Contacts of the helix formed by residues 400 - 415 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395J HIS* 4.6 11.3 - - - -
398J LEU 3.2 1.6 + - - -
399J PRO* 1.3 75.7 - - + +
401J MET* 1.3 65.8 + - - +
402J ASP* 3.3 7.9 - - - -
403J SER* 3.0 30.2 + - - +
404J VAL* 3.0 23.1 + - + +
13U GLN* 4.8 17.0 + - + +
14U ILE* 5.7 0.4 - - - +
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Residues in contact with MET 401 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394J LEU* 3.2 35.2 - - + +
395J HIS* 3.8 13.1 + - + -
397J LEU* 3.5 32.8 - - + -
398J LEU* 3.1 38.2 + - + +
399J PRO 4.3 0.9 - - - -
400J LYS* 1.3 74.1 - - - +
402J ASP* 1.3 64.7 + - - +
404J VAL* 3.0 22.3 + - - +
405J VAL* 3.0 20.3 + - - +
435J LEU* 3.8 27.4 - - + -
575J LEU* 5.5 0.2 - - + -
578J MET* 3.6 18.2 - - + -
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Residues in contact with ASP 402 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395J HIS* 2.9 24.3 + - + -
400J LYS* 4.0 5.5 - - - -
401J MET* 1.3 75.8 - - - +
403J SER* 1.3 71.2 + - - +
405J VAL* 3.3 12.4 + - - +
406J TYR* 3.3 10.2 + - - +
578J MET* 3.7 36.0 - - + +
579J LEU* 4.5 4.6 - - + +
582J TYR* 3.2 40.6 - - + +
583J ARG* 3.7 21.7 + - + +
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Residues in contact with SER 403 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400J LYS* 3.0 44.4 + - - +
402J ASP* 1.3 84.8 + - - +
404J VAL* 1.3 55.9 + - - +
406J TYR* 3.4 6.1 + - - +
407J ASP* 2.7 33.1 + - - +
583J ARG* 2.8 30.7 + - - +
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Residues in contact with VAL 404 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398J LEU* 5.7 5.6 - - + -
399J PRO 4.0 11.7 - - - +
400J LYS* 3.0 17.2 + - + +
401J MET* 3.4 15.0 - - - +
403J SER* 1.3 74.0 - - - +
405J VAL* 1.3 66.6 + - + +
407J ASP* 3.1 10.6 + - - +
408J PHE* 2.9 22.1 + - + +
422J TRP* 3.5 29.8 - - + -
435J LEU* 6.4 1.1 - - + -
543J LYS* 5.1 10.3 - - - -
545J ILE* 4.2 13.5 - - + -
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Residues in contact with VAL 405 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401J MET* 3.0 24.6 + - + +
402J ASP 3.5 6.5 - - - +
403J SER 3.3 0.2 - - - -
404J VAL* 1.3 77.6 - - + +
406J TYR* 1.3 56.9 + - - +
408J PHE* 3.3 6.7 + - - +
409J LEU* 2.9 37.1 + - + +
435J LEU* 5.5 0.7 - - + -
439J LEU* 4.5 13.9 - - + -
442J LEU* 3.7 26.2 - - + -
575J LEU* 4.7 7.0 - - + -
578J MET* 3.5 24.9 - - + -
579J LEU* 3.5 24.2 - - + -
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Residues in contact with TYR 406 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402J ASP 3.3 4.7 + - - +
403J SER 3.7 8.5 - - - +
404J VAL 3.3 0.4 - - - -
405J VAL* 1.3 79.1 - - - +
407J ASP* 1.3 69.8 + - - +
409J LEU* 3.5 17.3 + - + +
410J LYS* 3.2 63.1 + - + +
579J LEU* 4.6 2.2 - - + +
583J ARG* 3.9 33.4 - - + +
587J GLU* 3.1 60.5 + - + +
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Residues in contact with ASP 407 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403J SER* 2.7 24.8 - - - +
404J VAL* 3.1 9.7 + - - +
406J TYR* 1.3 82.5 - - - +
408J PHE* 1.3 60.1 + - - +
410J LYS* 3.5 4.3 + - - +
411J CYS* 2.8 30.2 + - - +
422J TRP* 4.2 15.0 - - + -
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Residues in contact with PHE 408 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404J VAL* 2.9 16.1 + - + +
