Contacts of the helix formed by residues 571 - 582 (chain D) in PDB entry 4E2I
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 SER 571 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387D TRP* 3.2 27.3 - - - -
438D ALA* 3.5 11.1 - - - +
441D GLU* 3.6 9.9 + - - -
567D ARG* 3.2 24.9 - - - -
568D ILE 3.1 9.0 + - - -
569D ILE 3.6 0.6 - - - -
570D GLN* 1.3 78.8 - - - +
572D GLY* 1.3 66.2 + - - +
573D ILE* 3.3 9.4 + - - +
574D ALA* 3.2 16.7 + - - +
575D LEU* 3.6 2.6 + - - +
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Residues in contact with GLY 572 (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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368D LEU* 4.6 3.0 - - - +
438D ALA* 3.4 22.6 + - - +
441D GLU* 2.8 21.5 + - - +
442D LEU* 3.6 26.3 - - - +
571D SER* 1.3 70.5 - - - +
573D ILE* 1.3 66.2 + - - +
575D LEU 3.3 1.8 + - - -
576D LEU* 3.1 17.3 + - - +
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Residues in contact with ILE 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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368D LEU* 3.3 49.8 - - + +
371D ARG* 4.1 18.8 - - + +
372D MET* 3.5 33.4 - - + -
375D MET* 4.4 12.1 - - + -
376D PHE* 4.7 0.2 - - + -
387D TRP* 3.6 25.6 - - + -
441D GLU* 4.6 4.5 - - - +
571D SER* 3.2 7.8 - - - +
572D GLY* 1.3 76.4 - - - +
574D ALA* 1.3 61.1 + - - +
576D LEU* 3.3 6.6 + - - +
577D LEU* 3.2 21.7 + - + +
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Residues in contact with ALA 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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387D TRP* 3.9 11.2 - - - +
391D VAL* 3.8 9.7 - - + +
394D LEU* 3.9 16.8 - - + +
568D ILE* 3.0 40.8 - - + +
571D SER* 3.2 9.7 + - - +
573D ILE* 1.3 77.0 - - - +
575D LEU* 1.3 64.1 + - - +
577D LEU* 3.2 18.8 + - - +
578D MET* 3.2 9.2 + - - +
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Residues in contact with LEU 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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394D LEU* 4.0 18.6 - - + -
401D MET* 5.5 0.4 - - + -
405D VAL* 4.7 4.0 - - + -
435D LEU* 4.2 15.5 - - + -
438D ALA* 3.5 34.3 - - + +
439D LEU* 3.5 35.7 - - + +
442D LEU* 3.6 20.6 - - + -
571D SER 3.6 1.8 + - - +
572D GLY 3.3 5.5 + - - +
574D ALA* 1.3 77.4 - - - +
576D LEU* 1.3 59.7 + - - +
578D MET* 3.1 31.9 + - + +
579D LEU* 2.9 33.8 + - - +
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Residues in contact with LEU 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D PHE* 3.5 39.0 - - + +
368D LEU* 3.5 28.7 - - + -
369D LEU* 3.5 17.5 - - + -
372D MET* 3.5 27.4 - - - -
442D LEU* 3.8 9.6 - - + +
572D GLY 3.1 12.3 + - - +
573D ILE* 3.3 11.4 - - - +
574D ALA 3.1 0.2 - - - -
575D LEU* 1.3 77.6 - - - +
577D LEU* 1.3 61.2 + - - +
579D LEU* 3.0 5.3 + - + +
580D ILE* 3.0 44.6 + - + +
588D PHE* 5.4 1.3 - - + -
596D ILE* 6.0 1.1 - - + -
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Residues in contact with LEU 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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372D MET* 3.4 32.3 - - + -
376D PHE* 4.6 2.2 - - + -
384D ILE* 4.3 9.9 - - + -
387D TRP* 3.6 36.3 - - + +
388D MET* 3.5 31.9 - - + +
391D VAL* 3.9 4.0 - - + -
573D ILE 3.2 10.3 + - - +
574D ALA* 3.2 9.3 + - - +
576D LEU* 1.3 79.3 - - - +
578D MET* 1.3 56.5 + - - +
580D ILE* 3.5 7.9 + - + +
581D TRP* 3.1 30.1 + - - +
599D TRP* 4.9 0.9 - - + -
603D LEU* 3.7 27.9 - - + +
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Residues in contact with MET 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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391D VAL* 3.5 37.7 - - + +
394D LEU* 4.4 11.4 - - + -
395D HIS* 4.5 5.6 - - - -
401D MET* 3.5 26.5 - - + -
402D ASP* 3.7 23.1 - - + +
405D VAL* 3.5 31.9 - - + -
574D ALA 3.2 9.6 + - - +
575D LEU* 3.1 27.9 + - + +
577D LEU* 1.3 78.5 - - - +
579D LEU* 1.3 62.1 + - + +
581D TRP* 4.4 1.8 - - - -
582D TYR* 3.4 30.0 + - + +
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Residues in contact with LEU 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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365D PHE* 3.5 29.6 - - + -
402D ASP* 4.5 4.7 - - - +
405D VAL* 3.5 28.9 - - + -
406D TYR* 4.6 3.1 - - + +
409D LEU* 3.9 13.7 - - + -
442D LEU* 3.8 26.0 - - + -
575D LEU 2.9 17.9 + - - +
576D LEU* 3.0 7.8 + - + +
578D MET* 1.3 81.6 - - + +
580D ILE* 1.3 59.0 + - - +
583D ARG* 3.2 48.0 + - + +
588D PHE* 3.4 17.8 - - + -
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Residues in contact with ILE 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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369D LEU* 3.9 28.7 - - + -
372D MET* 5.4 0.2 - - - -
576D LEU* 3.0 32.5 + - + +
577D LEU* 4.1 11.9 - - + +
579D LEU* 1.3 76.5 - - - +
581D TRP* 1.3 57.1 + - - +
583D ARG 4.6 0.9 - - - -
588D PHE* 4.4 13.2 - - + -
596D ILE* 3.6 39.3 - - + +
599D TRP* 4.1 20.9 - - + -
600D LYS* 2.7 41.2 + - + +
603D LEU* 5.0 5.8 - - + -
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Residues in contact with TRP 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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388D MET* 3.5 26.7 - - + -
391D VAL* 5.2 1.6 - - + -
577D LEU 3.1 20.3 + - - +
578D MET* 3.8 1.3 + - - +
579D LEU 3.3 0.2 - - - -
580D ILE* 1.3 81.4 - - - +
582D TYR* 1.3 90.8 + + + +
600D LYS* 4.2 4.7 + - - -
603D LEU* 3.6 40.4 - - + +
604D ASP* 5.1 8.1 - - - -
607D PHE* 3.8 26.9 - - + -
608D SER 3.8 9.9 - - - -
609D LEU* 4.6 17.4 - - + +
612D TYR* 3.4 47.6 - + + -
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Residues in contact with TYR 582 (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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391D VAL* 4.5 0.2 - - + -
395D HIS* 3.3 26.8 - + - -
402D ASP* 3.2 31.2 - - + +
578D MET* 3.4 24.7 + - + +
581D TRP* 1.3 97.2 - + + +
583D ARG* 1.3 68.5 + - - +
584D PRO* 3.4 7.1 - - - +
600D LYS* 4.6 1.9 + - - -
612D TYR* 2.8 42.4 + + - -
613D GLN* 5.1 1.3 + - - -
616D LYS* 3.3 19.4 + - - -
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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