Contacts of the helix formed by residues 387 - 408 (chain A) in PDB entry 3G9W
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 GLU 387 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A PHE* 3.7 30.2 - - + +
317A LEU 4.8 9.4 + - - +
385A THR* 2.9 13.2 + - - +
386A THR* 1.3 90.0 - - - +
388A GLY* 1.3 63.9 + - - +
389A GLU* 3.2 4.0 - - - +
390A GLN* 3.1 46.9 + - - +
391A ILE* 3.1 15.0 + - - +
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Residues in contact with GLY 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ALA* 3.8 18.9 - - - +
365A SER 4.8 4.3 + - - -
368A SER 4.3 4.0 - - - -
369A PHE* 3.8 21.4 - - - -
385A THR* 4.0 6.9 + - - +
386A THR 3.4 4.2 - - - -
387A GLU* 1.3 76.7 - - - +
389A GLU* 1.3 55.2 + - - +
391A ILE* 3.4 4.9 + - - +
392A SER* 2.8 32.6 + - - -
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ALA* 4.3 6.2 - - + +
365A SER 5.5 1.0 + - - -
386A THR 5.2 1.5 + - - +
387A GLU* 3.2 0.8 - - - -
388A GLY* 1.3 73.3 - - - +
390A GLN* 1.3 68.6 + - + +
392A SER* 3.4 9.9 + - - -
393A GLN* 2.7 53.6 + - - +
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Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PHE* 3.9 20.1 - - + -
386A THR 5.2 0.4 + - - -
387A GLU* 3.1 51.4 + - - +
389A GLU* 1.3 78.6 - - + +
391A ILE* 1.3 64.4 + - - +
393A GLN* 3.2 12.1 + - - +
394A LEU* 3.0 27.4 + - + +
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Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PHE* 3.7 48.9 - - + -
318A VAL* 4.7 1.3 - - + -
333A LEU* 4.3 15.3 - - + -
335A ILE* 4.2 13.7 - - + -
369A PHE* 3.6 33.9 - - + -
385A THR* 4.3 19.1 - - + +
387A GLU 3.1 20.1 + - - +
388A GLY* 3.6 8.3 - - - +
390A GLN* 1.3 77.6 - - - +
392A SER* 1.3 62.0 + - - +
394A LEU* 3.3 3.6 + - - +
395A ILE* 3.1 28.7 + - + +
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Residues in contact with SER 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TRP* 3.7 28.9 + - - +
364A ALA* 3.7 12.6 - - - +
369A PHE* 3.7 13.3 - - - -
388A GLY 2.8 18.9 + - - -
389A GLU* 3.6 12.9 + - - -
390A GLN 3.3 0.2 - - - -
391A ILE* 1.3 76.5 - - - +
393A GLN* 1.3 57.6 + - - +
395A ILE* 3.3 4.1 + - - +
396A ALA* 3.0 29.0 + - - +
776D ASP* 4.3 11.2 - - - +
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Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A GLU* 2.7 44.7 + - - +
390A GLN* 3.2 12.9 + - - +
392A SER* 1.3 75.7 - - - +
394A LEU* 1.3 64.5 + - + +
396A ALA* 3.5 6.0 + - + +
397A GLY* 2.8 27.9 + - - -
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 3.7 31.4 - - - +
316A PHE* 3.8 27.6 - - + -
335A ILE* 4.2 13.5 - - + -
390A GLN* 3.0 12.7 + - + +
391A ILE 3.3 7.6 + - - +
393A GLN* 1.3 77.9 - - + +
395A ILE* 1.3 57.9 + - - +
397A GLY* 3.3 1.2 + - - -
398A TYR* 2.9 50.5 + - + -
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ILE* 3.9 27.6 - - + -
340A VAL* 4.6 9.0 - - + -
356A LEU* 4.4 12.4 - - + +
359A VAL* 5.5 1.3 - - + -
362A TRP* 3.8 33.7 - - + -
369A PHE* 3.5 34.1 - - + -
371A LEU* 4.2 12.8 - - + -
391A ILE* 3.1 20.2 + - + +
392A SER* 3.6 7.4 - - - +
393A GLN 3.2 0.2 - - - -
394A LEU* 1.3 76.8 - - - +
396A ALA* 1.3 64.5 + - - +
398A TYR* 3.4 2.7 + - - +
399A ILE* 3.0 31.2 + - + +
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TRP* 4.2 17.3 - - + -
392A SER 3.0 17.0 + - - +
393A GLN* 3.8 6.5 - - - +
395A ILE* 1.3 78.0 - - - +
397A GLY* 1.3 63.6 + - - +
399A ILE* 3.3 7.2 + - - +
400A ASP* 3.0 24.1 + - - +
776D ASP* 4.6 6.5 - - - +
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Residues in contact with GLY 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A GLN 2.8 20.7 + - - -
394A LEU* 3.7 2.0 - - - -
