Contacts of the helix formed by residues 387 - 401 (chain A) in PDB entry 4G1T
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 CYS 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A GLN* 3.4 23.2 + - - +
382A LEU* 4.8 0.4 - - - -
385A MET* 3.2 6.2 - - + -
386A LYS* 1.3 81.6 - - - +
388A GLU* 1.3 63.8 + - - +
389A ASP* 3.2 6.5 - - - +
390A LYS* 3.7 43.1 - - + +
391A ALA 3.3 13.9 + - - -
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Residues in contact with GLU 388 (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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382A LEU* 4.3 21.6 - - + +
386A LYS 3.0 10.8 + - - +
387A CYS* 1.3 70.4 - - - +
389A ASP* 1.3 68.0 + - - +
391A ALA* 3.0 9.6 + - + +
392A ILE* 2.9 34.5 + - + +
418A ILE* 2.8 44.0 - - + +
421A MET* 4.3 9.7 - - - +
422A ARG* 3.6 16.8 + - - +
425A LYS* 6.0 0.2 + - - -
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Residues in contact with ASP 389 (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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387A CYS* 3.2 7.5 - - + +
388A GLU* 1.3 77.1 - - - +
390A LYS* 1.3 66.6 + - + +
392A ILE* 2.9 22.2 + - - +
393A HIS* 3.2 23.0 + - + +
422A ARG* 4.0 19.2 + - - -
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Residues in contact with LYS 390 (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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354A GLU* 5.5 2.8 + - - -
377A TYR* 6.4 0.2 - - + -
381A GLN* 3.5 40.0 + - + +
387A CYS* 3.5 27.5 + - + +
388A GLU 3.3 0.2 - - - -
389A ASP* 1.3 78.3 - - + +
391A ALA* 1.3 63.9 + - - +
392A ILE 3.2 0.7 + - - -
393A HIS* 3.2 23.5 + - + +
394A HIS* 3.3 21.7 - - + +
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Residues in contact with ALA 391 (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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378A GLY* 3.7 24.0 - - - +
381A GLN* 3.8 2.0 - - - +
382A LEU* 3.8 18.6 - - + -
387A CYS 3.3 6.8 + - - +
388A GLU* 3.0 13.8 + - + +
390A LYS* 1.3 78.8 - - - +
392A ILE* 1.3 61.6 + - + +
394A HIS* 3.2 5.9 + - - +
395A PHE* 3.0 48.5 + - + -
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Residues in contact with ILE 392 (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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388A GLU* 2.9 40.4 + - + +
389A ASP* 2.9 13.2 + - - +
391A ALA* 1.3 74.5 - - - +
393A HIS* 1.3 66.2 + - + +
395A PHE* 4.0 6.0 - - - +
396A ILE* 3.0 43.0 + - + +
415A LEU* 4.2 10.8 - - + -
418A ILE* 4.2 20.6 - - + -
422A ARG* 4.1 25.4 - - - +
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Residues in contact with HIS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ASP* 3.2 25.5 + - - +
390A LYS* 3.2 21.0 + - + +
392A ILE* 1.3 79.5 - - + +
394A HIS* 1.3 65.1 + - + +
396A ILE* 3.8 6.2 - - - +
397A GLU* 2.9 29.6 + - - +
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Residues in contact with HIS 394 (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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361A PHE* 4.1 9.1 - + - -
374A HIS* 3.0 55.8 + + - +
377A TYR* 3.1 39.8 - + - -
378A GLY* 4.2 9.9 - - - -
381A GLN* 4.9 2.7 - - + -
390A LYS* 3.3 24.6 + - - +
391A ALA 3.2 5.7 + - - +
392A ILE 3.1 0.8 - - - -
393A HIS* 1.3 82.0 + - + +
395A PHE* 1.3 58.4 + - - +
396A ILE 3.0 1.3 - - - -
397A GLU* 4.5 0.4 - - - +
398A GLY* 2.5 36.4 + - - -
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Residues in contact with PHE 395 (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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374A HIS 4.6 0.9 - - - -
375A LEU* 4.1 11.0 - - + -
378A GLY* 3.7 32.8 - - - -
379A ASN* 3.7 20.2 - - - -
382A LEU* 4.1 17.7 - - + -
391A ALA* 3.0 33.5 + - + +
392A ILE* 4.1 4.9 - - - -
394A HIS* 1.3 75.9 - - - +
396A ILE* 1.3 57.5 + - - +
398A GLY 3.6 0.5 - - - -
399A VAL* 2.8 35.0 + - - +
411A MET* 3.4 35.0 - - + +
414A LYS* 4.6 13.7 - - + -
415A LEU* 3.6 24.5 - - + -
418A ILE* 4.5 16.2 - - + -
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Residues in contact with ILE 396 (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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392A ILE* 3.0 35.2 + - + +
393A HIS* 3.8 5.6 - - - +
395A PHE* 1.3 72.0 - - - +
397A GLU* 1.3 68.7 + - - +
398A GLY 3.0 1.6 - - - -
399A VAL* 3.0 4.6 + - - +
400A LYS* 2.9 50.1 + - + +
415A LEU* 3.9 22.2 - - + -
435A VAL* 5.6 10.3 - - + -
438A PHE* 5.5 8.5 - - + -
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Residues in contact with GLU 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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370A LYS* 5.6 3.1 - - - +
374A HIS* 3.8 25.8 - - + +
393A HIS 2.9 23.6 + - - +
394A HIS* 4.0 1.1 - - - +
396A ILE* 1.3 76.5 - - + +
398A GLY* 1.3 61.0 + - - +
400A LYS* 3.7 28.4 + - - +
401A ILE* 3.4 23.2 + - - +
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Residues in contact with GLY 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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371A GLN* 3.3 31.0 + - - +
374A HIS* 3.6 22.4 - - - -
394A HIS 2.5 23.4 + - - -
395A PHE 3.6 2.0 - - - -
397A GLU* 1.3 73.5 - - - +
399A VAL* 1.3 60.2 + - - +
401A ILE* 3.5 5.1 - - - +
408A LYS* 4.4 0.2 - - - +
411A MET* 4.1 10.0 - - - +
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE 2.8 19.3 + - - +
396A ILE* 3.0 4.2 + - - +
398A GLY* 1.3 74.3 - - - +
400A LYS* 1.3 67.8 + - - +
401A ILE 3.1 3.0 + - - +
408A LYS* 3.3 53.7 + - + +
411A MET* 4.1 11.0 - - + +
412A LYS* 3.9 16.2 - - + +
415A LEU* 4.8 4.3 - - + -
438A PHE* 3.7 29.8 - - + -
439A LEU* 5.2 3.8 - - + -
442A LEU* 4.4 14.9 - - + +
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Residues in contact with LYS 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 2.9 34.5 + - + +
397A GLU* 3.9 30.8 + - - +
398A GLY 3.4 0.2 - - - -
399A VAL* 1.3 78.5 - - - +
401A ILE* 1.3 62.0 + - - +
402A ASN* 3.2 6.1 + - - +
438A PHE* 4.4 23.1 - - + -
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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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367A PRO* 3.8 33.7 - - + +
370A LYS* 3.6 37.2 - - + +
371A GLN* 3.0 26.4 + - + +
374A HIS* 4.1 10.3 - - + +
397A GLU* 3.4 22.0 - - + +
398A GLY 3.5 8.1 - - - +
399A VAL 3.1 0.8 - - - -
400A LYS* 1.3 74.2 - - - +
402A ASN* 1.3 60.6 + - - +
403A GLN* 2.9 13.7 + - + +
408A LYS* 3.3 12.3 + - - +
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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