Contacts of the helix formed by residues 400 - 415 (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 LYS 400 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135 GLN 5.0 9.4 + - - +
145 ILE* 5.7 0.6 - - - +
395E HIS* 4.6 11.2 - - - -
398E LEU 3.2 1.6 + - - -
399E PRO* 1.3 76.6 - - + +
401E MET* 1.3 66.3 + - - +
402E ASP* 3.3 7.4 - - - -
403E SER* 3.0 30.6 + - - +
404E VAL* 3.0 23.5 + - + +
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Residues in contact with MET 401 (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* 3.2 33.2 - - + +
395E HIS* 3.8 12.9 + - + -
397E LEU* 3.5 33.0 - - + -
398E LEU* 3.1 39.6 + - + +
399E PRO 4.3 0.9 - - - -
400E LYS* 1.3 75.1 - - - +
402E ASP* 1.3 65.8 + - - +
404E VAL* 3.0 21.7 + - - +
405E VAL* 3.0 19.9 + - - +
435E LEU* 3.8 28.0 - - + -
578E MET* 3.5 19.1 - - + -
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Residues in contact with ASP 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395E HIS* 2.9 23.9 + - + -
400E LYS* 3.9 5.4 - - - -
401E MET* 1.3 76.2 - - - +
403E SER* 1.3 71.0 + - - +
405E VAL* 3.3 11.2 + - - +
406E TYR* 3.3 13.3 + - - +
578E MET* 3.7 36.3 - - + +
579E LEU* 4.5 4.8 - - + +
582E TYR* 3.2 40.7 - - + +
583E ARG* 3.7 18.9 + - + +
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Residues in contact with SER 403 (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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400E LYS* 3.0 44.7 + - - +
402E ASP* 1.3 85.4 + - - +
404E VAL* 1.3 57.4 + - - +
406E TYR* 3.4 6.1 + - - +
407E ASP* 2.7 32.2 + - - +
583E ARG* 2.8 29.9 + - - +
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Residues in contact with VAL 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398E LEU* 5.8 5.6 - - + -
399E PRO 3.9 11.4 - - - +
400E LYS* 3.0 17.9 + - + +
401E MET* 3.0 15.0 + - - +
403E SER* 1.3 74.3 - - - +
405E VAL* 1.3 60.7 + - + +
407E ASP* 3.1 10.7 + - - +
408E PHE* 2.9 28.1 + - + +
422E TRP* 3.5 29.4 - - + -
435E LEU* 6.4 1.3 - - + -
543E LYS* 5.1 9.9 - - - -
545E ILE* 4.2 12.6 - - + -
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Residues in contact with VAL 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401E MET* 3.0 24.0 + - + +
402E ASP 3.5 6.5 - - - +
403E SER 3.3 0.2 - - - -
404E VAL* 1.3 77.4 - - + +
406E TYR* 1.3 56.6 + - - +
408E PHE* 3.3 7.0 + - - +
409E LEU* 2.9 37.2 + - + +
435E LEU* 5.5 0.9 - - + -
439E LEU* 4.4 14.4 - - + -
442E LEU* 3.7 25.6 - - + -
575E LEU* 4.7 6.5 - - + -
578E MET* 3.5 24.5 - - + -
579E LEU* 3.5 23.8 - - + -
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Residues in contact with TYR 406 (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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402E ASP 3.3 4.3 + - - +
403E SER 3.7 8.1 - - - +
404E VAL 3.3 0.4 - - - -
405E VAL* 1.3 79.5 - - - +
407E ASP* 1.3 69.8 + - - +
409E LEU* 3.6 16.7 - - + +
410E LYS* 3.2 63.4 + - + +
579E LEU* 4.6 2.4 - - + +
583E ARG* 3.9 34.5 - - + +
587E GLU* 3.1 59.2 + - + +
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Residues in contact with ASP 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403E SER* 2.7 24.4 - - - +
404E VAL* 3.1 10.4 + - - +
406E TYR* 1.3 83.6 - - - +
408E PHE* 1.3 61.1 + - - +
410E LYS* 3.5 4.2 + - - +
411E CYS* 2.8 31.0 + - - +
422E TRP* 4.2 15.0 - - + -
583E ARG* 6.3 0.2 - - - -
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Residues in contact with PHE 408 (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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404E VAL* 2.9 16.5 + - + +
405E VAL* 3.7 7.2 - - - +
