Contacts of the helix formed by residues 396 - 412 (chain B) in PDB entry 4S15
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 CYS 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B TRP* 4.7 3.1 - - - -
391B PHE 5.3 0.8 + - - -
392B LYS 4.8 0.6 + - - -
394B LEU* 3.8 25.5 - - - +
395B GLY* 1.3 81.0 - - - +
397B GLU* 1.3 64.7 + - - +
398B ASP 3.3 2.9 - - - -
399B PHE* 3.2 25.2 + - + +
400B ILE* 3.2 23.8 + - - +
487B LYS* 3.9 33.9 - - + +
601B 4D8 4.2 11.4 - - - -
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LYS* 6.6 0.2 - - - +
395B GLY 3.9 1.4 - - - -
396B CYS* 1.3 74.8 - - - +
398B ASP* 1.3 66.5 + - - +
400B ILE* 3.4 7.9 + - - +
401B SER* 3.0 33.9 + - - +
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Residues in contact with ASP 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B CYS 3.3 1.0 - - - -
397B GLU* 1.3 84.4 - - - +
399B PHE* 1.3 61.1 + - - +
401B SER* 3.4 9.3 + - - -
402B PHE* 3.0 26.9 + - - +
483B ARG* 3.3 23.2 + - - +
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Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 4.4 9.0 - + - -
396B CYS* 3.2 32.3 + - + +
398B ASP* 1.3 76.5 - - - +
400B ILE* 1.3 64.6 + - + +
402B PHE* 3.2 5.6 + + - +
403B VAL* 2.9 48.4 + - + +
480B LEU* 3.6 29.2 - - + -
483B ARG* 3.7 37.0 - - + +
484B HIS* 3.7 27.4 - + + -
487B LYS* 4.5 12.0 - - + +
601B 4D8 3.6 32.3 - - + -
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Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PRO* 3.9 24.9 - - + +
391B PHE* 4.0 19.1 - - + +
394B LEU* 3.9 13.7 - - + -
396B CYS* 3.2 20.6 + - - +
397B GLU* 3.7 8.5 - - - +
399B PHE* 1.3 82.7 - - + +
401B SER* 1.3 63.8 + - - +
403B VAL* 3.1 4.3 + - - +
404B PHE* 3.0 46.0 + - + -
601B 4D8 3.8 41.7 - - + -
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Residues in contact with SER 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PRO* 5.5 7.5 - - - +
397B GLU* 3.0 26.6 + - - +
398B ASP* 3.6 10.6 + - - -
400B ILE* 1.3 76.8 - - - +
402B PHE* 1.3 57.6 + - - +
404B PHE* 3.3 7.1 + - - +
405B GLU* 2.8 31.8 + - - +
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Residues in contact with PHE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASP 3.0 14.8 + - - +
399B PHE* 3.2 10.7 + + - +
401B SER* 1.3 74.3 - - - +
403B VAL* 1.3 65.3 + - - +
405B GLU* 3.3 22.8 + - + +
406B PHE* 3.0 22.3 + - + +
476B THR* 4.0 29.4 - - + -
479B ALA* 4.1 17.9 - - + -
480B LEU* 3.6 35.3 - - + +
483B ARG* 3.8 32.3 - - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 4.2 10.1 - - + -
368B MET* 3.6 30.5 - - + +
379B VAL* 6.6 0.2 - - + -
399B PHE* 2.9 49.0 + - + +
400B ILE* 3.3 9.4 - - - +
402B PHE* 1.3 75.4 - - - +
404B PHE* 1.3 68.8 + - + +
406B PHE* 3.2 5.8 + - - +
407B GLY 3.1 17.0 + - - -
480B LEU* 3.8 16.8 - - + -
601B 4D8 3.7 25.8 - - + -
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Residues in contact with PHE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B MET* 6.5 0.2 - - - -
372B PHE* 3.4 23.5 - + - -
377B ASN* 3.4 48.1 - - - +
378B THR* 4.0 3.4 - - - -
379B VAL* 3.7 18.8 - - + -
386B ALA 3.5 22.2 - - - -
387B SER 3.8 2.2 - - - -
388B PRO* 3.6 27.1 - - + -
391B PHE* 4.0 9.4 - + - -
400B ILE* 3.0 45.4 + - + +
401B SER* 3.8 5.6 - - - +
