Contacts of the helix formed by residues 400 - 415 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395L HIS* 4.6 11.0 - - - -
398L LEU 3.2 1.6 + - - -
399L PRO* 1.3 76.7 - - + +
401L MET* 1.3 66.3 + - - +
402L ASP* 3.4 7.6 - - - -
403L SER* 3.1 30.4 + - - +
404L VAL* 3.0 23.3 + - + +
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Residues in contact with MET 401 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394L LEU* 3.2 33.7 - - + +
395L HIS* 3.8 13.3 + - + -
397L LEU* 3.5 33.0 - - + -
398L LEU* 3.1 40.5 + - + +
399L PRO 4.3 1.1 - - - -
400L LYS* 1.3 74.4 - - - +
402L ASP* 1.3 65.4 + - - +
404L VAL* 3.0 21.6 + - - +
405L VAL* 3.0 20.3 + - - +
435L LEU* 3.8 28.0 - - + -
575L LEU* 5.5 0.2 - - + -
578L MET* 3.5 19.3 - - + -
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Residues in contact with ASP 402 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395L HIS* 2.9 24.1 + - + -
400L LYS* 3.9 4.7 - - - -
401L MET* 1.3 75.9 - - - +
403L SER* 1.3 71.8 + - - +
405L VAL* 3.3 12.8 + - - +
406L TYR* 3.3 13.2 + - - +
578L MET* 3.7 36.0 - - + +
579L LEU* 4.5 4.4 - - + +
582L TYR* 3.2 41.0 - - + +
583L ARG* 3.7 19.7 + - + +
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Residues in contact with SER 403 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400L LYS* 3.1 45.2 + - - +
402L ASP* 1.3 85.6 + - - +
404L VAL* 1.3 57.4 + - - +
406L TYR* 3.4 6.1 + - - +
407L ASP* 2.7 32.4 + - - +
583L ARG* 2.8 29.9 + - - +
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Residues in contact with VAL 404 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398L LEU* 5.7 5.8 - - + -
399L PRO 3.9 11.9 - - - +
400L LYS* 3.0 16.8 + - + +
401L MET* 3.0 14.1 + - - +
403L SER* 1.3 74.5 - - - +
405L VAL* 1.3 62.0 + - + +
407L ASP* 3.1 11.0 + - - +
408L PHE* 2.9 27.1 + - + +
422L TRP* 3.5 29.6 - - + -
435L LEU* 6.4 1.3 - - + -
543L LYS* 5.1 10.8 - - - -
545L ILE* 4.2 13.5 - - + -
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Residues in contact with VAL 405 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L MET* 3.0 24.4 + - + +
402L ASP 3.4 7.2 - - - +
403L SER 3.3 0.2 - - - -
404L VAL* 1.3 77.6 - - - +
406L TYR* 1.3 56.5 + - - +
408L PHE* 3.3 7.1 + - + +
409L LEU* 2.9 37.7 + - + +
435L LEU* 5.5 0.9 - - + -
439L LEU* 4.5 13.2 - - + -
442L LEU* 3.7 26.0 - - + -
575L LEU* 4.7 6.7 - - + -
578L MET* 3.5 24.5 - - + -
579L LEU* 3.5 24.0 - - + -
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Residues in contact with TYR 406 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402L ASP 3.3 4.7 + - - +
403L SER 3.7 8.3 - - - +
404L VAL 3.3 0.4 - - - -
405L VAL* 1.3 78.7 - - - +
407L ASP* 1.3 69.5 + - - +
409L LEU* 3.5 17.5 + - + +
410L LYS* 3.2 64.0 + - + +
579L LEU* 4.6 3.1 - - + +
583L ARG* 3.9 33.0 - - + +
587L GLU* 3.1 58.7 + - + +
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Residues in contact with ASP 407 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403L SER* 2.7 24.9 - - - +
404L VAL* 3.1 10.0 + - - +
406L TYR* 1.3 82.7 - - - +
408L PHE* 1.3 60.4 + - - +
410L LYS* 3.5 3.6 + - - +
411L CYS* 2.8 30.7 + - - +
422L TRP* 4.2 15.0 - - + -
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Residues in contact with PHE 408 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404L VAL* 2.9 16.1 + - + +
