Contacts of the helix formed by residues 572 - 581 (chain D) in PDB entry 4IVE
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 LEU 572 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569D HIS* 3.5 9.3 + - + +
571D THR* 1.3 88.1 - - + +
573D ALA* 1.3 59.0 + - - +
574D GLY 3.3 3.1 - - - -
575D LYS* 3.1 19.0 + - + +
576D ILE* 2.9 45.0 + - + +
606D VAL* 4.6 23.8 - - + +
609D LEU* 4.5 24.7 - - + -
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Residues in contact with ALA 573 (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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562D PHE* 3.7 17.9 - - + -
565D ILE* 3.8 10.7 - - + +
566D GLN* 3.7 26.7 - - + +
569D HIS 3.0 18.2 + - - +
570D PRO 3.6 11.0 + - - +
571D THR 3.5 2.2 - - - -
572D LEU* 1.3 74.6 - - - +
574D GLY* 1.3 54.4 + - - +
576D ILE* 4.0 0.2 - - - +
577D THR* 2.6 39.6 + - - -
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Residues in contact with GLY 574 (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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562D PHE* 3.6 19.1 - - - -
570D PRO 5.0 0.8 + - - -
571D THR 5.2 1.2 + - - -
572D LEU 3.3 0.8 - - - -
573D ALA* 1.3 77.5 - - - +
575D LYS* 1.3 59.3 + - - +
577D THR* 3.7 3.5 - - - +
578D GLY* 3.3 17.7 + - - -
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Residues in contact with LYS 575 (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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554C LYS* 5.4 5.3 - - - +
582C GLU* 3.0 57.9 + - + +
584C ASP* 5.7 5.6 + - - -
572D LEU* 3.1 21.1 + - + +
574D GLY* 1.3 70.4 - - - +
576D ILE* 1.3 65.5 + - - +
578D GLY* 3.3 3.2 + - - -
579D MSE 3.1 28.5 + - - +
609D LEU* 4.1 21.8 - - + -
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Residues in contact with ILE 576 (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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565D ILE* 3.8 20.6 - - + -
569D HIS* 4.3 9.4 - - + -
572D LEU* 2.9 43.0 + - + +
573D ALA 4.3 0.4 - - - +
575D LYS* 1.3 71.3 - - - +
577D THR* 1.3 60.0 + - - +
579D MSE 3.1 9.3 + - - +
580D LEU* 2.8 43.3 + - + +
602D VAL* 4.1 16.4 - - + -
605D ALA* 3.8 22.2 - - + -
606D VAL* 3.7 24.7 - - + -
609D LEU* 4.3 12.8 - - + -
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Residues in contact with THR 577 (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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551B GLN* 5.4 2.5 - - - +
558D GLY* 3.9 34.1 - - - +
561D LEU* 4.2 6.5 - - + +
562D PHE* 3.6 25.9 - - + +
565D ILE* 3.4 20.7 - - - +
573D ALA 2.6 23.4 + - - -
574D GLY 3.7 5.4 - - - -
576D ILE* 1.3 75.4 - - - +
578D GLY* 1.3 63.6 + - - +
580D LEU* 3.3 1.9 + - - +
581D LEU* 3.0 32.6 + - + +
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Residues in contact with GLY 578 (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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550B PRO* 3.5 31.4 - - - +
551B GLN* 5.3 3.6 - - - -
582C GLU* 4.6 12.3 - - - -
574D GLY 3.3 11.9 + - - -
575D LYS* 3.3 4.8 + - - -
577D THR* 1.3 78.5 - - - +
579D MSE 1.3 60.6 + - - +
581D LEU* 3.5 12.5 + - - -
582D GLU* 4.2 2.8 - - - +
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Residues in contact with MSE 579 (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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579C MSE 3.6 40.8 - - + +
582C GLU* 3.5 19.3 - - + -
575D LYS 3.1 16.5 + - - +
576D ILE* 3.5 11.7 - - - +
578D GLY* 1.3 74.5 - - - +
580D LEU* 1.4 60.0 + - + +
582D GLU* 3.1 31.2 + - - +
583D ILE* 5.1 0.2 - - - +
605D ALA* 3.7 25.4 - - + +
608D VAL* 3.6 32.3 - - + -
609D LEU* 3.7 39.0 - - + -
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Residues in contact with LEU 580 (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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608C VAL* 3.7 27.4 - - + -
561D LEU* 4.1 11.0 - - + -
565D ILE* 3.8 22.0 - - + -
576D ILE* 2.8 24.6 + - + +
577D THR 4.0 3.1 - - - +
579D MSE 1.4 67.2 - - - +
581D LEU* 1.4 56.4 + - - +
582D GLU 3.0 5.6 - - - -
583D ILE* 3.1 40.5 + - + +
588D LEU* 3.2 9.3 - - - +
591D MSE 3.9 19.1 - - + -
598D LEU* 3.9 9.9 - - + -
601D LYS* 3.8 18.6 - - + +
602D VAL* 3.9 13.0 - - + -
605D ALA* 4.1 8.3 - - + -
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Residues in contact with LEU 581 (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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550B PRO* 3.8 15.8 - - + +
551B GLN* 3.4 39.3 - - + +
554D LYS* 2.9 58.3 + - + +
557D LEU* 3.9 12.6 - - + -
558D GLY* 3.6 21.8 - - - +
561D LEU* 4.0 11.0 - - + -
577D THR* 3.0 26.0 + - + +
578D GLY* 3.6 9.6 - - - +
579D MSE 3.2 1.0 - - - -
580D LEU* 1.4 74.4 - - - +
582D GLU* 1.3 56.4 + - - +
583D ILE 3.3 0.9 - - - -
588D LEU* 4.0 7.6 - - + -
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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