Contacts of the helix formed by residues 540 - 553 (chain A) in PDB entry 1U9J
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 ILE 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A PHE* 3.5 31.9 - - + -
327A ILE* 5.1 1.6 - - + -
330A HIS* 3.7 41.5 - - + +
493A TRP* 3.5 33.4 - - + -
494A MET 2.8 18.1 + - - +
495A GLY* 3.8 14.6 - - - -
496A PRO* 4.1 4.5 - - + -
538A THR 3.4 1.3 + - - -
539A ASP* 1.3 75.8 + - - +
541A ARG* 1.3 63.2 + - + +
543A GLY* 3.7 2.7 - - - +
544A ILE* 2.7 47.6 + - + +
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Residues in contact with ARG 541 (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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330A HIS* 6.3 1.3 - - + -
496A PRO* 5.9 1.1 - - + +
539A ASP* 2.7 26.4 + - - +
540A ILE* 1.3 78.5 - - + +
542A ASP* 1.3 56.3 + - - +
544A ILE* 4.0 7.2 - - - +
545A GLU* 3.2 24.4 + - - +
636A ILE* 4.1 18.3 - - + +
640A GLU* 5.1 7.9 + - - -
644A GLU* 2.6 44.7 + - - -
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Residues in contact with ASP 542 (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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538A THR* 4.3 6.7 - - + +
539A ASP* 2.9 14.2 + - - +
541A ARG* 1.3 79.2 - - - +
543A GLY* 1.3 65.3 + - - +
545A GLU* 3.3 3.1 + - - +
546A ALA 3.2 8.0 + - - -
567A ASN* 4.6 1.6 - - - +
632A TRP* 2.9 40.3 + - + +
633A GLU 4.5 0.5 - - - +
634A PRO* 3.7 10.1 - - + +
635A LYS* 3.0 31.0 + - - +
636A ILE* 3.1 44.9 + - - +
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Residues in contact with GLY 543 (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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493A TRP* 3.6 30.5 - - - -
538A THR* 4.1 3.3 - - - +
539A ASP 2.9 13.0 + - - -
540A ILE 3.9 1.1 - - - -
542A ASP* 1.3 77.3 - - - +
544A ILE* 1.3 56.7 + - - +
546A ALA* 3.2 5.5 + - - +
547A LEU 3.0 21.8 + - - -
565A ILE* 3.8 19.7 - - - -
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Residues in contact with ILE 544 (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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327A ILE* 4.1 7.2 - - + +
330A HIS* 3.8 21.3 - - + +
331A LEU* 3.7 43.9 - - + +
334A ARG* 4.3 15.9 - - + -
337A ARG* 6.1 0.7 - - - +
493A TRP* 4.4 6.3 - - + -
540A ILE* 2.7 39.4 + - + +
541A ARG* 4.0 8.1 - - - +
543A GLY* 1.3 70.3 - - - +
545A GLU* 1.3 65.3 + - - +
547A LEU* 3.7 17.2 - - + +
548A TYR* 2.9 29.5 + - - +
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Residues in contact with GLU 545 (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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334A ARG* 2.6 42.2 + - - +
337A ARG* 5.4 0.5 + - - -
541A ARG 3.2 17.9 + - - +
542A ASP* 3.3 7.8 + - - +
543A GLY 3.2 0.4 - - - -
544A ILE* 1.3 82.6 - - + +
546A ALA* 1.3 63.7 + - - +
548A TYR* 3.4 7.1 - - - +
549A ARG* 3.0 64.7 + - - +
632A TRP* 4.3 7.6 - - + +
635A LYS* 5.8 5.8 - - - +
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Residues in contact with ALA 546 (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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542A ASP 3.2 2.6 + - - -
543A GLY 3.2 8.3 + - - +
545A GLU* 1.3 78.0 - - - +
547A LEU* 1.3 65.0 + - - +
549A ARG* 3.2 7.1 + - - +
550A ILE* 3.0 25.7 + - - +
565A ILE* 3.8 21.3 - - + -
630A LEU* 3.7 12.8 - - + +
632A TRP* 3.6 36.5 - - + +
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Residues in contact with LEU 547 (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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327A ILE* 4.2 12.8 - - + -
