Contacts of the helix formed by residues 406 - 427 (chain B) in PDB entry 4GDY
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 SER 406 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLN* 5.2 0.2 - - - -
404B SER 3.6 2.5 + - - -
405B ALA* 1.3 75.6 - - - +
407B PRO* 1.4 68.3 - - - +
408B GLU* 3.5 18.0 + - - +
409B GLN* 2.8 58.0 + - - +
410B MET* 3.0 12.2 + - - +
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Residues in contact with PRO 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLN* 4.8 9.6 - - - +
332B ALA* 4.1 21.7 - - + +
336B ALA* 5.2 2.1 - - - +
405B ALA 4.6 1.1 - - - +
406B SER* 1.4 86.0 - - - +
408B GLU* 1.3 69.6 + - - +
410B MET* 3.5 16.3 - - - +
411B ASP* 3.3 22.2 + - - +
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Residues in contact with GLU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B SER* 3.5 23.3 + - - +
407B PRO* 1.3 86.5 - - - +
409B GLN* 1.4 59.5 + - - +
410B MET 3.2 1.3 - - - -
411B ASP* 3.7 8.3 - - + +
412B VAL* 3.1 36.5 + - + +
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Residues in contact with GLN 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A MET 5.2 1.5 - - - +
34A ILE* 3.5 41.5 - - + +
35A SER 4.9 3.3 + - - +
404B SER 5.1 1.6 + - - -
405B ALA* 3.7 18.9 - - + +
406B SER* 2.8 43.4 + - - +
408B GLU* 1.4 75.6 - - - +
410B MET* 1.4 56.6 + - - +
412B VAL* 3.6 1.2 + - - -
413B ALA* 3.1 30.7 + - - +
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Residues in contact with MET 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.4 4.9 - - + -
329B GLN* 3.8 15.7 - - - +
332B ALA* 3.7 14.1 - - - -
333B ILE* 3.7 37.2 - - + -
336B ALA* 4.0 14.4 - - + -
402B PHE* 3.7 35.2 - - + -
405B ALA* 3.4 31.0 - - + +
406B SER 3.0 13.2 + - - +
407B PRO* 3.5 10.1 - - - +
409B GLN* 1.4 74.2 - - - +
411B ASP* 1.3 59.0 + - - +
413B ALA* 3.4 4.9 + - - +
414B PHE* 2.9 36.9 + - + +
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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
----------------------------------------------------------
336B ALA* 4.1 12.7 - - + +
339B LYS* 2.9 36.6 + - - +
340B TRP* 3.3 25.1 + - - +
407B PRO 3.3 12.0 + - - +
408B GLU* 3.7 12.1 - - + +
409B GLN 3.5 0.4 - - - -
410B MET* 1.3 78.2 - - - +
412B VAL* 1.3 64.8 + - + +
414B PHE 3.5 0.2 + - - -
415B GLN* 3.1 26.3 + - - +
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 3.4 24.0 - - + -
379B VAL* 5.5 0.2 - - + -
408B GLU* 3.1 19.3 + - + +
409B GLN* 3.9 4.3 - - - +
411B ASP* 1.3 79.0 - - + +
413B ALA* 1.3 60.9 + - - +
415B GLN* 3.4 19.6 + - - +
416B VAL* 3.3 28.3 + - + +
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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
----------------------------------------------------------
34A ILE* 3.8 6.7 - - + -
36A LEU* 3.5 30.7 - - + -
379B VAL* 3.7 28.9 - - + +
381B MET* 4.4 2.0 - - + +
409B GLN 3.1 18.7 + - - +
410B MET 3.8 2.5 - - - +
411B ASP 3.4 0.2 - - - -
412B VAL* 1.3 72.1 - - - +
414B PHE* 1.4 61.3 + - + +
415B GLN 3.2 1.8 - - - -
416B VAL* 3.1 6.4 + - - +
417B LEU* 3.0 24.1 + - - +
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Residues in contact with PHE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 5.2 1.8 - - + -
333B ILE* 3.5 47.1 - - + -
336B ALA* 3.5 10.5 - - + -
337B ALA* 3.4 28.9 - - + -
340B TRP* 3.6 24.9 - - + +
341B LEU* 3.5 18.0 - - + +
356B LEU* 4.2 1.3 - - + -
358B ILE* 3.8 29.4 - - + -
381B MET* 3.6 28.3 - - + -
400B ALA* 4.2 4.0 - - + -
410B MET* 2.9 18.6 + - - +
413B ALA* 1.4 69.8 - - + +
415B GLN* 1.3 59.2 + - - +
417B LEU* 3.6 12.5 - - + +
418B ALA* 3.1 20.8 + - - +
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TRP* 3.3 47.5 - - + -
411B ASP* 3.1 18.9 + - - +
412B VAL* 3.4 21.0 + - - +
413B ALA 3.2 0.4 - - - -
414B PHE* 1.3 75.0 - - - +
416B VAL* 1.4 67.1 + - + +
418B ALA* 3.6 4.2 + - - +
419B GLN* 3.3 19.9 + - - +
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Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ALA* 5.1 1.1 - - - +
377B MET* 3.7 44.2 - - + +
379B VAL* 4.2 25.4 - - + -
