Contacts of the helix formed by residues 400 - 415 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133 GLN 5.6 7.4 + - - +
143 ILE* 5.9 1.0 - - - +
395C HIS* 4.6 11.5 - - - -
398C LEU 3.2 1.6 + - - -
399C PRO* 1.3 76.7 - - + +
401C MET* 1.3 67.0 + - - +
402C ASP* 3.4 7.4 - - - -
403C SER* 3.1 31.7 + - - +
404C VAL* 3.0 23.1 + - + +
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Residues in contact with MET 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 3.2 34.1 - - + +
395C HIS* 3.9 12.9 + - - -
397C LEU* 3.5 33.4 - - + -
398C LEU* 3.1 38.4 + - + +
399C PRO 4.3 0.9 - - - -
400C LYS* 1.3 74.9 - - - +
402C ASP* 1.3 65.7 + - - +
404C VAL* 3.0 21.4 + - - +
405C VAL* 3.0 19.8 + - - +
435C LEU* 3.8 27.8 - - + -
575C LEU* 5.5 0.2 - - + -
578C MET* 3.5 19.5 - - + -
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Residues in contact with ASP 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C HIS* 2.9 23.9 + - + -
400C LYS* 3.9 4.9 - - - -
401C MET* 1.3 75.7 - - - +
403C SER* 1.3 71.0 + - - +
405C VAL* 3.3 11.9 + - - +
406C TYR* 3.3 13.7 + - - +
578C MET* 3.7 36.9 - - + +
579C LEU* 4.5 3.8 - - + +
582C TYR* 3.2 41.0 - - + +
583C ARG* 3.6 20.6 + - + -
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Residues in contact with SER 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C LYS* 3.1 44.7 + - - +
402C ASP* 1.3 85.8 + - - +
404C VAL* 1.3 57.2 + - - +
406C TYR* 3.4 6.1 + - - +
407C ASP* 2.7 31.9 + - - +
583C ARG* 2.9 30.0 + - - +
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Residues in contact with VAL 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C LEU* 5.7 5.8 - - + -
399C PRO 3.9 11.7 - - - +
400C LYS* 3.0 17.2 + - + +
401C MET* 3.0 14.8 + - - +
403C SER* 1.3 75.3 - - - +
405C VAL* 1.3 61.5 + - + +
407C ASP* 3.1 11.1 + - - +
408C PHE* 2.9 27.6 + - + +
422C TRP* 3.5 29.8 - - + -
435C LEU* 6.4 1.3 - - + -
543C LYS* 5.1 10.3 - - - -
545C ILE* 4.2 13.7 - - + -
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Residues in contact with VAL 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C MET* 3.0 24.1 + - + +
402C ASP 3.4 7.0 - - - +
403C SER 3.3 0.4 - - - -
404C VAL* 1.3 77.6 - - + +
406C TYR* 1.3 56.3 + - - +
408C PHE* 3.3 7.0 + - + +
409C LEU* 2.9 37.2 + - + +
435C LEU* 5.5 0.7 - - + -
439C LEU* 4.5 14.6 - - + -
442C LEU* 3.7 25.6 - - + -
575C LEU* 4.7 6.5 - - + -
578C MET* 3.5 25.4 - - + -
579C LEU* 3.5 24.0 - - + -
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Residues in contact with TYR 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C ASP 3.3 4.5 + - - +
403C SER 3.7 8.1 - - - +
404C VAL 3.3 0.6 - - - -
405C VAL* 1.3 78.4 - - - +
407C ASP* 1.3 70.0 + - - +
409C LEU* 3.5 16.9 + - + +
410C LYS* 3.2 63.7 + - + +
579C LEU* 4.6 2.2 - - + +
583C ARG* 3.9 33.2 - - + +
587C GLU* 3.1 61.0 + - + +
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Residues in contact with ASP 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C SER* 2.7 25.7 + - - +
404C VAL* 3.1 11.4 + - - +
406C TYR* 1.3 81.3 - - - +
408C PHE* 1.3 58.2 + - - +
410C LYS* 3.5 4.2 + - - +
411C CYS* 2.8 31.4 + - - +
422C TRP* 4.2 14.5 - - + -
583C ARG* 5.9 0.8 + - - -
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Residues in contact with PHE 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C VAL* 2.9 15.3 + - + +
