Contacts of the helix formed by residues 382 - 395 (chain A) in PDB entry 3GSB
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 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A PHE* 3.0 22.4 + - + +
380A LYS 3.9 1.4 + - - -
381A SER* 1.3 67.6 - - - +
383A LEU* 1.3 65.0 + - - +
384A GLN* 3.1 21.3 + - - +
385A LYS* 3.2 40.0 + - + +
386A PHE* 3.1 22.0 + - - +
388A ARG* 5.0 2.6 + - - -
404A GLN* 4.8 0.2 - - - +
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Residues in contact with LEU 383 (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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36A SER* 5.4 7.7 - - - +
167A THR 5.7 4.0 - - - +
379A LYS 5.1 4.5 - - - +
381A SER* 2.9 43.2 + - - +
382A ASP* 1.3 72.3 + - - +
384A GLN* 1.3 62.3 + - - +
386A PHE* 4.1 8.1 - - + +
387A SER* 3.3 22.9 + - - -
404A GLN* 4.3 13.0 - - + -
405A PHE* 4.0 34.3 - - + -
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Residues in contact with GLN 384 (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 ASP* 3.1 13.3 + - - +
383A LEU* 1.3 77.6 + - - +
385A LYS* 1.3 64.8 + - - +
387A SER* 3.3 28.7 + - - -
388A ARG* 3.5 35.1 + - - +
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Residues in contact with LYS 385 (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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352A HIS* 3.2 42.6 - - + +
353A ALA* 4.9 6.5 + - - +
367A PHE* 3.7 36.9 + - + +
382A ASP* 3.2 33.4 + - + +
384A GLN* 1.3 76.7 - - - +
386A PHE* 1.3 64.9 + - - +
388A ARG* 3.0 27.8 + - - +
389A PHE* 2.9 19.4 + - - +
433A LEU* 4.1 12.7 - - + +
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Residues in contact with PHE 386 (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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37A VAL* 4.2 15.9 - - + -
365A PHE* 5.0 6.7 - + - -
367A PHE* 3.7 16.2 - + + -
382A ASP 3.1 12.6 + - - +
383A LEU* 4.1 9.2 - - + +
385A LYS* 1.3 77.7 - - - +
387A SER* 1.3 59.6 + - - +
389A PHE* 3.6 21.2 - + - +
390A HIS* 2.9 36.2 + + - +
400A LEU* 5.5 5.2 - - + -
401A ALA 3.8 10.8 - - - -
403A SER* 3.2 40.6 - - - -
404A GLN* 3.9 42.2 - - + +
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Residues in contact with SER 387 (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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36A SER 4.0 10.1 + - - -
37A VAL* 3.7 34.6 + - - +
38A GLY* 4.1 3.8 + - - -
383A LEU 3.3 13.8 + - - -
384A GLN* 3.3 25.4 + - - -
385A LYS 3.0 0.2 + - - -
386A PHE* 1.3 81.2 - - - +
388A ARG* 1.3 63.0 + - - +
390A HIS* 3.4 3.3 + - - +
391A ARG* 3.3 20.6 + - - +
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Residues in contact with ARG 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 ASP* 5.0 2.0 + - - -
384A GLN* 3.5 41.0 + - - +
385A LYS* 3.0 36.7 + - - +
387A SER* 1.3 78.0 - - - +
389A PHE* 1.3 63.1 + - - +
390A HIS 3.3 0.2 - - - -
391A ARG* 4.0 6.3 - - - +
392A GLY* 3.2 18.7 + - - -
429A VAL* 4.5 1.0 - - - +
433A LEU* 3.6 39.1 + - + +
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Residues in contact with PHE 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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343A LEU* 5.1 13.0 - - + -
365A PHE* 4.8 15.5 - + - -
367A PHE* 3.6 32.5 - + + -
385A LYS 2.9 14.5 + - - +
386A PHE* 3.6 20.9 - + - +