405L VAL* 3.7 6.5 - - - +
407L ASP* 1.3 73.5 - - - +
409L LEU* 1.3 69.7 + - + +
411L CYS* 3.1 3.5 + - - +
412L MET* 2.9 62.3 + - + +
422L TRP* 3.9 39.0 - + + -
424L PHE* 6.1 0.2 - + - -
439L LEU* 4.4 26.7 - - + -
443L CYS* 3.9 15.9 - - - -
469L LEU* 3.7 23.1 - - + -
524L GLY 4.2 2.9 - - - -
525L ILE* 3.5 39.7 - - + -
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Residues in contact with LEU 409 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361L LEU* 4.2 10.4 - - + +
365L PHE* 3.9 27.1 - - + -
405L VAL* 2.9 28.0 + - + +
406L TYR* 3.6 20.9 - - + +
408L PHE* 1.3 79.1 - - + +
410L LYS* 1.3 64.6 + - + +
412L MET* 3.0 17.4 + - - +
413L VAL* 3.0 17.8 + - + +
442L LEU* 4.4 7.6 - - + -
443L CYS* 3.5 29.2 - - - -
579L LEU* 3.9 29.2 - - + -
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Residues in contact with LYS 410 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358L GLU* 3.3 31.1 + - - +
406L TYR* 3.2 57.0 + - + +
407L ASP* 4.0 3.8 - - - +
409L LEU* 1.3 78.5 - - + +
411L CYS* 1.3 58.3 + - - +
413L VAL* 2.9 11.8 + - + +
414L TYR* 2.7 62.8 + - + -
587L GLU 4.0 11.3 + - - -
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Residues in contact with CYS 411 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407L ASP 2.8 19.9 + - - +
408L PHE 3.1 6.7 + - - +
410L LYS* 1.3 77.9 - - - +
412L MET* 1.3 63.5 + - + +
414L TYR* 4.3 5.3 - - - +
415L ASN* 3.4 17.3 + - - -
416L ILE* 4.7 4.6 + - - +
419L LYS 4.2 15.2 - - - +
420L ARG* 3.9 16.1 - - - +
422L TRP* 3.2 33.4 - - + +
542L VAL* 4.4 10.5 - - - -
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Residues in contact with MET 412 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357L ARG* 2.8 33.1 + - - +
408L PHE* 2.9 56.0 + - + +
409L LEU* 3.2 9.4 - - - +
411L CYS* 1.3 84.7 - - - +
413L VAL* 1.3 56.2 + - - +
415L ASN* 3.7 5.7 + - - +
420L ARG 3.2 27.4 - - - +
443L CYS* 5.2 0.7 - - - -
468L PHE* 3.7 24.9 - - + -
469L LEU* 4.0 12.3 - - + -
523L PRO* 3.6 32.8 - - + +
524L GLY 4.0 7.2 - - - +
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Residues in contact with VAL 413 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357L ARG* 3.7 23.4 - - + +
358L GLU* 3.5 43.5 - - + +
361L LEU* 3.5 25.1 - - + -
409L LEU* 3.1 16.8 - - + +
410L LYS* 2.9 19.9 + - + +
412L MET* 1.3 77.6 - - - +
414L TYR* 1.3 73.6 + - + +
415L ASN* 3.1 0.9 + - - +
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Residues in contact with TYR 414 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561G GLU* 5.9 2.0 - - + -
565G GLU* 3.2 62.6 + - + +
410L LYS* 2.7 56.9 + - + +
411L CYS* 4.3 5.2 - - - +
413L VAL* 1.3 80.1 - - + +
415L ASN* 1.3 71.5 + - - +
416L ILE* 4.0 23.9 - - + +
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Residues in contact with ASN 415 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564G LEU 4.2 1.9 - - - +
565G GLU 4.8 0.3 - - - +
567G ARG* 2.8 49.6 + - - +
357L ARG* 3.7 36.8 + - - +
411L CYS 3.4 9.9 + - - -
412L MET 4.0 4.0 - - - -
413L VAL 3.1 2.2 - - - +
414L TYR* 1.3 84.7 - - - +
416L ILE* 1.3 58.7 + - - +
417L PRO* 3.6 0.2 - - - +
420L ARG* 3.0 36.2 + - - +
520L ILE* 5.3 3.3 - - - +
523L PRO* 5.1 2.2 - - - +
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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