405J VAL* 3.7 7.4 - - - +
407J ASP* 1.3 73.4 - - - +
409J LEU* 1.3 70.2 + - + +
411J CYS* 3.1 2.8 + - - +
412J MET* 2.9 62.4 + - + +
422J TRP* 3.9 39.0 - + + -
424J PHE* 6.1 0.4 - + - -
439J LEU* 4.4 24.5 - - + -
443J CYS* 4.0 15.9 - - - -
469J LEU* 3.7 22.7 - - + -
524J GLY 4.2 3.1 - - - -
525J ILE* 3.5 39.9 - - + -
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Residues in contact with LEU 409 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J LEU* 4.2 11.7 - - + +
365J PHE* 3.9 26.9 - - + -
405J VAL* 2.9 27.4 + - + +
406J TYR* 3.6 21.5 - - + +
407J ASP 3.3 0.2 - - - -
408J PHE* 1.3 78.6 - - + +
410J LYS* 1.3 65.8 + - + +
412J MET* 3.0 17.9 + - - +
413J VAL* 3.0 17.6 + - - +
442J LEU* 4.4 7.9 - - + -
443J CYS* 3.5 28.9 - - - -
579J LEU* 3.9 28.9 - - + -
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Residues in contact with LYS 410 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358J GLU* 3.3 30.7 + - - +
406J TYR* 3.2 57.6 + - + +
407J ASP* 4.0 3.8 - - - +
409J LEU* 1.3 77.9 - - + +
411J CYS* 1.3 58.2 + - - +
413J VAL* 3.8 12.3 - - + +
414J TYR* 2.7 63.6 + - + +
587J GLU 4.0 11.5 + - - -
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Residues in contact with CYS 411 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407J ASP 2.8 21.6 + - - +
408J PHE 3.1 6.5 + - - +
410J LYS* 1.3 76.1 - - - +
412J MET* 1.3 63.5 + - + +
414J TYR* 4.3 4.6 - - - +
415J ASN* 3.4 17.2 + - - -
416J ILE* 4.7 5.6 + - - +
419J LYS 4.2 14.7 - - - +
420J ARG* 3.9 16.4 - - - +
422J TRP* 3.2 32.3 - - + +
542J VAL* 4.4 11.2 - - - -
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Residues in contact with MET 412 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357J ARG* 2.8 32.8 + - - +
408J PHE* 2.9 57.3 + - + +
409J LEU* 3.2 9.0 - - - +
411J CYS* 1.3 83.3 - - - +
413J VAL* 1.3 56.3 + - - +
415J ASN* 3.7 5.7 + - - +
420J ARG 3.2 27.1 - - - +
443J CYS* 5.2 0.7 - - - -
468J PHE* 3.7 25.4 - - + -
469J LEU* 4.0 11.4 - - + -
523J PRO* 3.6 33.0 - - + +
524J GLY 4.0 7.0 - - - +
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Residues in contact with VAL 413 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357J ARG* 3.7 22.5 - - + +
358J GLU* 3.5 43.1 - - + +
361J LEU* 3.5 25.4 - - + -
409J LEU 3.1 16.4 - - - +
410J LYS* 2.9 21.4 + - + +
412J MET* 1.3 78.1 - - - +
414J TYR* 1.3 73.5 + - + +
415J ASN* 3.2 1.4 + - - +
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Residues in contact with TYR 414 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410J LYS* 2.7 57.2 + - + +
411J CYS* 4.3 5.4 - - - +
413J VAL* 1.3 78.4 - - + +
415J ASN* 1.3 70.4 + - - +
416J ILE* 4.0 25.1 - - + +
561K GLU* 6.0 2.5 - - + -
565K GLU* 3.6 56.6 - - + +
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Residues in contact with ASN 415 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J ARG* 3.7 36.6 + - - +
411J CYS 3.4 9.7 + - - -
412J MET* 3.7 4.2 + - - +
413J VAL 3.1 1.6 - - - +
414J TYR* 1.3 85.0 - - - +
416J ILE* 1.3 58.2 + - - +
417J PRO* 3.6 7.8 - - - +
420J ARG* 3.0 36.8 + - - +
520J ILE* 5.3 2.6 - - - +
523J PRO* 5.1 2.6 - - - +
564K LEU 4.2 3.1 - - - +
565K GLU 4.9 0.5 - - - +
567K ARG* 3.0 33.1 + - - +
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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