405C VAL* 3.7 6.7 - - - +
407C ASP* 1.3 73.9 - - - +
409C LEU* 1.3 69.4 + - + +
411C CYS* 3.1 3.1 + - - +
412C MET* 2.9 61.5 + - + +
422C TRP* 3.9 38.3 - + + -
424C PHE* 6.1 0.2 - + - -
439C LEU* 4.4 24.9 - - + -
443C CYS* 4.0 16.2 - - - -
469C LEU* 3.7 22.9 - - + -
524C GLY 4.3 3.1 - - - -
525C ILE* 3.5 39.0 - - + -
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Residues in contact with LEU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C LEU* 4.2 10.6 - - + +
365C PHE* 3.9 27.1 - - + -
405C VAL* 2.9 27.3 + - + +
406C TYR* 3.6 21.3 - - + +
408C PHE* 1.3 78.4 - - + +
410C LYS* 1.3 65.3 + - + +
412C MET* 3.0 17.1 + - - +
413C VAL* 3.0 17.6 + - + +
442C LEU* 4.3 7.9 - - + -
443C CYS* 3.5 29.4 - - - -
579C LEU* 3.9 29.4 - - + -
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Residues in contact with LYS 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C GLU* 3.3 31.1 + - - +
406C TYR* 3.2 58.5 + - + +
407C ASP* 4.0 3.6 - - - +
409C LEU* 1.3 78.5 - - + +
411C CYS* 1.3 60.1 + - - +
413C VAL* 2.9 12.3 + - + +
414C TYR* 2.7 61.0 + - + -
587C GLU 4.0 11.3 + - - -
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Residues in contact with CYS 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C ASP 2.8 19.5 + - - +
408C PHE 3.1 6.9 + - - +
410C LYS* 1.3 77.4 - - - +
412C MET* 1.3 63.5 + - + +
414C TYR* 4.3 5.3 - - - +
415C ASN* 3.4 17.0 + - - -
416C ILE* 4.7 5.5 + - - +
419C LYS 4.2 14.2 - - - +
420C ARG* 3.9 15.7 - - - +
422C TRP* 3.2 32.8 - - + +
542C VAL* 4.4 10.5 - - - -
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Residues in contact with MET 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ARG* 2.8 32.3 + - - +
408C PHE* 2.9 58.0 + - + +
409C LEU* 3.2 9.4 - - - +
411C CYS* 1.3 82.6 - - - +
413C VAL* 1.3 56.9 + - - +
415C ASN* 3.7 5.4 + - - +
420C ARG 3.2 27.4 - - - +
443C CYS* 5.2 0.2 - - - -
468C PHE* 3.7 26.7 - - + -
469C LEU* 4.0 11.9 - - + -
523C PRO* 3.6 32.7 - - + +
524C GLY 4.0 7.6 - - - +
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Residues in contact with VAL 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ARG* 3.7 24.9 - - + +
358C GLU* 3.5 42.2 - - + +
361C LEU* 3.5 25.4 - - + -
409C LEU 3.1 16.4 - - - +
410C LYS* 2.9 21.6 + - + +
412C MET* 1.3 77.6 - - - +
414C TYR* 1.3 72.5 + - + +
415C ASN* 3.1 0.9 + - - +
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Residues in contact with TYR 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C LYS* 2.7 58.4 + - + +
411C CYS* 4.3 4.9 - - - +
413C VAL* 1.3 80.4 - - + +
415C ASN* 1.3 71.3 + - - +
416C ILE* 4.0 22.6 - - + +
561D GLU* 5.5 5.8 - - + -
565D GLU* 3.5 61.7 - - + +
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Residues in contact with ASN 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C ARG* 3.7 37.0 + - - +
411C CYS 3.4 10.3 + - - -
412C MET* 3.7 4.2 + - - +
413C VAL 3.1 1.8 - - - +
414C TYR* 1.3 84.1 - - - +
416C ILE* 1.3 59.0 + - - +
417C PRO* 3.6 7.4 - - - +
420C ARG* 3.0 34.3 + - - +
520C ILE* 5.4 1.6 - - - +
523C PRO* 5.1 2.1 - - - +
564D LEU 3.8 4.2 - - - +
565D GLU 4.7 1.3 - - - +
567D ARG* 2.8 36.6 + - - +
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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
------------------------------------------------------------
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