Contacts of the helix formed by residues 381 - 393 (chain A) in PDB entry 6XWQ
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 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER* 6.0 0.2 - - - -
376A ASP* 2.8 33.9 + - - -
378A THR* 3.2 10.9 + - - +
379A PRO 3.9 1.4 - - - +
380A GLY* 1.3 79.8 - - - +
382A PRO* 1.3 73.8 - - - +
383A VAL* 3.1 17.0 - - - -
384A ALA* 3.1 18.9 + - - +
385A LEU* 4.0 1.0 + - - +
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Residues in contact with PRO 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.4 39.0 - - + +
118A GLY 4.6 1.6 - - - +
119A SER* 4.2 30.5 - - - +
332A ILE* 4.4 7.2 - - + -
380A GLY 4.3 2.5 - - - +
381A SER* 1.3 84.4 - - - +
383A VAL* 1.3 59.9 + - + +
384A ALA 3.1 0.2 - - - -
385A LEU* 2.9 27.3 + - + +
386A ALA 3.0 10.7 + - - -
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 5.6 1.1 - - - +
328A VAL* 4.7 11.6 - - + +
332A ILE* 3.8 20.4 - - + -
370A LEU* 5.5 5.0 - - + +
375A LEU* 3.6 30.3 - - + -
376A ASP* 3.2 35.2 - - - +
377A LEU* 4.4 5.6 - - + -
378A THR 4.6 0.9 - - - +
381A SER* 3.1 22.4 - - - -
382A PRO* 1.3 78.0 - - + +
384A ALA* 1.3 60.6 + - - +
386A ALA* 3.4 8.4 + - - +
387A TYR* 2.8 29.6 + - - +
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU 5.0 3.8 - - - +
378A THR 3.7 4.7 - - - +
379A PRO* 3.6 32.5 - - + +
381A SER 3.1 13.6 + - - +
383A VAL* 1.3 82.4 - - - +
385A LEU* 1.3 56.7 - - - +
387A TYR* 3.3 8.0 + - - +
388A ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.8 27.6 - - + -
225A ARG* 6.2 2.2 - - - +
381A SER 4.0 0.8 + - - +
382A PRO* 2.9 16.7 + - + +
384A ALA* 1.3 79.6 - - - +
386A ALA* 1.3 57.7 + - - +
388A ALA* 3.3 10.4 + - + +
389A MET* 2.9 31.5 + - + +
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Residues in contact with ALA 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.9 13.6 - - + +
327A PHE* 4.4 11.9 - - + -
328A VAL* 3.6 29.6 - - + -
331A ALA* 5.0 4.0 - - + -
332A ILE* 5.6 0.7 - - + -
382A PRO 3.0 11.6 + - - +
383A VAL* 3.8 3.6 - - - +
385A LEU* 1.3 75.2 - - - +
387A TYR* 1.3 59.5 + - - +
389A MET* 3.2 18.0 - - - +
390A ILE* 2.9 32.3 + - - +
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Residues in contact with TYR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A VAL* 5.2 1.5 - - - +
363A ALA* 2.3 33.9 + - + -
364A ILE* 3.7 11.6 + - - -
366A LEU* 4.3 12.8 - - + -
367A ALA* 3.9 22.9 + - + +
370A LEU* 3.8 26.7 - - + -
377A LEU* 4.5 10.5 - - + -
383A VAL 2.8 19.6 + - - +
384A ALA* 3.5 8.1 - - - +
385A LEU 3.3 0.2 - - - -
386A ALA* 1.3 76.1 - - - +
388A ALA* 1.3 59.5 + - - +
390A ILE* 3.3 6.9 + - + +
391A LEU* 2.9 49.3 + - + +
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Residues in contact with ALA 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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225A ARG* 4.4 12.2 + - - +
384A ALA 2.9 16.5 + - - +
385A LEU* 3.7 12.3 - - + +
386A ALA 3.3 0.2 - - - -
387A TYR* 1.3 79.7 - - - +
389A MET* 1.3 57.1 + - - +
391A LEU* 3.3 8.3 + - - +
392A GLY* 2.9 26.2 + - - -
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Residues in contact with MET 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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115A VAL* 4.3 30.3 - - + -
117A LEU* 5.1 3.6 - - + -
225A ARG* 4.5 13.9 - - - +
229A PRO* 5.5 9.2 - - + -
230A LEU* 3.3 46.6 - - + +
327A PHE* 3.5 29.2 - - + -
331A ALA* 6.0 0.4 - - - -
385A LEU* 2.9 15.6 + - + +
386A ALA* 3.2 27.3 + - - +
388A ALA* 1.3 75.2 - - - +
390A ILE* 1.3 60.1 + - - +
392A GLY* 3.8 5.9 + - - +
393A ILE* 4.2 1.4 - - - +
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Residues in contact with ILE 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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230A LEU* 4.6 5.2 - - + -
233A VAL* 4.2 20.9 - - + -
320A TYR* 3.3 28.5 - - + +
324A THR* 3.6 27.4 - - + +
327A PHE* 3.5 35.2 - - + -
328A VAL* 6.0 0.7 - - + -
363A ALA* 5.6 1.1 - - + -
366A LEU* 4.2 7.9 - - + -
386A ALA 2.9 20.1 + - - +
387A TYR* 3.7 6.7 - - + +
389A MET* 1.3 76.2 - - - +
391A LEU* 1.3 63.5 + - - +
392A GLY 2.9 5.7 + - - -
393A ILE* 3.1 10.5 + - + +
394A ASP* 2.9 18.2 + - - -
397A LEU* 4.6 3.3 - - + +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA* 4.7 11.4 - - + +
364A ILE* 6.6 0.4 - - + -
387A TYR* 2.9 39.9 + - + +
388A ALA* 3.8 8.1 - - - +
390A ILE* 1.3 76.4 - - - +
392A GLY* 1.3 63.1 + - - +
394A ASP* 3.2 30.6 - - - +
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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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218A VAL* 5.1 2.9 - - - +
222A GLN* 3.6 29.1 + - - +
225A ARG* 4.2 20.2 - - - -
230A LEU* 5.7 0.9 - - - -
388A ALA 2.9 14.8 + - - -
389A MET 3.8 5.1 + - - -
390A ILE 2.9 2.4 + - - -
391A LEU* 1.3 81.0 - - - +
393A ILE* 1.3 58.6 + - - -
394A ASP 3.4 1.4 + - - -
395A ALA* 4.3 5.0 + - - +
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Residues in contact with ILE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLN* 5.4 4.9 - - + -
225A ARG* 4.4 2.9 - - - +
226A VAL* 4.1 16.8 - - + -
230A LEU* 3.7 53.4 - - + +
233A VAL* 4.4 9.6 - - + -
234A VAL* 4.5 11.9 - - + -
389A MET 4.2 7.1 + - - +
390A ILE* 3.1 9.6 + - + +
392A GLY* 1.3 73.3 - - - +
394A ASP* 1.3 64.5 + - - +
395A ALA* 3.1 2.9 - - - -
396A ILE* 3.1 29.3 + - + +
397A LEU* 3.0 40.3 + - + +
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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