Contacts of the helix formed by residues 389 - 407 (chain B) in PDB entry 5CHG
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 ARG 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B MET 3.7 0.2 + - - -
388B PRO* 1.3 72.4 - - - +
390B GLU* 1.3 83.7 + - - +
392B ALA* 3.0 12.1 + - - +
393B THR* 3.0 27.2 + - - +
418B TYR* 2.6 66.5 + - + -
421B GLY* 3.9 12.9 - - - -
422B LYS 3.1 25.3 + - - +
423B ALA* 3.0 17.7 + - - +
425B CYS* 4.4 6.5 - - - -
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PRO* 3.1 13.8 - - + +
389B ARG* 1.3 98.3 + - - +
391B GLU* 1.3 60.9 + - - +
393B THR* 3.3 11.6 + - - -
394B GLU* 3.2 24.4 + - - +
423B ALA 5.3 0.3 - - - +
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B MET* 3.4 12.1 - - + +
388B PRO* 3.0 24.7 + - + +
390B GLU* 1.3 77.2 - - - +
392B ALA* 1.3 64.5 + - - +
394B GLU* 3.3 12.5 + - - +
395B ILE* 3.1 22.6 + - + +
479B LEU* 3.6 23.0 + - + +
484B ARG* 4.1 16.1 + - - +
485B ARG 4.4 7.8 + - - +
487B ARG* 2.7 56.1 + - - +
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Residues in contact with ALA 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B MET* 3.3 17.5 - - + +
388B PRO 3.5 1.6 + - - +
389B ARG* 3.0 16.5 + - - +
391B GLU* 1.3 76.0 - - - +
393B THR* 1.3 60.0 + - - +
395B ILE* 3.2 4.0 + - - +
396B GLU* 2.9 29.3 + - - +
414B ALA* 5.3 0.3 - - - +
418B TYR* 3.6 23.1 - - + -
425B CYS* 4.2 11.9 - - - -
428B VAL* 4.0 17.5 - - + +
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Residues in contact with THR 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ARG* 3.0 15.0 + - - +
390B GLU* 3.4 12.7 - - - -
392B ALA* 1.3 76.5 - - - +
394B GLU* 1.3 56.9 + - + +
396B GLU* 3.2 10.7 + - - +
397B GLN* 2.9 41.5 + - + +
418B TYR* 2.7 29.9 + - - +
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Residues in contact with GLU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B GLU* 3.2 9.0 + - - +
391B GLU* 3.3 18.7 + - - +
393B THR* 1.3 80.2 - - - +
395B ILE* 1.3 55.8 - - - +
397B GLN* 3.3 7.7 + - - +
398B THR* 2.9 33.3 + - - -
479B LEU* 3.6 15.1 - - + +
484B ARG* 2.7 40.3 + - - -
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Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B MET* 3.5 23.8 - - + -
391B GLU* 3.1 11.9 + - - +
392B ALA 3.2 6.9 + - - +
394B GLU* 1.3 71.9 - - - +
396B GLU* 1.3 65.0 + - - +
398B THR* 3.3 8.0 + - - -
399B VAL* 3.1 22.4 + - - +
428B VAL* 4.0 12.8 - - + -
430B VAL* 5.4 0.2 - - + -
456B PHE* 3.7 15.0 - - + -
477B CYS* 3.5 22.7 - - - -
479B LEU* 4.1 21.8 - - + +
487B ARG* 3.8 16.2 - - + -
489B LEU* 3.8 26.7 - - + -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA 2.9 13.3 + - - +
393B THR* 3.4 12.8 - - - +
395B ILE* 1.3 77.6 - - - +
397B GLN* 1.3 66.6 + - - +
399B VAL* 3.2 4.9 + - - +
400B GLN* 2.8 39.4 + - + +
412B CYS* 4.0 9.3 - - + +
413B VAL* 3.6 9.5 - - - +
414B ALA* 2.8 46.9 + - + +
418B TYR* 4.2 17.4 + - - -
428B VAL* 4.8 0.6 - - + +
430B VAL* 4.8 15.9 - - + +
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Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B THR* 2.9 30.9 + - + +
394B GLU* 3.7 7.2 - - - +
396B GLU* 1.3 89.2 - - - +
398B THR* 1.3 54.2 + - - +
400B GLN* 3.3 31.2 + - - +
401B LYS* 2.7 38.2 + - - +
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Residues in contact with THR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B GLU 2.9 14.7 + - - -
395B ILE 3.5 8.7 - - - -
397B GLN* 1.3 76.7 - - - +
399B VAL* 1.3 62.0 + - - +
401B LYS* 3.9 5.3 - - - +
402B ALA* 3.1 24.1 + - - +
451B LEU* 4.5 5.2 - - + -
454B GLU* 4.3 14.5 - - - +
456B PHE* 3.6 39.9 - - + -
479B LEU* 3.8 14.2 - - - +
480B PRO* 5.5 1.9 - - - +
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Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ILE 3.1 14.1 + - - +