396A ALA* 1.3 73.2 - - - +
398A TYR* 1.3 62.8 + - - +
400A ASP* 3.4 7.6 + - - +
401A ILE* 3.2 26.8 + - - +
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Residues in contact with TYR 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLY 4.7 9.8 + - - -
314A SER* 4.7 8.3 + - - -
335A ILE* 4.0 15.4 + - + -
336A THR* 3.5 23.3 - - - +
337A LYS* 3.4 40.8 - - + +
356A LEU* 4.1 5.6 - - + -
394A LEU* 2.9 43.0 + - + +
395A ILE* 3.9 3.1 - - - +
397A GLY* 1.3 73.8 - - - +
399A ILE* 1.3 66.1 + - - +
400A ASP 3.1 0.2 - - - -
401A ILE* 3.3 22.8 + - + +
402A ILE* 3.2 26.2 + - - +
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 4.0 14.6 - - + +
359A VAL* 5.8 0.4 - - + -
362A TRP* 3.7 29.8 - - + -
395A ILE* 3.0 23.0 + - + +
396A ALA* 3.7 5.4 - - - +
398A TYR* 1.3 75.7 - - - +
400A ASP* 1.3 60.4 + - - +
402A ILE* 3.1 5.5 + - - +
403A LEU* 2.8 26.3 + - + +
780D ASN* 3.2 41.5 - - - +
781D PRO* 4.1 18.6 - - + -
782D ILE* 4.0 25.6 - - + +
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Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA 3.0 17.3 + - - +
397A GLY* 3.5 8.1 - - - +
399A ILE* 1.3 76.5 - - - +
401A ILE* 1.3 65.2 + - + +
403A LEU* 3.0 12.9 + - - +
404A LYS* 3.0 63.4 + - - +
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LYS* 6.3 2.5 - - + -
397A GLY 3.2 14.5 + - - +
398A TYR* 3.3 28.5 + - + +
400A ASP* 1.3 77.5 - - + +
402A ILE* 1.3 61.3 + - + +
404A LYS* 3.5 7.6 + - - +
405A LYS* 3.3 45.3 + - + +
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Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LYS 3.2 26.0 - - - +
338A ASP* 4.1 17.0 - - + -
356A LEU* 4.5 4.7 - - + -
357A THR* 6.0 2.7 - - + -
398A TYR 3.2 9.7 + - - +
399A ILE 3.1 7.8 + - - +
400A ASP 3.1 0.6 - - - -
401A ILE* 1.3 75.0 - - + +
403A LEU* 1.3 64.5 + - - +
404A LYS 3.1 2.0 - - - -
405A LYS* 3.1 35.1 + - + +
406A LYS* 3.4 19.9 + - + +
782D ILE* 3.9 35.7 - - + -
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ILE* 2.8 19.7 + - + +
400A ASP* 3.0 15.2 + - - +
402A ILE* 1.3 73.1 - - - +
404A LYS* 1.3 60.8 + - + +
405A LYS 3.4 0.2 - - - -
406A LYS* 3.9 29.1 - - + +
407A GLN* 3.5 26.4 - - + +
781D PRO* 3.5 33.7 - - + +
782D ILE* 4.1 15.7 - - + -
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Residues in contact with LYS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ASP* 3.0 42.2 + - - +
401A ILE* 3.9 7.2 - - - +
402A ILE 3.1 0.2 - - - -
403A LEU* 1.3 80.6 - - + +
405A LYS* 1.3 61.2 + - - +
406A LYS 3.5 0.4 - - - -
407A GLN* 3.7 29.3 + - - +
408A SER* 3.5 21.3 + - - -
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Residues in contact with LYS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LYS* 5.4 14.3 - - - +
401A ILE* 3.3 35.9 + - - +
402A ILE* 3.1 27.6 + - + +
404A LYS* 1.3 77.3 - - - +
406A LYS* 1.3 65.8 + - - +
407A GLN 3.1 0.2 - - - -
408A SER* 3.0 27.9 + - - +
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ILE* 3.4 14.7 + - + +
403A LEU* 3.9 27.3 - - + +
405A LYS* 1.3 79.7 - - - +
407A GLN* 1.3 62.1 + - + +
408A SER 3.5 4.2 + - - +
781D PRO 4.9 2.6 + - - -
782D ILE* 4.4 27.5 + - - +
784D LYS* 4.9 16.3 - - - +
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Residues in contact with GLN 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 3.5 28.5 + - + +
404A LYS* 3.7 29.8 - - - +
405A LYS 3.1 0.4 - - - -
406A LYS* 1.3 79.1 - - + +
408A SER* 1.3 59.5 + - - +
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LYS 3.5 12.7 + - - -
405A LYS* 3.0 19.5 + - - +
406A LYS 3.9 4.0 - - - +
407A GLN* 1.3 82.4 - - - +
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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