407E ASP* 1.3 72.0 - - - +
409E LEU* 1.3 69.6 + - + +
411E CYS* 3.1 3.5 + - - +
412E MET* 2.9 63.2 + - + +
422E TRP* 3.9 40.1 - + + -
439E LEU* 4.4 26.0 - - + -
443E CYS* 3.9 15.3 - - - -
469E LEU* 3.7 23.3 - - + -
524E GLY 4.3 2.7 - - - -
525E ILE* 3.5 39.9 - - + -
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Residues in contact with LEU 409 (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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361E LEU* 4.2 11.3 - - + +
365E PHE* 3.9 26.7 - - + -
405E VAL* 2.9 26.9 + - + +
406E TYR* 3.6 21.1 - - + +
408E PHE* 1.3 79.0 - - + +
410E LYS* 1.3 64.4 + - + +
412E MET* 3.0 18.3 + - - +
413E VAL* 3.0 17.6 + - - +
442E LEU* 4.4 7.2 - - + -
443E CYS* 3.5 28.7 - - - -
579E LEU* 3.9 29.6 - - + -
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Residues in contact with LYS 410 (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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358E GLU* 3.4 29.9 + - - +
406E TYR* 3.2 55.8 + - + +
407E ASP* 4.0 4.5 - - - +
409E LEU* 1.3 78.5 - - + +
411E CYS* 1.3 58.8 + - - +
413E VAL* 3.8 12.1 - - + +
414E TYR* 2.7 62.9 + - + +
587E GLU 4.0 11.5 + - - -
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Residues in contact with CYS 411 (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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407E ASP 2.8 19.7 + - - +
408E PHE 3.1 7.1 + - - +
410E LYS* 1.3 76.4 - - - +
412E MET* 1.3 63.9 + - + +
414E TYR* 4.3 4.9 - - - +
415E ASN* 3.4 17.7 + - - -
416E ILE* 4.7 4.9 + - - +
419E LYS 4.2 15.1 - - - +
420E ARG* 3.9 15.7 - - - +
422E TRP* 3.2 32.3 - - + +
542E VAL* 4.4 10.5 - - - -
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Residues in contact with MET 412 (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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357E ARG* 2.8 33.2 + - - +
408E PHE* 2.9 56.6 + - + +
409E LEU* 3.2 8.5 - - - +
411E CYS* 1.3 84.3 - - - +
413E VAL* 1.3 57.0 + - - +
415E ASN* 3.7 5.7 + - - +
420E ARG 3.2 26.9 - - - +
443E CYS* 5.2 0.4 - - - -
468E PHE* 3.7 25.8 - - + -
469E LEU* 4.0 11.7 - - + -
523E PRO* 3.5 33.1 - - + +
524E GLY 4.0 7.0 - - - +
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Residues in contact with VAL 413 (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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357E ARG* 3.7 24.6 - - + +
358E GLU* 3.5 42.2 - - + +
361E LEU* 3.5 24.7 - - + -
409E LEU 3.1 16.8 - - - +
410E LYS* 2.9 20.8 + - + +
412E MET* 1.3 76.9 - - - +
414E TYR* 1.3 72.4 + - + +
415E ASN* 3.1 0.9 + - - +
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Residues in contact with TYR 414 (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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410E LYS* 2.7 57.9 + - + +
411E CYS* 4.3 4.7 - - - +
413E VAL* 1.3 78.9 - - + +
415E ASN* 1.3 72.2 + - - +
416E ILE* 4.0 22.0 - - + -
561F GLU* 5.8 3.6 - - + -
565F GLU* 3.3 62.2 - - + +
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Residues in contact with ASN 415 (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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357E ARG* 3.7 36.6 + - - +
411E CYS 3.4 10.5 + - - -
412E MET 4.0 4.3 - - - +
413E VAL 3.1 2.2 - - - +
414E TYR* 1.3 84.4 - - - +
416E ILE* 1.3 58.0 + - - +
417E PRO* 3.6 0.5 - - - +
420E ARG* 3.0 32.5 + - - +
520E ILE* 5.3 2.3 - - - +
523E PRO* 5.1 2.4 - - - +
564F LEU 3.9 3.3 - - - +
565F GLU 4.4 1.4 - - - +
567F ARG* 2.9 42.9 + - - +
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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