76.8 - - - +
550A LYS* 1.3 63.4 + - + +
552A GLN 3.3 0.5 + - - -
553A ARG* 2.9 38.0 + - - +
410B VAL* 3.5 22.4 - - + +
426B LEU* 3.8 39.7 - - + -
429B PHE* 5.3 2.2 - - + -
430B LEU* 4.0 32.5 - - + -
478B VAL* 4.3 22.7 - - + -
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Residues in contact with LYS 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A GLU 2.9 28.5 + - - -
529A LEU* 3.6 8.7 - - + +
530A ASP 3.5 7.3 + - - -
531A GLY 2.9 25.3 + - - +
532A SER* 4.2 10.8 - - - +
533A ALA* 2.7 32.4 + - - +
534A GLN* 5.2 4.3 - - - +
535A VAL* 4.2 2.7 - - - +
546A ILE* 2.9 32.8 + - + +
547A ASN* 3.8 11.7 - - - +
549A ILE* 1.3 76.9 - - + +
551A GLN* 1.3 63.7 + - - +
553A ARG* 3.3 35.7 + - - +
554A GLU* 3.9 11.1 - - - +
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Residues in contact with GLN 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ASN 3.0 15.4 + - - +
548A PHE* 3.4 20.6 - - - +
550A LYS* 1.3 79.3 - - - +
552A GLN* 1.3 89.2 + - - +
554A GLU* 3.4 20.3 + - - +
555A ALA* 4.3 1.7 + - - +
50B HIS* 5.0 4.3 + - - -
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Residues in contact with GLN 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A PHE* 2.9 42.0 + - + +
551A GLN* 1.3 97.6 + - - +
553A ARG* 1.3 66.6 + - - +
554A GLU 3.0 2.8 + - - -
555A ALA* 3.1 25.3 + - - +
50B HIS* 3.6 31.0 + - - -
410B VAL* 3.9 22.9 - - + -
411B GLN* 2.9 19.6 + - - +
480B THR* 2.6 28.5 + - + +
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Residues in contact with ARG 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 2.8 31.5 + - - +
530A ASP* 5.0 0.4 - - - +
531A GLY* 2.7 37.0 + - - +
532A SER* 4.8 0.8 - - - +
549A ILE* 2.9 23.3 + - - +
550A LYS* 3.3 33.4 + - - +
552A GLN* 1.3 77.9 - - - +
554A GLU* 1.3 74.0 + - - +
555A ALA 3.5 1.4 + - - +
410B VAL* 3.7 9.8 - - + +
411B GLN* 3.5 14.7 + - - +
426B LEU* 6.1 1.4 - - - +
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Residues in contact with GLU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A LYS 3.9 9.5 - - - +
551A GLN* 3.7 13.9 - - - +
552A GLN 3.0 1.4 - - - -
553A ARG* 1.3 98.5 + - - +
555A ALA* 1.3 61.1 + - - +
556A ARG* 3.8 5.7 + - - +
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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