Contacts of the helix formed by residues 400 - 413 (chain B) in PDB entry 6G4N
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 400 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B SER* 3.8 33.0 - - - +
227B GLY 4.5 1.1 - - - +
228B SER* 5.0 0.2 + - - -
231B CYS* 4.8 4.3 - - - -
233B TRP* 4.5 3.1 - - + +
288B PHE* 3.9 23.6 - - + -
323B VAL* 3.8 10.1 - - + -
327B GLU* 3.5 42.0 - - + +
396B GLY 3.2 8.6 + - - +
398B HIS 3.7 0.6 - - - -
399B ASN* 1.3 85.8 - - + +
401B ILE* 1.3 69.5 + - - +
402B CYS 3.3 1.6 - - - -
403B PRO* 3.2 4.3 - - - +
404B LEU* 2.9 24.6 + - + +
440B HIS* 4.8 0.9 - - + +
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Residues in contact with ILE 401 (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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323B VAL* 3.4 39.2 - - + +
324B ASN 4.2 9.4 - - - +
325B LYS 5.4 3.6 - - - +
327B GLU* 4.8 5.6 - - + +
396B GLY* 3.1 19.1 + - - +
397B ASP* 3.7 15.9 - - - +
400B VAL* 1.3 78.1 - - - +
402B CYS* 1.3 59.9 + - - +
404B LEU* 3.3 3.8 + - - +
405B MET* 3.0 31.4 + - - +
422B PHE* 4.2 7.2 - - + -
516B LEU* 4.0 14.1 - - + -
517B ARG* 3.9 28.9 - - - -
521B CYS* 4.0 14.1 - - - -
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Residues in contact with CYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ASP* 3.0 26.5 + - - +
401B ILE* 1.3 75.3 - - - +
403B PRO* 1.3 73.9 - - + +
405B MET* 3.2 1.4 + - - +
406B HIS* 2.9 20.1 + - - +
520B MET* 4.0 0.7 - - - -
521B CYS* 2.2 61.7 - - + -
524B TRP* 3.8 28.0 - - + -
525B ASN* 3.4 12.8 - - - +
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Residues in contact with PRO 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B SER* 4.2 0.4 - - - -
230B ASN* 2.7 37.5 + - - +
231B CYS* 4.1 22.7 - - - -
232B PRO* 3.7 14.1 - - + -
397B ASP 3.3 13.0 - - - +
398B HIS* 3.2 20.0 - - - +
399B ASN 3.8 4.5 - - - -
400B VAL 3.2 11.0 - - - +
402B CYS* 1.3 92.4 - - + +
404B LEU* 1.3 61.8 + - - +
406B HIS* 3.3 3.0 + - + -
407B PHE 3.0 9.4 + - - -
524B TRP* 6.0 0.2 - - + -
525B ASN* 4.4 4.9 - - - +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU 4.8 0.4 - - - +
226B SER 4.5 0.7 - - - +
227B GLY 3.7 20.2 - - - +
228B SER* 2.9 25.0 + - - +
321B LEU* 4.0 23.6 - - + -
322B GLY* 3.8 23.1 - - - +
323B VAL* 4.0 17.5 - - + -
400B VAL* 2.9 19.0 + - + +
401B ILE 3.6 2.9 - - - +
403B PRO* 1.3 75.7 - - - +
405B MET* 1.3 60.8 + - - +
407B PHE* 2.8 6.1 + - - +
408B VAL* 2.7 33.6 + - + +
420B LEU* 3.8 28.5 - - + -
516B LEU* 6.4 0.2 - - + -
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Residues in contact with MET 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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401B ILE 3.0 19.3 + - - +
402B CYS* 3.7 5.2 - - - +
404B LEU* 1.3 83.1 - - - +
406B HIS* 1.3 65.0 + - - +
408B VAL* 3.2 18.8 - - + +
409B ASN* 2.9 41.3 + - - +
420B LEU* 3.8 18.8 - - + -
495B PHE* 4.5 6.3 - - + -
500B GLN* 5.3 3.8 - - - +
515B ARG* 5.6 0.2 - - - -
516B LEU* 3.6 59.0 - - + +
521B CYS* 4.2 13.0 - - + -
525B ASN* 5.1 0.4 - - - +
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Residues in contact with HIS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASN* 3.7 19.7 - - + +
306B GLU* 2.3 33.5 + - - +
309B LEU* 4.6 3.1 - - + -
402B CYS 2.9 12.5 + - - +
403B PRO 3.3 9.4 - - - +
405B MET* 1.3 76.1 - - - +
407B PHE* 1.3 58.3 + - - +
409B ASN* 3.9 3.9 - - - +