388A ARG* 1.3 75.1 - - - +
390A HIS* 1.3 63.6 + - - +
392A GLY 3.4 0.2 + - - -
393A MET* 2.9 57.1 + - + +
400A LEU* 4.0 20.6 - - + -
426A ALA* 4.9 2.2 - - - -
429A VAL* 3.7 16.4 - - + +
430A MET* 4.2 24.5 - - + -
433A LEU* 3.8 13.0 - - + +
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Residues in contact with HIS 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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34A PHE* 4.1 23.9 - + - -
37A VAL* 3.4 32.3 + - + +
386A PHE* 2.9 25.9 + + + +
387A SER 3.6 1.3 - - - +
388A ARG 3.3 0.2 - - - -
389A PHE* 1.3 78.6 - - - +
391A ARG* 1.3 68.4 + - - +
393A MET* 3.0 6.4 + - - +
394A LEU* 2.8 43.3 + - + +
399A TYR* 5.3 0.7 - + - -
400A LEU* 2.8 46.0 + - + +
401A ALA 3.8 11.7 - - - -
402A PRO* 3.6 10.0 - - + +
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Residues in contact with ARG 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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7A PHE* 4.0 29.5 + - - -
9A THR* 4.4 14.6 + - - +
34A PHE* 5.7 2.0 - - - -
37A VAL 5.7 2.9 + - - +
38A GLY 5.3 10.6 + - - -
40A GLN 4.7 11.5 + - - -
42A ILE* 5.3 3.0 - - - +
387A SER 3.3 12.6 + - - +
388A ARG* 4.0 7.2 - - - +
390A HIS* 1.3 80.0 + - - +
392A GLY* 1.3 62.5 + - - +
394A LEU* 3.0 28.1 + - - +
395A GLU* 3.0 47.2 + - - +
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Residues in contact with GLY 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 ARG 3.2 10.0 + - - -
389A PHE 3.4 3.8 + - - -
390A HIS 3.1 0.8 - - - -
391A ARG* 1.3 81.6 - - - +
393A MET* 1.3 63.1 + - - +
394A LEU 3.0 0.7 + - - -
395A GLU* 3.4 16.4 + - - +
396A GLN* 3.5 18.7 + - - +
429A VAL* 3.6 22.3 - - - +
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Residues in contact with MET 393 (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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343A LEU* 5.4 2.5 - - + -
389A PHE* 2.9 45.0 + - + +
390A HIS* 3.0 5.4 + - + +
392A GLY* 1.3 76.1 - - - +
394A LEU* 1.3 59.1 + - - +
396A GLN* 3.5 2.3 + - - +
397A GLY 3.5 3.6 + - - -
398A ILE* 2.9 68.8 + - + +
400A LEU* 3.8 22.9 - - + -
422A THR* 3.9 21.5 - - + +
425A ALA* 3.9 4.7 - - - +
426A ALA* 3.9 19.7 - - + +
429A VAL* 3.7 18.3 - - + +
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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
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7A PHE* 4.2 9.8 - - + -
34A PHE* 4.2 22.4 - - + -
42A ILE* 4.7 9.2 - - + -
60A TYR* 4.1 22.8 - - + -
390A HIS* 2.8 27.3 + - + +
391A ARG* 3.0 38.1 - - - +
392A GLY 3.0 0.2 - - - -
393A MET* 1.3 74.3 - - - +
395A GLU* 1.3 56.7 + - + +
396A GLN 2.7 14.5 + - - -
397A GLY* 2.7 17.7 + - - -
398A ILE 3.5 15.7 + - - +
399A TYR* 4.0 25.4 - - + -
400A LEU 5.0 0.2 - - - +
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Residues in contact with GLU 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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7A PHE* 3.8 48.0 - - + +
391A ARG* 3.0 43.4 + - - +
392A GLY* 3.4 10.1 + - - +
394A LEU* 1.3 77.1 - - + +
396A GLN* 1.3 64.0 + - - +
397A GLY 3.4 0.9 - - - -
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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
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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