412B VAL* 3.3 20.4 + - + +
413B ALA 3.1 7.5 + - - +
415B GLN* 1.4 77.3 - - + +
417B LEU* 1.4 62.0 + - - +
419B GLN* 3.3 7.5 + - - +
420B LEU* 3.2 31.9 + - + +
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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
----------------------------------------------------------
341B LEU* 3.9 28.3 - - + -
358B ILE* 4.9 1.3 - - + -
369B LEU* 4.2 14.6 - - + -
370B ILE* 4.2 6.1 - - + -
379B VAL* 5.9 0.4 - - + +
381B MET* 4.1 13.7 - - - -
398B LEU* 4.1 33.9 - - + -
413B ALA 3.0 13.1 + - - +
414B PHE* 3.6 26.5 - - + +
416B VAL* 1.4 75.9 - - - +
418B ALA* 1.3 62.8 + - - +
420B LEU* 3.2 8.5 + - + +
421B ILE* 3.0 47.5 + - + +
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TRP* 3.9 22.4 - - + +
341B LEU* 5.6 2.0 - - + +
344B LEU* 3.9 23.4 - - + +
414B PHE 3.1 14.6 + - - +
415B GLN* 3.7 7.0 - - - +
417B LEU* 1.3 77.8 - - - +
419B GLN* 1.4 56.7 + - - +
421B ILE* 3.3 6.8 + - - +
422B LYS* 2.9 39.9 + - + +
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Residues in contact with GLN 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B MET* 3.5 29.5 - - - +
415B GLN 3.3 10.2 + - - +
416B VAL* 3.3 11.4 + - - +
418B ALA* 1.4 76.6 - - - +
420B LEU* 1.3 57.0 + - + +
422B LYS* 3.3 20.8 + - + +
423B GLU* 2.8 55.3 + - + +
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 3.7 32.9 - - + +
373B LYS* 3.7 27.8 - - + +
374B ALA* 3.7 36.3 - - + +
377B MET* 4.4 12.8 - - + -
416B VAL* 3.2 27.8 + - + +
417B LEU* 3.2 9.4 + - + +
419B GLN* 1.3 71.5 - - - +
421B ILE* 1.4 64.0 + - - +
423B GLU* 3.3 34.7 + - - +
424B SER* 3.3 10.4 + - - -
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Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 5.3 5.8 - - + -
344B LEU* 3.9 29.6 - - + +
345B ALA* 5.3 2.2 - - + -
360B VAL* 3.7 43.1 - - + -
363B ILE* 4.0 3.3 - - + +
369B LEU* 4.4 11.7 - - + -
417B LEU* 3.0 46.1 + - + +
418B ALA* 3.6 10.5 - - - +
420B LEU* 1.4 73.1 - - - +
422B LYS* 1.3 63.2 + - - +
423B GLU 3.2 0.5 + - - -
424B SER* 3.2 5.2 + - - -
425B LEU* 3.1 44.3 + - + +
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Residues in contact with LYS 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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344B LEU* 4.6 22.0 - - + -
418B ALA* 2.9 28.0 + - + +
419B GLN* 3.5 18.6 - - + +
421B ILE* 1.3 76.1 - - - +
423B GLU* 1.4 59.2 + - - +
425B LEU* 3.7 9.3 + - + +
426B LEU* 3.5 28.0 + - + +
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Residues in contact with GLU 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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373B LYS* 5.5 3.5 - - - +
377B MET* 5.0 1.1 - - - +
419B GLN* 2.8 52.4 + - + +
420B LEU* 3.4 27.7 + - - +
421B ILE 3.2 0.2 - - - -
422B LYS* 1.4 73.8 - - - +
424B SER* 1.4 62.1 - - - +
426B LEU* 3.3 26.6 + - + +
427B VAL* 3.8 6.8 + - - +
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ILE* 3.6 34.4 - - - +
369B LEU* 3.5 22.1 - - - +
420B LEU 3.3 3.5 + - - -
421B ILE 3.2 4.1 + - - -
423B GLU* 1.4 77.3 - - - +
425B LEU* 1.3 60.6 + - - +
427B VAL* 3.3 31.1 - - - +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 4.3 16.8 - - + +
362B GLY* 3.8 31.9 - - - +
363B ILE* 3.9 11.7 - - + -
421B ILE* 3.1 35.6 + - + +
422B LYS* 4.0 9.2 - - + +
423B GLU 3.3 0.4 - - - -
424B SER* 1.3 74.8 - - - +
426B LEU* 1.3 62.3 + - - +
427B VAL 3.3 5.0 + - - +
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Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LYS* 3.5 17.2 + - + +
423B GLU* 3.3 17.0 + - + +
424B SER 3.2 0.8 - - - -
425B LEU* 1.3 78.3 - - - +
427B VAL* 1.3 58.9 + - - +
428B PRO* 4.0 5.9 - - - +
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLU 3.8 3.9 + - - +
424B SER* 3.3 28.2 - - - +
425B LEU 4.1 4.2 - - - +
426B LEU* 1.3 78.8 - - + +
428B PRO* 1.4 78.5 - - + +
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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
------------------------------------------------------------
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