410B LYS* 3.0 62.8 + - + +
525B ASN* 3.9 28.0 + - + +
526B GLN* 4.6 15.8 + - - -
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Residues in contact with PHE 407 (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 GLY* 4.9 0.2 - - - -
210B ILE* 3.3 33.4 - - + -
211B LEU* 4.9 2.5 - - + -
224B LEU* 4.2 18.4 - - + -
228B SER* 4.4 2.7 - - - +
229B PRO* 3.6 34.3 - - + -
230B ASN* 3.4 20.6 - - - +
309B LEU* 3.7 29.4 - - + -
314B PHE* 6.2 0.2 - + - -
319B ILE* 4.1 21.1 - - + -
321B LEU* 4.0 14.6 - - + -
403B PRO 3.0 5.5 + - - +
404B LEU* 2.8 10.6 + - - +
406B HIS* 1.3 74.0 - - - +
408B VAL* 1.3 63.3 + - - +
410B LYS* 3.8 4.0 - - - +
411B TYR* 2.7 45.9 + + + +
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Residues in contact with VAL 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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319B ILE* 4.7 1.1 - - + -
321B LEU* 3.5 26.5 - - + -
404B LEU 2.7 14.5 + - - +
405B MET* 3.2 40.6 - - + +
407B PHE* 1.3 78.2 - - - +
409B ASN* 1.3 60.6 + - - +
411B TYR* 4.3 3.0 - - - +
412B THR* 2.3 37.1 + - - +
418B THR* 3.4 29.4 - - + -
420B LEU* 4.1 9.0 - - + -
495B PHE* 3.7 15.4 - - + -
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Residues in contact with ASN 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B MET* 2.9 30.5 + - - +
406B HIS* 4.1 4.0 - - - +
408B VAL* 1.3 82.6 - - - +
410B LYS* 1.3 66.6 + - + +
411B TYR 3.3 0.3 + - - -
412B THR* 3.4 11.5 + - - -
413B LYS* 3.5 22.5 + - - +
495B PHE* 3.9 15.2 - - - -
497B THR* 4.8 12.5 + - - +
500B GLN* 3.5 32.1 + - - +
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLU* 4.0 3.7 + - - -
309B LEU* 3.8 40.9 - - + +
310B ASN* 2.6 33.4 + - - +
314B PHE* 4.2 1.2 - - - -
406B HIS* 3.0 52.8 + - + +
407B PHE 3.8 2.5 - - - +
409B ASN* 1.3 76.5 - - + +
411B TYR* 1.3 63.7 + - - +
413B LYS* 3.6 31.2 + - + +
414B PHE* 3.9 9.7 - - - -
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Residues in contact with TYR 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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210B ILE* 3.5 24.0 - - + -
309B LEU* 5.1 1.3 - - - +
314B PHE* 3.1 42.5 - + + -
315B LYS 2.9 8.9 + - - -
317B THR* 2.8 45.7 + - - +
319B ILE* 3.4 41.5 - - + -
407B PHE* 2.7 34.8 + + + +
408B VAL 4.3 1.1 - - - +
410B LYS* 1.3 70.7 - - - +
412B THR* 1.3 60.2 + - - +
413B LYS 3.1 2.0 - - - -
414B PHE* 2.8 22.9 + - - +
415B GLY* 2.9 32.1 + - - -
417B GLY 5.1 0.7 - - - -
418B THR* 4.1 6.7 - - - -
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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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408B VAL 2.3 25.8 + - - -
409B ASN 3.4 5.1 + - - -
411B TYR* 1.3 77.0 - - - +
413B LYS* 1.3 60.0 + - - +
414B PHE 3.1 1.9 + - - -
415B GLY* 4.2 10.2 + - - +
418B THR* 3.0 23.4 + - - +
495B PHE* 3.3 40.5 - - + +
496B THR* 4.3 0.9 - - - -
497B THR* 3.8 25.2 + - - +
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Residues in contact with LYS 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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309B LEU 6.0 0.2 - - - +
409B ASN* 3.5 20.9 - - - +
410B LYS* 3.7 28.7 - - + +
411B TYR 3.0 0.6 + - - -
412B THR* 1.3 76.5 - - - +
414B PHE* 1.3 79.5 + - + +
497B THR* 4.2 28.7 - - + +
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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