Contacts of the helix formed by residues 407 - 424 (chain B) in PDB entry 4QGC
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 ASP 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B SER* 1.3 78.3 + - - +
408B PRO* 1.3 77.4 - - - +
409B THR* 3.7 15.3 + - - -
410B GLU* 3.1 32.3 + - + +
411B ALA* 3.0 24.2 + - - +
440B GLN* 4.0 6.8 + - - -
521B PHE* 4.4 6.9 - - - -
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Residues in contact with PRO 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A VAL* 5.4 1.1 - - + -
527A VAL* 3.2 42.4 - - + +
529A PRO* 4.0 21.1 - - + -
406B SER 3.3 9.8 - - - +
407B ASP* 1.3 92.4 - - - +
409B THR* 1.3 52.8 + - - +
411B ALA* 3.6 1.4 + - - +
412B THR* 2.6 37.9 + - - -
521B PHE* 3.7 25.8 - - + -
523B ASN* 3.9 10.3 - - + -
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ASP* 3.2 12.2 + - - -
408B PRO* 1.3 74.6 - - - +
410B GLU* 1.3 61.0 + - - +
412B THR* 3.3 2.9 + - - -
413B ALA* 3.0 27.6 + - + +
437B SER* 4.6 7.2 - - - +
440B GLN* 3.4 27.6 - - + +
520B GLY 4.5 1.9 + - - -
521B PHE* 3.6 14.9 - - - -
522B THR* 3.2 47.0 + - - +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ALA* 5.1 1.1 - - + +
403B PRO* 6.2 2.4 - - - +
407B ASP* 3.1 28.6 + - + +
409B THR* 1.3 76.5 - - - +
411B ALA* 1.3 62.5 + - - +
413B ALA* 3.3 5.0 + - - +
414B VAL* 3.2 28.9 + - + +
436B ARG* 5.0 1.9 + - - -
440B GLN* 2.8 32.0 + - - +
443B ARG* 4.6 9.5 + - - -
444B TYR* 2.3 39.8 + - - +
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ALA* 5.8 1.9 - - + +
422A ARG* 4.1 11.6 + - - +
423A CYS* 3.5 32.1 - - - -
527A VAL* 4.5 11.9 - - + -
406B SER* 5.7 1.8 - - - +
407B ASP 3.0 16.6 + - - +
408B PRO 3.9 4.3 - - - +
410B GLU* 1.3 76.2 - - - +
412B THR* 1.3 59.3 + - - +
414B VAL* 3.5 7.0 + - - +
415B GLY* 3.1 23.6 + - - -
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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
----------------------------------------------------------
525A MET* 5.7 5.6 - - + -
527A VAL* 3.7 12.3 - - + +
408B PRO 2.6 22.9 + - - -
409B THR 3.6 4.7 - - - -
411B ALA* 1.3 73.8 - - - +
413B ALA* 1.3 60.9 + - - +
415B GLY* 3.8 1.2 - - - +
416B ALA* 2.9 28.8 + - - +
512B LEU* 3.7 26.2 - - + -
522B THR 3.7 15.7 - - - +
523B ASN* 3.2 28.7 + - - +
524B THR 4.2 0.2 - - - +
525B MET* 4.2 12.4 - - + +
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Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR* 3.0 14.3 + - + +
410B GLU* 3.4 12.6 - - - +
411B ALA 3.3 0.4 - - - -
412B THR* 1.3 76.3 - - - +
414B VAL* 1.3 62.1 + - - +
416B ALA* 3.3 4.3 + - - +
417B VAL* 3.2 28.5 + - - +
437B SER 5.3 0.2 - - - +
440B GLN* 4.0 28.5 - - + +
441B VAL* 4.1 21.8 - - + +
444B TYR* 4.2 5.8 - - + -
512B LEU* 4.8 1.3 - - - +
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Residues in contact with VAL 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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422A ARG* 3.6 31.6 - - - +
395B PHE* 4.0 6.8 - - + -
399B ARG* 4.0 24.0 - - + -
402B ALA* 6.0 0.4 - - + -
410B GLU* 3.2 17.2 + - + +
411B ALA* 3.8 7.4 - - - +
413B ALA* 1.3 75.5 - - - +
415B GLY* 1.3 57.5 + - - +
417B VAL* 3.3 5.2 + - - +
418B GLU* 2.9 31.2 + - - +
444B TYR* 3.4 36.1 - - + +
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Residues in contact with GLY 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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415A GLY* 6.2 0.5 - - - -
419A ALA* 6.4 0.2 - - - -
422A ARG* 3.8 17.7 - - - +
525A MET* 5.4 7.0 - - - -
411B ALA 3.1 10.8 + - - -
412B THR* 3.4 3.6 + - - -
413B ALA 3.3 0.2 - - - -
414B VAL* 1.3 79.9 - - - +
416B ALA* 1.3 56.8 + - - +
418B GLU* 3.8 5.3 - - - +
419B ALA* 2.9 30.3 + - - +
525B MET* 3.8 10.0 - - - +
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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
----------------------------------------------------------
412B THR 2.9 18.6 + - - +
413B ALA 3.6 4.9 - - - +
