Contacts of the helix formed by residues 542 - 554 (chain A) in PDB entry 3IAD
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 542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A HIS* 3.6 31.9 - - + +
443A MET* 5.0 2.7 - - + -
485A LEU* 4.3 6.7 - - + -
538A PHE* 3.1 22.0 + - + +
540A ASP 3.7 0.4 - - - -
541A TYR* 1.3 81.4 - - - +
543A VAL* 1.3 70.5 + - - +
544A HIS 3.5 1.3 - - - -
545A PRO* 3.4 4.6 - - - +
546A LEU* 3.3 22.2 + - - +
600A ILE* 3.3 33.7 - - + -
604A PHE* 3.1 63.0 - - + -
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LEU* 3.8 23.6 - - + +
488A PRO* 4.1 8.3 - - + -
489A THR* 4.6 0.2 - - + -
538A PHE* 2.9 63.3 + - + +
539A ILE* 3.8 7.9 - - + -
542A ILE* 1.3 74.8 - - + +
544A HIS* 1.3 63.7 + - - +
546A LEU* 3.3 5.8 + - - +
547A TRP* 3.1 33.1 + - + +
565A LEU* 3.8 23.6 - - + -
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Residues in contact with HIS 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ILE* 2.7 35.3 + - + +
540A ASP* 4.6 4.0 + - - +
543A VAL* 1.3 71.5 - - - +
545A PRO* 1.3 68.2 - - + +
548A GLU* 2.9 57.3 + - + +
562A LEU* 3.8 21.8 - - + +
565A LEU* 3.6 15.6 - - + +
566A GLU* 3.0 36.0 + - + +
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Residues in contact with PRO 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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446A LEU* 3.9 21.0 - - + +
450A LYS* 5.6 3.9 - - - +
539A ILE 3.5 2.0 - - - +
540A ASP 3.3 27.6 - - - +
541A TYR* 3.6 16.8 - - - +
542A ILE 3.4 11.0 - - - +
544A HIS* 1.3 93.6 - - + +
546A LEU* 1.3 58.7 + - - +
548A GLU* 4.0 7.5 - - + +
549A THR* 2.9 29.5 + - - -
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Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A HIS* 4.1 9.6 - - + -
446A LEU* 3.8 23.9 - - + +
449A LEU* 4.3 3.8 - - + +
478A ASN* 4.1 15.5 - - - +
481A HIS* 3.5 34.1 - - + +
482A CYS* 3.9 31.0 - - - -
485A LEU* 3.7 23.1 - - + -
542A ILE 3.3 10.3 + - - +
543A VAL* 3.5 9.2 - - - +
544A HIS 3.2 0.6 - - - -
545A PRO* 1.3 79.5 - - - +
547A TRP* 1.3 61.8 + - + +
549A THR* 3.0 8.3 + - - -
550A TRP* 3.0 25.2 + - - +
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Residues in contact with TRP 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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268A TRP* 3.6 34.5 - + - -
341A LEU* 3.8 27.4 - - + -
482A CYS* 3.3 36.1 + - + +
485A LEU 3.2 18.9 + - - -
486A SER* 4.0 2.9 - - - -
489A THR* 3.7 14.1 - - + +
543A VAL* 3.1 35.3 + - + +
544A HIS 4.3 0.4 - - - +
546A LEU* 1.3 85.1 - - + +
548A GLU* 1.3 60.4 + - - +
550A TRP* 3.8 24.5 - + + +
551A ALA* 2.8 28.9 + - - +
558A ALA* 5.2 4.9 - - + +
561A ILE* 3.9 23.6 - - + -
562A LEU* 4.2 19.0 - - + +
565A LEU* 4.3 4.5 - - + -
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Residues in contact with GLU 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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544A HIS* 2.9 46.7 + - + +
545A PRO* 4.0 8.1 - - - +
547A TRP* 1.3 76.1 - - - +
549A THR* 1.3 58.6 + - - +
551A ALA* 3.3 7.1 + - - +
552A ASP* 2.9 41.1 + - - +
562A LEU* 4.2 13.3 - - + +
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Residues in contact with THR 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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446A LEU* 3.9 9.2 - - + +
449A LEU* 3.4 28.9 - - + -
450A LYS* 3.8 29.7 - - + +
453A VAL* 3.6 20.6 - - + +
545A PRO 2.9 13.5 + - - -
546A LEU 3.0 9.2 + - - -
548A GLU* 1.3 75.9 - - - +
550A TRP* 1.3 60.7 - - - +
552A ASP* 3.3 9.6 + - - +
553A LEU* 3.0 24.1 + - - +
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Residues in contact with TRP 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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341A LEU* 3.6 24.5 - - + +
344A THR* 5.5 2.4 - - + +
347A LEU* 4.4 5.6 - - + -
449A LEU* 3.9 13.6 - - + +
475A VAL* 3.8 26.9 - - + -
478A ASN* 4.3 5.2 - - + -
479A MET* 3.8 48.0 - - + -
482A CYS* 4.1 24.9 - - - -
546A LEU 3.0 12.6 + - - +
547A TRP* 3.8 30.1 - + + +
549A THR* 1.3 76.8 - - - +
551A ALA* 1.3 62.6 + - - +
553A LEU* 3.1 26.1 + - + +
554A VAL* 3.0 55.0 + - + +
558A ALA* 4.6 4.5 - - + +
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Residues in contact with ALA 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 TRP 2.8 20.1 + - - +
548A GLU 3.5 5.4 - - - +
549A THR 3.3 0.2 - - - -
550A TRP* 1.3 77.7 - - - +
552A ASP* 1.3 57.7 + - - +
554A VAL* 3.6 1.0 - - - -
555A HIS* 2.8 35.0 + - + +
556A PRO* 5.1 0.5 - - - +
558A ALA* 4.0 27.4 - - + +
559A GLN* 5.8 2.2 - - - +
562A LEU* 3.9 22.0 - - + -
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Residues in contact with ASP 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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453A VAL* 3.9 22.0 - - + +
456A LYS* 4.0 12.6 - - - +
548A GLU* 2.9 31.2 + - - +
549A THR* 3.6 11.7 - - - +
550A TRP 3.2 0.2 - - - -
551A ALA* 1.3 75.3 - - - +
553A LEU* 1.3 65.6 + - - +
554A VAL 3.4 0.2 + - - -
555A HIS* 3.6 21.6 + - - +
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Residues in contact with LEU 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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346A ALA* 5.1 2.1 - - - +
347A LEU* 5.7 0.2 - - + -
449A LEU* 4.2 11.4 - - + -
452A MET* 4.2 28.0 - - + +
453A VAL* 4.1 21.2 - - + +
456A LYS* 3.2 29.5 + - + -
464A LEU* 4.0 36.4 - - + +
475A VAL* 4.4 12.6 - - + -
549A THR 3.0 13.3 + - - +
550A TRP* 3.1 38.6 + - + +
552A ASP* 1.3 75.1 - - - +
554A VAL* 1.3 64.2 + - + +
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A THR* 4.4 18.6 - - + +
346A ALA* 4.0 20.7 - - + +
347A LEU* 4.6 8.7 - - + -
456A LYS* 5.8 0.2 - - - -
464A LEU* 5.4 0.4 - - + -
550A TRP* 3.0 56.0 + - + +
551A ALA* 4.0 6.1 - - - +
553A LEU* 1.3 87.4 - - + +
555A HIS* 1.3 67.3 + - - +
557A ASP* 3.1 26.7 + - + +
558A ALA* 4.1 13.0 - - + +
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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