Contacts of the helix formed by residues 403 - 422 (chain B) in PDB entry 3GWX
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 VAL 403 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B GLY 4.0 12.6 - - - +
397B ARG 5.7 0.2 - - - +
400B LEU* 4.0 39.2 - - + +
401B MET 3.4 3.3 + - - +
402B ASN* 1.3 71.0 - - - +
404B PRO* 1.3 78.0 - - + +
405B ARG 3.1 0.3 + - - -
406B VAL* 3.1 1.5 + - - +
407B GLU* 2.8 55.0 + - + +
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Residues in contact with PRO 404 (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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401B MET 5.0 1.3 - - - +
402B ASN* 3.6 10.3 - - - +
403B VAL* 1.3 96.6 - - + +
405B ARG* 1.3 62.1 + - - +
407B GLU* 3.6 8.9 + - + +
408B ALA* 3.1 23.6 + - - +
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Residues in contact with ARG 405 (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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305B SER* 5.9 1.8 - - - -
308B SER* 4.8 19.1 + - - -
309B LEU* 3.8 21.3 - - + +
402B ASN* 2.8 48.0 + - + +
404B PRO* 1.3 74.8 - - - +
406B VAL* 1.3 66.1 + - - +
408B ALA* 3.1 9.8 + - - +
409B ILE* 3.0 40.3 + - + +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 4.2 24.7 - - + -
313B ASP* 5.6 0.4 - - - +
317B LEU* 4.2 9.4 - - + -
393B LEU* 4.0 16.2 - - + -
394B CYS 3.5 33.7 - - - +
395B GLY* 4.3 0.7 - - - -
400B LEU* 3.6 28.5 - - + -
402B ASN 3.1 13.7 + - - +
403B VAL 3.1 4.6 + - - +
405B ARG* 1.3 74.3 - - - +
407B GLU* 1.3 65.2 + - - +
409B ILE* 2.9 11.1 + - - +
410B GLN* 2.8 21.5 + - - +
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLY* 4.1 16.9 - - - +
396B ASP* 5.0 4.4 - - - +
403B VAL* 2.8 46.7 + - + +
404B PRO* 3.8 8.0 - - - +
406B VAL* 1.3 72.7 - - - +
408B ALA* 1.3 57.2 + - - +
410B GLN* 3.4 13.3 + - - +
411B ASP* 3.1 27.4 + - - +
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Residues in contact with ALA 408 (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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404B PRO 3.1 14.6 + - - +
405B ARG* 3.4 12.8 - - - +
406B VAL 3.0 0.8 - - - -
407B GLU* 1.3 74.5 - - - +
409B ILE* 1.3 66.8 + - + +
411B ASP* 3.3 13.1 + - - +
412B THR* 3.3 19.7 - - - +
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Residues in contact with ILE 409 (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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214B PHE* 5.5 4.5 - - + -
303B ILE* 5.2 1.3 - - + -
305B SER* 2.8 58.6 - - - +
308B SER* 5.9 0.2 - - - -
309B LEU* 4.6 10.8 - - + -
393B LEU* 3.7 28.3 - - + -
405B ARG* 3.0 36.7 + - + +
406B VAL* 2.9 9.9 + - - +
408B ALA* 1.3 76.4 - - + +
410B GLN* 1.3 62.7 + - - +
411B ASP 3.5 0.2 + - - -
412B THR* 3.6 9.9 + - + +
413B ILE* 3.2 23.8 + - + +
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Residues in contact with GLN 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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390B ALA* 3.6 15.6 + - - +
393B LEU* 3.1 29.9 + - - +
394B CYS* 3.9 13.1 - - - +
395B GLY* 3.7 15.0 + - - +
396B ASP* 5.6 1.7 - - - +
406B VAL 2.8 13.4 + - - +
407B GLU* 3.6 10.3 - - - +
409B ILE* 1.3 79.5 - - - +
411B ASP* 1.3 64.2 + - - +
413B ILE* 3.0 12.5 + - + +
414B LEU* 2.9 39.9 + - + +
439B MET* 4.5 12.9 - - - +
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Residues in contact with ASP 411 (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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407B GLU 3.1 13.2 + - - +
408B ALA* 3.5 12.3 - - - +
410B GLN* 1.3 78.6 - - - +
412B THR* 1.3 59.2 + - + +
414B LEU* 3.2 11.7 + - - +
415B ARG* 2.5 72.7 + - - +
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Residues in contact with THR 412 (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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211B LEU* 4.1 10.3 - - - +
214B PHE* 3.5 26.0 - - - -
408B ALA 3.3 18.4 - - - +
409B ILE* 3.8 7.6 + - + +
410B GLN 3.3 0.2 - - - -
411B ASP* 1.3 73.8 - - + +
413B ILE* 1.3 62.9 + - - +
415B ARG* 3.7 11.5 - - - +
416B ALA* 2.8 31.7 + - - +
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Residues in contact with ILE 413 (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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214B PHE* 3.2 35.9 - - + -
218B ILE* 3.4 15.9 - - + -
303B ILE* 5.1 1.1 - - + -
386B LEU* 3.5 13.8 - - + +
389B ALA* 4.1 9.2 - - + +
390B ALA* 3.4 40.2 - - + +
393B LEU* 4.0 21.1 - - + -