414B VAL 3.2 0.2 - - - -
415B GLY* 1.3 74.5 - - - +
417B VAL* 1.3 60.9 + - + +
419B ALA* 3.3 2.3 + - - +
420B SER* 2.9 28.1 + - - -
428B ILE* 3.9 9.6 - - + +
441B VAL* 5.2 1.1 - - + -
510B ILE* 4.0 12.7 - - + +
512B LEU* 3.7 33.9 - - + -
525B MET* 3.7 10.5 - - - -
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Residues in contact with VAL 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.5 29.6 - - + -
413B ALA 3.2 15.1 + - - +
414B VAL 3.8 5.2 - - - +
416B ALA* 1.3 72.6 - - - +
418B GLU* 1.3 62.7 + - - +
420B SER* 2.5 23.0 + - - -
421B PHE* 3.2 19.3 - - + -
428B ILE* 4.1 2.2 - - - -
441B VAL* 3.8 36.1 - - + +
444B TYR* 3.8 11.7 - - + +
446B PRO* 3.7 24.9 - - + -
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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
----------------------------------------------------------
399A ARG* 4.2 1.7 + - - -
418A GLU* 2.8 32.9 - - + +
422A ARG* 2.9 23.0 + - - +
395B PHE* 3.7 13.0 - - + -
399B ARG* 3.1 42.8 + - - +
414B VAL* 2.9 16.1 + - - +
415B GLY* 3.8 6.3 - - - +
417B VAL* 1.3 79.1 - - - +
419B ALA* 1.3 60.1 + - - +
421B PHE* 3.5 5.2 + - - +
422B ARG* 3.2 38.7 + - - +
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Residues in contact with ALA 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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411A ALA* 5.7 4.3 - - + +
415A GLY* 6.2 2.0 - - - -
415B GLY 2.9 19.4 + - - +
416B ALA 3.7 4.7 - - - +
418B GLU* 1.3 73.5 - - - +
420B SER* 1.3 60.9 + - - +
422B ARG* 3.7 15.7 - - - +
423B CYS* 2.9 39.6 + - - +
510B ILE* 3.9 17.2 - - + +
525B MET* 4.2 16.8 - - + -
527B VAL* 5.4 2.0 - - + -
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Residues in contact with SER 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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416B ALA 2.9 14.8 + - - -
417B VAL* 2.5 23.6 + - - -
419B ALA* 1.3 75.8 - - - +
421B PHE* 1.3 61.4 + - - +
424B CYS* 3.1 7.6 + - - -
425B SER* 3.0 48.1 + - - +
428B ILE* 3.8 17.7 - - - -
446B PRO* 4.0 12.5 - - - +
447B ARG* 5.2 1.4 + - - -
448B ALA* 4.5 8.0 + - - +
510B ILE* 4.2 2.0 - - - +
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Residues in contact with PHE 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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391B HIS* 4.0 24.0 - - + -
392B LEU* 3.5 33.4 - - + -
395B PHE* 3.9 26.5 - + + -
417B VAL* 3.2 39.3 + - + -
418B GLU 3.8 5.4 - - - +
420B SER* 1.3 84.1 + - - +
422B ARG* 1.3 62.6 + - - +
424B CYS* 3.3 18.9 + - - +
445B ARG 4.2 0.4 - - - -
446B PRO* 4.2 4.5 - - + -
447B ARG* 3.4 60.3 + - + +
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Residues in contact with ARG 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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399A ARG* 3.5 20.9 - - - +
411A ALA* 5.3 8.5 + - - +
414A VAL* 3.6 33.6 - - - +
415A GLY* 5.0 6.1 - - - +
418A GLU* 2.6 34.8 + - - +
418B GLU* 3.2 30.9 + - - +
419B ALA* 4.0 14.8 - - - +
420B SER 3.4 0.4 - - - -
421B PHE* 1.3 79.5 - - - +
423B CYS* 1.3 67.4 + - - +
424B CYS* 3.6 4.3 + - - -
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Residues in contact with CYS 423 (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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411A ALA* 3.6 31.2 - - - -
419B ALA* 2.9 25.6 + - - +
422B ARG* 1.3 82.7 - - - +
424B CYS* 1.3 71.5 + - - +
425B SER* 3.3 6.8 + - - +
508B VAL* 4.1 24.2 - - + +
510B ILE* 4.7 4.0 - - + -
527B VAL* 4.5 12.1 - - - -
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Residues in contact with CYS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B SER 3.1 9.6 + - - -
421B PHE* 3.3 12.8 + - - +
422B ARG 4.6 4.0 - - - -
423B CYS* 1.3 80.9 - - - +
425B SER* 1.3 66.0 + - - +
426B GLY* 3.7 1.0 + - - -
447B ARG* 4.8 15.9 - - - +
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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