403B VAL* 1.3 84.8 - - + +
405B GLU* 1.3 63.3 + - - +
407B GLY 3.2 0.9 + - - -
408B LYS* 3.0 22.2 + - - +
601B 4D8 5.3 2.9 - - + -
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Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B SER 2.8 16.8 + - - +
402B PHE* 3.4 28.3 - - + +
403B VAL 3.2 0.2 - - - -
404B PHE* 1.3 77.0 - - - +
406B PHE* 1.3 61.4 + - - +
408B LYS* 3.4 10.1 + - + +
409B SER* 3.1 23.9 + - - -
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 3.5 25.4 - - + -
366B ILE* 4.9 0.2 - - + -
368B MET* 4.1 6.3 - - + -
369B CYS* 6.3 0.2 - - + -
402B PHE* 3.0 10.8 + - + +
403B VAL 3.2 7.6 + - - +
405B GLU* 1.3 72.5 - - - +
407B GLY* 1.3 67.8 + - - +
409B SER* 3.0 10.6 + - - -
410B LEU* 3.0 51.0 + - + +
423B PHE* 5.5 0.2 - + - -
473B LYS* 4.1 26.9 - - + -
476B THR* 3.8 25.4 - - + -
477B LEU* 3.5 39.5 - - + -
480B LEU* 3.6 24.0 - - + -
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Residues in contact with GLY 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B MET* 3.9 17.7 - - - -
369B CYS* 5.3 3.6 - - - -
372B PHE* 3.8 20.9 - - - -
403B VAL 3.1 10.7 + - - -
404B PHE 3.2 4.0 + - - -
406B PHE* 1.3 77.9 - - - +
408B LYS* 1.3 63.8 + - - +
410B LEU* 3.9 2.7 - - - +
411B CYS* 3.0 29.2 + - - -
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Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PHE* 3.6 6.9 - - + -
374B SER* 3.1 42.0 + - - +
375B GLN 5.2 0.8 + - - -
377B ASN* 2.9 41.2 + - - +
404B PHE 3.0 11.4 + - - +
405B GLU* 3.5 13.0 - - + +
406B PHE 3.2 0.2 - - - -
407B GLY* 1.3 77.0 - - - +
409B SER* 1.3 62.6 + - - +
411B CYS* 3.3 2.6 + - - +
412B SER* 3.1 22.3 + - - -
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Residues in contact with SER 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLU* 3.1 12.3 + - - -
406B PHE* 3.0 15.8 + - - -
408B LYS* 1.3 79.1 - - - +
410B LEU* 1.3 63.9 + - - +
412B SER* 2.6 25.8 + - - -
413B MET* 3.4 9.9 - - - +
469B LYS* 4.4 2.7 - - - -
473B LYS* 3.2 36.3 + - - +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B ILE* 3.9 24.0 - - + +
369B CYS* 3.8 32.7 - - + -
406B PHE* 3.0 46.8 + - + +
409B SER* 1.3 78.6 + - - +
411B CYS* 1.3 62.5 + - - +
413B MET* 3.2 27.1 + - - +
414B HIS 3.9 1.9 + - - -
415B LEU* 4.1 15.4 + - + +
423B PHE* 4.6 5.6 - - + -
470B LEU* 4.0 25.8 - - + -
473B LYS* 4.4 12.8 - - + +
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Residues in contact with CYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B CYS* 3.5 31.2 - - - -
372B PHE* 3.7 30.1 - - - -
374B SER* 3.8 18.8 - - - -
407B GLY 3.0 24.8 + - - +
408B LYS 3.6 4.7 - - - +
410B LEU* 1.3 72.9 - - - +
412B SER* 1.3 55.0 + - - +
413B MET 2.9 5.4 - - - -
414B HIS* 2.9 34.0 + - - +
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Residues in contact with SER 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B SER* 5.0 3.1 + - - -
408B LYS 3.1 12.1 + - - -
409B SER* 2.6 25.5 + - - -
411B CYS* 1.3 74.4 - - - +
413B MET* 1.3 59.3 + - - +
414B HIS* 3.4 20.2 + - - -
469B LYS* 4.3 8.3 + - - -
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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
------------------------------------------------------------
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