409B ILE* 3.2 16.8 + - + +
410B GLN* 3.0 11.9 + - - +
412B THR* 1.3 81.5 + - - +
414B LEU* 1.3 57.4 + - - +
416B ALA* 3.1 3.7 + - - +
417B LEU* 2.8 26.8 + - + +
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Residues in contact with LEU 414 (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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390B ALA* 4.2 17.0 - - + -
410B GLN* 2.9 36.5 + - + +
411B ASP* 3.6 12.1 - - - +
413B ILE* 1.3 78.2 - - - +
415B ARG* 1.3 57.4 + - + +
417B LEU* 4.1 19.5 - - + -
418B GLU 2.8 22.7 + - - -
432B PHE* 3.0 22.9 - - + -
436B LEU* 4.1 35.0 - - + -
439B MET* 4.4 8.1 - - + -
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Residues in contact with ARG 415 (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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211B LEU* 4.4 13.0 - - + -
411B ASP* 2.5 51.5 + - - +
412B THR* 3.8 9.4 - - - +
414B LEU* 1.3 74.7 - - + +
416B ALA* 1.3 64.6 + - - +
418B GLU* 3.1 13.5 - - + +
419B PHE* 3.0 34.9 - - + -
432B PHE* 5.1 0.2 - - - -
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Residues in contact with ALA 416 (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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211B LEU* 3.9 26.0 - - + +
214B PHE* 3.9 20.6 - - + -
215B SER* 4.4 14.6 - - - -
386B LEU* 3.9 6.5 - - + +
412B THR 2.8 17.5 + - - +
413B ILE 3.3 4.9 - - - +
415B ARG* 1.3 76.2 - - - +
417B LEU* 1.3 65.0 + - - +
419B PHE* 3.5 2.0 + - - +
420B HIS* 2.9 25.1 + - - +
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Residues in contact with LEU 417 (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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383B ASP* 4.4 9.9 - - + +
386B LEU* 3.7 30.2 - - + +
387B PHE* 4.5 25.4 - - + +
390B ALA* 5.2 1.3 - - + -
413B ILE 2.8 13.6 + - - +
414B LEU* 3.4 23.6 - - + +
416B ALA* 1.3 74.3 - - - +
418B GLU* 1.3 66.2 + - - +
420B HIS* 3.0 3.8 + - - +
421B LEU* 2.9 53.6 + - + +
432B PHE* 3.8 20.0 - - + -
435B LEU* 4.3 13.7 - - + -
436B LEU* 5.3 4.0 - - + -
439B MET* 5.8 0.9 - - - -
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Residues in contact with GLU 418 (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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414B LEU 2.8 15.3 + - - +
415B ARG* 3.1 16.4 - - + +
417B LEU* 1.3 77.5 - - - +
419B PHE* 1.3 75.3 + - + +
421B LEU* 3.4 11.1 + - - +
422B GLN* 3.5 22.9 + - - +
431B LEU* 5.0 1.6 - - - +
432B PHE* 3.2 39.9 - - + +
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Residues in contact with PHE 419 (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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207B GLN* 4.4 18.6 - - - -
211B LEU* 3.9 22.9 - - + +
212B LYS* 6.5 1.6 - - + -
415B ARG* 3.0 34.1 + - + +
416B ALA* 4.1 2.9 - - - +
418B GLU* 1.3 88.4 - - + +
420B HIS* 1.3 59.2 + - - +
422B GLN* 2.7 51.9 + - - +
423B ALA* 3.1 8.3 + - - +
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Residues in contact with HIS 420 (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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212B LYS* 6.1 3.9 - - - +
215B SER* 4.7 13.1 - - - -
382B SER* 2.7 38.7 + - - -
383B ASP* 2.8 28.0 + - + -
386B LEU* 3.5 23.4 - - + +
416B ALA 2.9 19.5 + - - +
417B LEU 3.0 4.9 + - - +
419B PHE* 1.3 76.7 - - - +
421B LEU* 1.3 62.4 + - + +
423B ALA* 3.4 8.0 + - - +
424B ASN* 3.1 35.3 + - - +
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Residues in contact with LEU 421 (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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379B LEU* 4.9 4.0 - - + -
383B ASP* 4.2 26.0 - - + +
417B LEU* 2.9 43.7 + - + +
418B GLU* 3.7 7.2 - - - +
419B PHE 3.1 0.4 - - - -
420B HIS* 1.3 78.5 - - + +
422B GLN* 1.3 57.2 - - - +
424B ASN* 3.8 3.8 - - - -
425B HIS* 2.9 36.4 + - - +
430B TYR* 4.7 1.3 - - + -
431B LEU* 3.7 29.2 - - + +
432B PHE* 3.6 38.1 - - + +
435B LEU* 4.2 13.7 - - + -
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Residues in contact with GLN 422 (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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418B GLU* 3.5 22.2 + - - +
419B PHE* 2.7 39.1 + - - +
421B LEU* 1.3 81.3 - - - +
423B ALA* 1.3 55.4 + - + +
424B ASN 3.2 2.8 + - - -
425B HIS 5.5 0.4 - - - -
426B PRO* 4.0 21.0 - - - +
431B LEU* 5.9 2.5 - - + -
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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