Contacts of the helix formed by residues 542 - 554 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D HIS* 3.8 33.9 + - + +
443D MET* 4.7 2.0 - - + -
485D LEU* 3.8 13.0 - - + -
538D PHE* 3.1 32.1 + - + +
540D ASP 3.7 0.8 - - - -
541D TYR* 1.3 81.3 - - - +
543D VAL* 1.3 66.9 + - - +
544D HIS 3.6 0.9 - - - -
545D PRO* 3.6 4.1 - - - +
546D LEU* 3.3 23.2 + - - +
600D ILE* 3.3 40.4 - - + -
604D PHE* 3.1 43.3 - - + -
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Residues in contact with VAL 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D LEU* 3.7 15.7 - - + +
488D PRO* 4.1 10.1 - - + -
489D THR* 4.4 1.6 - - + -
538D PHE* 3.0 58.5 + - + +
539D ILE* 4.1 7.0 - - + -
542D ILE* 1.3 72.3 - - + +
544D HIS* 1.3 61.0 + - - +
546D LEU* 3.4 5.5 + - - +
547D TRP* 2.9 50.9 + - + +
565D LEU* 4.0 21.8 - - + -
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Residues in contact with HIS 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539D ILE* 2.9 27.8 + - + +
540D ASP* 4.7 3.4 - - - +
543D VAL* 1.3 73.9 - - - +
545D PRO* 1.3 64.1 - - + +
547D TRP 4.6 0.2 - - - +
548D GLU* 2.9 60.3 + - + +
562D LEU* 4.3 9.3 - - + +
565D LEU* 3.8 24.2 - - + +
566D GLU* 3.2 39.0 + - + -
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Residues in contact with PRO 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D LEU* 3.9 17.4 - - + +
450D LYS* 5.2 5.9 - - - +
539D ILE 3.6 2.2 - - - +
540D ASP 3.4 22.2 - - - +
541D TYR* 3.9 14.6 - - - +
542D ILE 3.6 12.8 - - - +
544D HIS* 1.3 94.9 - - + +
546D LEU* 1.3 55.4 + - - +
548D GLU* 4.0 8.4 - - - +
549D THR* 2.6 34.5 + - - -
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Residues in contact with LEU 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D HIS* 4.1 12.6 - - + -
446D LEU* 3.8 23.6 - - + +
449D LEU* 4.2 3.9 - - + +
478D ASN* 4.3 17.0 - - - +
481D HIS* 4.0 16.6 - - + -
482D CYS* 3.8 34.1 - - - -
485D LEU* 3.9 31.4 - - + -
542D ILE 3.3 17.1 + - - +
543D VAL* 3.6 3.4 - - - +
545D PRO* 1.3 78.8 - - - +
547D TRP* 1.3 63.1 + - + +
549D THR* 3.3 5.4 + - - -
550D TRP* 3.0 25.7 + - - +
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Residues in contact with TRP 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D TRP* 3.5 36.8 - + - -
341D LEU* 3.7 19.5 - - + -
482D CYS* 3.5 34.2 + - + +
485D LEU 3.2 18.7 + - - -
486D SER* 4.1 2.2 - - - -
489D THR* 3.8 15.4 - - + +
543D VAL* 2.9 42.4 + - + +
546D LEU* 1.3 78.4 - - + +
548D GLU* 1.3 55.6 + - - +
550D TRP* 3.5 30.8 - + + +
551D ALA* 2.6 37.1 + - + +
558D ALA* 4.9 4.5 - - + -
561D ILE* 3.8 24.9 - - + -
562D LEU* 3.9 18.6 - - + +
565D LEU* 4.4 4.0 - - + -
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Residues in contact with GLU 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D HIS* 2.9 48.2 + - + +
545D PRO* 4.0 7.0 - - - +
547D TRP* 1.3 76.2 - - - +
549D THR* 1.3 58.7 + - - +
551D ALA* 3.4 2.3 + - - +
552D ASP* 3.1 36.7 + - - +
562D LEU* 3.7 20.9 - - + +
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Residues in contact with THR 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D LEU* 3.7 10.9 - - + +
449D LEU* 3.7 42.0 - - + +
450D LYS* 3.8 27.5 - - + +
453D VAL* 3.6 10.7 - - + +
545D PRO 2.6 20.6 + - - -
546D LEU 3.5 7.9 - - - -
548D GLU* 1.3 73.8 - - - +
550D TRP* 1.3 64.2 + - - +
552D ASP* 3.3 10.1 + - - +
553D LEU* 3.1 17.2 + - - +
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Residues in contact with TRP 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D LEU* 3.8 24.7 - - + +
344D THR* 5.6 1.4 - - + +
347D LEU* 4.5 4.3 - - + -
449D LEU* 3.9 16.5 - - + +
475D VAL* 3.9 22.9 - - + -
478D ASN* 4.4 5.2 - - + -
479D MET* 3.6 49.8 - - + -
482D CYS* 4.0 22.7 - - - -
546D LEU 3.0 13.9 + - - +
547D TRP* 3.5 29.2 - + + +
549D THR* 1.3 71.9 - - - +
551D ALA* 1.3 68.0 + - - +
553D LEU* 2.9 36.4 + - + +
554D VAL* 3.1 42.5 + - + +
558D ALA* 4.4 4.8 - - + +
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Residues in contact with ALA 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D TRP* 2.6 20.8 + - + +
548D GLU 3.5 6.3 - - - +
549D THR 3.3 0.2 - - - -
550D TRP* 1.3 72.6 - - - +
552D ASP* 1.3 58.4 + - - +
554D VAL* 3.6 1.8 + - - +
555D HIS* 3.0 32.8 + - + +
556D PRO* 5.1 0.3 - - - +
558D ALA* 4.0 27.7 + - + +
559D GLN* 5.7 2.0 - - - +
562D LEU* 3.8 25.8 - - + -
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Residues in contact with ASP 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D VAL* 3.9 22.7 - - + +
456D LYS* 3.0 24.6 + - - +
548D GLU* 3.1 26.3 + - - +
549D THR* 3.5 10.6 - - - +
550D TRP 3.2 0.2 - - - -
551D ALA* 1.3 77.1 - - - +
553D LEU* 1.3 60.7 + - - +
554D VAL 3.4 0.2 + - - -
555D HIS* 3.6 17.7 + - - +
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Residues in contact with LEU 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ALA* 4.9 2.4 - - - +
347D LEU* 5.9 0.4 - - + -
449D LEU* 4.0 12.3 - - + -
452D MET* 4.4 26.5 - - + +
453D VAL* 4.0 21.5 - - + +
456D LYS* 3.0 24.7 + - + +
464D LEU* 3.7 40.2 - - + +
475D VAL* 4.4 11.2 - - + -
549D THR 3.1 11.7 + - - +
550D TRP* 2.9 44.9 + - + +
552D ASP* 1.3 76.2 - - - +
554D VAL* 1.3 63.3 + - + +
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Residues in contact with VAL 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D THR* 4.1 20.2 - - + +
346D ALA* 3.8 18.2 - - + +
347D LEU* 4.7 7.6 - - + -
456D LYS* 4.7 0.4 - - - -
464D LEU* 5.9 0.4 - - + -
550D TRP* 3.1 48.6 + - + +
551D ALA 4.0 0.4 - - - +
553D LEU* 1.3 86.7 - - + +
555D HIS* 1.3 67.6 + - - +
557D ASP* 2.9 32.2 + - + +
558D ALA* 4.0 19.5 - - + +
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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