Contacts of the helix formed by residues 400 - 415 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395G HIS* 4.6 11.3 - - - -
398G LEU 3.2 2.0 + - - -
399G PRO* 1.3 75.3 - - + +
401G MET* 1.3 65.9 + - - +
402G ASP* 3.3 8.3 - - - -
403G SER* 3.1 29.3 + - - +
404G VAL* 3.0 24.0 + - + +
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Residues in contact with MET 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G LEU* 3.2 34.1 - - + +
395G HIS* 3.9 12.7 + - - -
397G LEU* 3.5 32.8 - - + -
398G LEU* 3.1 38.5 + - + +
399G PRO 4.3 0.9 - - - -
400G LYS* 1.3 74.1 - - - +
402G ASP* 1.3 63.6 + - - +
404G VAL* 3.0 21.4 + - - +
405G VAL* 3.0 20.1 + - - +
435G LEU* 3.8 27.4 - - + -
575G LEU* 5.5 0.2 - - + -
578G MET* 3.5 19.5 - - + -
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Residues in contact with ASP 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G HIS* 2.9 23.5 + - + -
400G LYS* 3.9 5.4 - - - -
401G MET* 1.3 75.8 - - - +
403G SER* 1.3 72.7 + - - +
405G VAL* 3.3 12.0 + - - +
406G TYR* 3.3 10.0 + - - +
578G MET* 3.7 35.6 - - + +
579G LEU* 4.5 5.2 - - + +
582G TYR* 3.2 41.7 - - + +
583G ARG* 3.7 22.7 + - + +
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Residues in contact with SER 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400G LYS* 3.1 44.1 + - - +
402G ASP* 1.3 84.0 + - - +
404G VAL* 1.3 58.2 + - - +
406G TYR* 3.4 5.7 + - - +
407G ASP* 2.7 32.3 + - - +
583G ARG* 2.8 31.3 + - - +
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Residues in contact with VAL 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G LEU* 5.7 5.4 - - + -
399G PRO 3.9 11.2 - - - +
400G LYS* 3.0 17.7 + - + +
401G MET* 3.0 14.8 + - - +
403G SER* 1.3 74.1 - - - +
405G VAL* 1.3 60.4 + - - +
407G ASP* 3.1 10.8 + - - +
408G PHE* 2.9 28.0 + - + +
422G TRP* 3.5 30.3 - - + -
435G LEU* 6.4 1.1 - - + -
543G LYS* 5.1 9.9 - - - -
545G ILE* 4.2 13.2 - - + -
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Residues in contact with VAL 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401G MET* 3.0 24.2 + - + +
402G ASP 3.5 6.5 - - - +
403G SER 3.3 0.2 - - - -
404G VAL* 1.3 78.2 - - + +
406G TYR* 1.3 56.9 + - - +
408G PHE* 3.3 5.9 + - - +
409G LEU* 2.9 37.0 + - + +
435G LEU* 5.5 0.7 - - + -
439G LEU* 4.5 13.5 - - + -
442G LEU* 3.7 26.5 - - + -
575G LEU* 4.7 6.7 - - + -
578G MET* 3.5 24.9 - - + -
579G LEU* 3.5 23.6 - - + -
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Residues in contact with TYR 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402G ASP 3.3 4.1 + - - +
403G SER 3.7 8.7 - - - +
404G VAL 3.3 0.8 - - - -
405G VAL* 1.3 78.8 - - - +
407G ASP* 1.3 70.8 + - - +
409G LEU* 3.5 16.9 + - + +
410G LYS* 3.2 63.3 + - + +
579G LEU* 4.6 2.4 - - + +
583G ARG* 3.9 33.2 - - + +
587G GLU* 3.1 59.2 + - + +
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Residues in contact with ASP 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403G SER* 2.7 24.3 - - - +
404G VAL* 3.1 11.1 + - - +
406G TYR* 1.3 82.3 - - - +
408G PHE* 1.3 59.9 - - - +
410G LYS* 3.5 3.8 + - - +
411G CYS* 2.8 30.9 + - - +
422G TRP* 4.2 14.4 - - + -
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Residues in contact with PHE 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404G VAL* 2.9 16.7 + - + +