396B GLU 3.8 6.1 - - - +
398B THR* 1.3 76.7 - - - +
400B GLN* 1.3 62.6 + - - +
402B ALA* 3.6 5.9 + - - +
403B ALA* 3.1 22.2 + - - +
412B CYS* 4.8 0.4 - - - -
430B VAL* 4.2 17.3 - - + -
432B ILE* 4.0 22.2 - - + -
447B LEU* 4.4 6.7 - - + +
451B LEU* 4.5 7.9 - - + -
456B PHE* 4.1 20.0 - - + -
489B LEU* 4.2 11.0 - - + -
491B ILE* 3.9 31.4 - - + -
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Residues in contact with GLN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLU* 2.8 21.4 + - - +
397B GLN* 3.3 34.8 + - - +
399B VAL* 1.3 76.6 - - - +
401B LYS* 1.3 65.3 + - - +
403B ALA* 3.1 3.3 + - - +
404B GLN* 2.9 54.1 + - + +
410B LEU 5.7 0.2 - - - +
411B LEU* 5.4 2.4 - - - +
412B CYS* 3.3 46.5 + - + +
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Residues in contact with LYS 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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397B GLN 2.7 22.7 + - - +
398B THR* 3.9 5.4 - - - +
400B GLN* 1.3 72.2 - - - +
402B ALA* 1.3 65.0 + - - +
404B GLN* 3.2 17.6 + - - +
405B ALA* 3.5 10.4 + - - +
454B GLU* 6.0 2.9 - - - +
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Residues in contact with ALA 402 (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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398B THR 3.1 15.5 + - - +
399B VAL 3.8 1.8 - - - +
401B LYS* 1.3 79.2 - - - +
403B ALA* 1.3 61.6 + - - +
405B ALA* 3.4 11.6 + - - +
406B PHE* 3.1 22.0 - - - -
447B LEU* 3.7 13.0 - - + -
450B SER* 4.7 9.4 + - - +
451B LEU* 3.6 24.9 - - + -
454B GLU* 5.0 8.7 - - - +
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Residues in contact with ALA 403 (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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399B VAL 3.1 18.2 + - - +
400B GLN 3.1 4.2 + - - +
402B ALA* 1.3 77.3 - - - +
404B GLN* 1.3 62.4 + - + +
405B ALA 3.4 0.3 + - - -
406B PHE* 3.4 7.5 + - - +
407B ASN 3.3 19.0 + - - +
410B LEU* 3.4 23.8 - - + +
412B CYS* 4.1 17.3 - - - -
432B ILE* 4.8 1.8 - - + -
443B ILE* 5.4 0.2 - - + -
447B LEU* 3.7 23.8 - - + +
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Residues in contact with GLN 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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400B GLN* 2.9 48.2 + - + +
401B LYS* 3.2 8.4 + - - +
403B ALA* 1.3 75.8 - - + +
405B ALA* 1.3 64.3 + - - +
407B ASN 3.3 24.4 - - - +
408B SER* 3.5 24.4 + - - +
410B LEU* 4.2 19.1 + - + +
412B CYS* 6.2 0.4 - - - -
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Residues in contact with ALA 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 LYS 3.5 7.0 + - - +
402B ALA* 3.4 14.2 + - - +
403B ALA 3.2 0.6 - - - -
404B GLN* 1.3 80.1 - - - +
406B PHE* 1.3 67.6 + - + +
407B ASN 3.5 0.2 + - - -
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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
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402B ALA 3.1 29.2 - - - -
403B ALA* 3.8 11.2 - - - +
405B ALA* 1.3 81.0 - - + +
407B ASN* 1.3 61.6 + - - +
410B LEU* 5.9 0.4 - - + -
443B ILE* 4.5 23.5 - - + +
446B ARG* 3.4 65.1 - - + -
447B LEU* 3.9 20.6 - - + -
450B SER* 3.7 17.3 - - - -
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Residues in contact with ASN 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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403B ALA 3.3 4.7 + - - +
404B GLN* 3.3 16.5 - - - -
405B ALA 3.3 1.6 - - - -
406B PHE* 1.3 83.8 + - + +
408B SER* 1.3 62.5 + - - +
409B GLY 2.8 28.2 + - - -
410B LEU* 3.3 24.7 + - + +
434B HIS* 3.1 18.8 + - - -
439B SER* 3.4 32.1 + - - -
443B ILE* 5.1 5.5 - - + +
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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