331A LEU* 3.6 35.0 - - + -
387A LEU* 4.2 9.2 - - + -
428A ILE* 3.9 27.6 - - + -
488A PHE* 4.0 24.9 - - + -
493A TRP* 4.2 14.4 - - + -
543A GLY 3.0 12.5 + - - +
544A ILE* 3.7 19.5 - - + +
546A ALA* 1.3 75.2 - - - +
548A TYR* 1.3 63.8 + - - +
550A ILE* 3.0 20.2 + - + +
551A ILE* 3.0 16.9 + - + +
565A ILE* 4.1 3.0 - - - +
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Residues in contact with TYR 548 (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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331A LEU* 4.7 3.8 - - + +
334A ARG* 3.4 51.6 - - + +
335A LEU* 4.0 17.9 - - + -
338A GLU* 3.1 36.8 + - + +
340A HIS* 4.0 3.1 - - - -
341A TYR* 3.8 21.3 - + - -
544A ILE 2.9 17.9 + - - +
545A GLU* 3.4 11.4 - - - +
547A LEU* 1.3 78.8 - - - +
549A ARG* 1.3 63.1 + - + +
551A ILE* 3.0 12.8 + - - +
552A GLU* 2.9 55.9 + - + +
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Residues in contact with ARG 549 (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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545A GLU* 3.0 46.6 + - - +
546A ALA* 3.2 7.2 + - - +
548A TYR* 1.3 80.9 - - + +
550A ILE* 1.3 61.0 + - - +
552A GLU* 3.4 12.1 - - + +
553A ASN* 2.8 26.3 + - - -
554A ALA 4.5 1.2 + - - -
630A LEU* 2.9 38.9 + - + +
631A ASP* 2.7 34.1 + - - +
632A TRP* 3.7 12.3 - - - +
635A LYS* 4.4 18.2 - - - +
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Residues in contact with ILE 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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426A ARG* 2.7 37.2 + - - +
428A ILE* 3.9 15.3 - - + -
486A THR* 3.6 27.6 - - + -
488A PHE* 4.0 17.9 - - + -
546A ALA 3.0 16.3 + - - +
547A LEU* 3.0 14.1 + - + +
549A ARG* 1.3 75.9 - - - +
551A ILE* 1.3 58.5 + - - +
553A ASN* 3.3 6.8 + - - +
558A CYS* 4.0 6.7 - - - -
563A ILE* 3.9 19.5 - - + -
565A ILE* 4.0 25.6 - - + -
630A LEU* 3.9 16.4 - - + -
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Residues in contact with ILE 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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316A THR* 5.6 1.1 - - + +
318A VAL* 4.6 14.1 - - + -
331A LEU* 3.7 42.2 - - + -
335A LEU* 4.2 14.8 - - + -
341A TYR* 3.6 32.3 + - + +
385A VAL* 5.1 12.5 - - + +
387A LEU* 5.3 3.1 - - + -
426A ARG* 3.1 17.9 + - - +
428A ILE* 3.6 18.8 - - + -
547A LEU* 3.0 19.7 + - + +
548A TYR* 3.0 8.0 + - - +
550A ILE* 1.3 78.0 - - - +
552A GLU* 1.3 62.4 + - - +
553A ASN* 4.0 0.2 - - - +
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Residues in contact with GLU 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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340A HIS* 3.2 19.5 + - - -
341A TYR* 2.5 25.7 + - - +
548A TYR* 2.9 46.5 + - + +
549A ARG* 3.4 15.0 - - + +
551A ILE* 1.3 78.6 - - - +
553A ASN* 1.3 69.4 + - - +
554A ALA* 3.3 9.6 + - + +
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Residues in contact with ASN 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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426A ARG* 3.6 26.5 - - - +
484A GLN* 3.7 8.7 - - - +
549A ARG 2.8 13.6 + - - -
550A ILE 3.6 11.0 - - - +
551A ILE 3.3 0.6 - - - +
552A GLU* 1.3 80.1 - - - +
554A ALA* 1.3 56.0 + - - +
555A GLY 3.2 0.5 + - - -
556A ASN* 2.7 47.9 + - - +
558A CYS* 2.9 35.3 + - - +
559A ASP* 3.0 24.2 + - - -
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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