405G VAL* 3.3 6.7 + - - +
407G ASP* 1.3 73.5 - - - +
409G LEU* 1.3 70.4 + - + +
411G CYS* 3.0 3.4 + - - +
412G MET* 2.9 63.3 + - + +
422G TRP* 3.9 40.8 - + + -
424G PHE* 6.1 0.4 - + - -
439G LEU* 4.4 25.4 - - + -
443G CYS* 3.9 15.9 - - - -
469G LEU* 3.7 22.4 - - + -
524G GLY 4.3 0.9 - - - -
525G ILE* 3.5 39.9 - - + -
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Residues in contact with LEU 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G LEU* 4.2 10.0 - - + +
365G PHE* 3.9 26.5 - - + -
405G VAL* 2.9 28.0 + - + +
406G TYR* 3.6 21.1 - - + +
408G PHE* 1.3 79.1 - - + +
410G LYS* 1.3 60.4 + - + +
412G MET* 3.0 23.4 + - - +
413G VAL* 3.0 18.4 + - + +
442G LEU* 4.3 7.9 - - + -
443G CYS* 3.5 29.6 - - - -
579G LEU* 3.9 28.9 - - + -
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Residues in contact with LYS 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358G GLU* 3.4 30.3 + - - +
406G TYR* 3.2 57.0 + - + +
407G ASP* 4.0 3.6 - - - +
409G LEU* 1.3 78.5 - - + +
411G CYS* 1.3 59.0 + - - +
413G VAL* 3.8 12.0 - - + +
414G TYR* 2.7 62.3 + - + -
587G GLU 4.0 11.7 + - - -
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Residues in contact with CYS 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407G ASP 2.8 20.5 + - - +
408G PHE 3.0 6.7 + - - +
410G LYS* 1.3 76.0 - - - +
412G MET* 1.3 64.2 + - + +
414G TYR* 4.3 5.1 - - - +
415G ASN* 3.4 17.2 + - - -
416G ILE* 4.7 5.5 + - - +
419G LYS 4.2 15.1 - - - +
420G ARG* 3.9 15.7 - - - +
422G TRP* 3.2 32.1 - - + +
523G PRO* 5.8 0.2 - - - +
542G VAL* 4.4 11.0 - - - -
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Residues in contact with MET 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G ARG* 2.8 32.8 + - - +
408G PHE* 2.9 58.0 + - + +
409G LEU* 3.0 8.7 + - - +
411G CYS* 1.3 83.2 - - - +
413G VAL* 1.3 55.6 + - - +
415G ASN* 3.7 6.1 + - - +
420G ARG 3.2 27.4 - - - +
443G CYS* 5.2 0.7 - - - -
468G PHE* 3.7 25.4 - - + -
469G LEU* 4.0 11.2 - - + -
523G PRO* 3.6 32.3 - - + +
524G GLY 4.0 7.4 - - - +
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Residues in contact with VAL 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G ARG* 3.7 23.0 - - + +
358G GLU* 3.5 43.3 - - + +
361G LEU* 3.5 25.6 - - + -
409G LEU 3.1 15.9 - - - +
410G LYS* 2.9 20.6 + - + +
412G MET* 1.3 77.5 - - - +
414G TYR* 1.3 73.6 + - + +
415G ASN 3.2 0.5 + - - -
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Residues in contact with TYR 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410G LYS* 2.7 57.0 + - + +
411G CYS* 4.3 4.9 - - - +
413G VAL* 1.3 80.4 - - + +
415G ASN* 1.3 71.4 + - - +
416G ILE* 4.0 24.4 - - + +
561H GLU* 5.7 4.5 - - + -
565H GLU* 3.8 55.2 - - + +
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Residues in contact with ASN 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357G ARG* 3.6 36.1 + - - +
411G CYS 3.4 10.3 + - - -
412G MET 3.7 3.8 + - - +
413G VAL 3.1 2.2 - - - +
414G TYR* 1.3 84.3 - - - +
416G ILE* 1.3 59.0 + - - +
417G PRO* 3.6 7.4 - - - +
420G ARG* 3.0 35.7 + - - +
520G ILE* 5.3 2.1 - - - +
523G PRO* 5.1 3.0 - - - +
564H LEU 4.1 3.3 - - - +
565H GLU 4.9 0.9 - - - +
567H ARG* 2.9 33.4 + - - +
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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