Contacts of the helix formed by residues 571 - 582 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387E TRP* 3.2 27.3 - - - -
438E ALA* 3.5 11.0 - - - +
441E GLU* 3.6 9.7 + - - -
567E ARG* 3.2 25.6 - - - -
568E ILE 3.1 9.6 + - - -
569E ILE 3.6 0.4 - - - -
570E GLN* 1.3 79.6 - - - +
572E GLY* 1.3 66.8 + - - +
573E ILE* 3.3 9.0 + - - +
574E ALA* 3.2 16.3 + - - +
575E LEU 3.6 2.6 + - - -
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Residues in contact with GLY 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368E LEU* 4.6 2.6 - - - +
438E ALA* 3.4 23.3 + - - +
441E GLU* 2.8 20.8 + - - +
442E LEU* 3.6 25.8 - - - +
571E SER* 1.3 70.2 - - - +
573E ILE* 1.3 66.8 + - - +
575E LEU* 3.3 2.4 + - - +
576E LEU* 3.1 18.0 + - - +
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Residues in contact with ILE 573 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368E LEU* 3.3 50.0 - - + +
371E ARG* 4.1 20.0 - - + +
372E MET* 3.5 33.2 - - + -
375E MET* 4.4 12.1 - - + -
376E PHE* 4.7 0.4 - - + -
387E TRP* 3.6 24.9 - - + -
441E GLU* 4.6 4.5 - - - +
571E SER* 3.2 7.6 - - - +
572E GLY* 1.3 77.1 - - - +
574E ALA* 1.3 62.2 + - - +
576E LEU* 3.3 6.2 + - - +
577E LEU* 3.2 21.7 + - + +
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Residues in contact with ALA 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E TRP* 3.9 10.4 - - - +
390E GLY 5.6 0.7 - - - -
391E VAL* 3.8 9.1 - - + +
394E LEU* 3.9 17.2 - - + +
568E ILE* 3.0 40.4 - - + +
571E SER* 3.2 9.5 + - - +
572E GLY 3.1 0.2 - - - -
573E ILE* 1.3 77.1 - - - +
575E LEU* 1.3 65.2 + - - +
577E LEU* 3.2 19.1 + - - +
578E MET* 3.2 9.4 + - - +
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Residues in contact with LEU 575 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E LEU* 4.0 18.4 - - + -
405E VAL* 4.7 4.3 - - + -
435E LEU* 4.3 15.9 - - + -
438E ALA* 3.5 35.0 - - + +
439E LEU* 3.5 34.8 - - + +
442E LEU* 3.6 20.0 - - + -
571E SER 3.6 1.1 + - - +
572E GLY 3.3 5.9 + - - +
574E ALA* 1.3 76.6 - - - +
576E LEU* 1.3 60.6 + - - +
578E MET* 3.1 32.5 + - + +
579E LEU* 2.9 33.4 + - - +
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Residues in contact with LEU 576 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E PHE* 3.5 39.3 - - + +
368E LEU* 3.5 27.8 - - + -
369E LEU* 3.5 16.4 - - + -
372E MET* 3.5 28.3 - - - -
442E LEU* 3.8 10.3 - - + +
572E GLY 3.1 13.4 + - - +
573E ILE* 3.4 11.0 - - - +
574E ALA 3.1 0.4 - - - -
575E LEU* 1.3 76.7 - - - +
577E LEU* 1.3 61.5 + - - +
579E LEU* 3.0 6.0 + - + +
580E ILE* 3.0 44.9 + - + +
588E PHE* 5.4 1.3 - - + -
596E ILE* 6.0 0.7 - - + -
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Residues in contact with LEU 577 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372E MET* 3.4 32.1 - - + -
376E PHE* 4.6 2.2 - - + -
384E ILE* 4.3 9.9 - - + -
387E TRP* 3.6 36.6 - - + +
388E MET* 3.5 33.5 - - + +
391E VAL* 3.9 3.8 - - + -
573E ILE 3.2 10.3 + - - +
574E ALA* 3.2 9.0 + - - +
576E LEU* 1.3 80.1 - - - +
578E MET* 1.3 56.4 + - - +
580E ILE* 3.6 8.4 + - + +
581E TRP* 3.1 30.0 + - - +
599E TRP* 4.9 0.4 - - + -
603E LEU* 3.6 27.5 - - + +
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Residues in contact with MET 578 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E VAL* 3.5 39.5 - - + +
394E LEU* 4.4 11.0 - - - -
395E HIS* 4.5 6.1 - - - -
401E MET* 3.5 25.1 - - + -
402E ASP* 3.7 22.9 - - + +
405E VAL* 3.5 32.5 - - + -
574E ALA 3.2 9.3 + - - +
575E LEU* 3.1 28.8 + - + +
577E LEU* 1.3 78.2 - - - +
579E LEU* 1.3 61.3 + - + +
581E TRP* 4.4 1.3 - - - -
582E TYR* 3.4 29.0 + - + +
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Residues in contact with LEU 579 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E PHE* 3.5 30.1 - - + -
402E ASP* 4.5 5.2 - - - +
405E VAL* 3.5 29.6 - - + -
406E TYR* 4.6 3.1 - - + +
409E LEU* 3.9 14.6 - - + -
442E LEU* 3.8 24.7 - - + -
575E LEU 2.9 18.3 + - - +
576E LEU* 3.5 7.2 - - + +
578E MET* 1.3 81.4 - - + +
580E ILE* 1.3 57.8 + - - +
583E ARG* 3.2 48.4 + - + +
588E PHE* 3.5 17.2 - - + -
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Residues in contact with ILE 580 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E LEU* 3.9 28.7 - - + -
372E MET* 5.4 0.2 - - - -
576E LEU* 3.0 31.8 + - + +
577E LEU* 4.1 12.1 - - + +
579E LEU* 1.3 76.7 - - - +
581E TRP* 1.3 59.7 + - - +
583E ARG 4.6 1.1 - - - -
588E PHE* 4.4 12.6 - - + -
596E ILE* 3.6 37.7 - - + +
599E TRP* 4.1 21.8 - - + -
600E LYS* 2.7 41.2 + - + +
603E LEU* 5.0 6.0 - - + +
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Residues in contact with TRP 581 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388E MET* 3.5 26.5 - - + -
391E VAL* 5.2 2.5 - - + -
577E LEU 3.1 19.3 + - - +
578E MET* 4.4 1.3 - - - -
579E LEU 3.3 0.2 - - - -
580E ILE* 1.3 81.4 - - - +
582E TYR* 1.3 90.0 + + + +
600E LYS* 4.2 4.2 + - - -
603E LEU* 3.6 38.8 - - + -
604E ASP* 5.0 9.0 - - - -
607E PHE* 3.8 26.7 - - + -
608E SER 3.8 9.9 - - - -
609E LEU* 4.5 17.0 - - + +
612E TYR* 3.4 47.6 - + + -
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Residues in contact with TYR 582 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E VAL* 4.5 0.2 - - + -
395E HIS* 3.3 26.6 - + - -
402E ASP* 3.2 32.3 - - + +
578E MET* 3.4 25.3 + - + +
581E TRP* 1.3 99.0 - + + +
583E ARG* 1.3 67.6 + - - +
584E PRO* 3.4 7.7 - - - +
600E LYS* 4.6 1.9 + - - -
612E TYR* 2.8 42.7 + + - -
613E GLN* 5.1 1.9 + - - -
616E LYS* 3.3 19.0 + - - -
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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