Contacts of the helix formed by residues 371 - 383 (chain A) in PDB entry 2WU4
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 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ARG* 3.3 7.3 + - - +
369A GLN 3.7 2.8 + - - -
370A ALA* 1.3 79.0 - - - +
372A ASP* 1.3 64.2 + - - +
373A LEU* 3.5 9.2 + - - +
374A ALA* 3.2 22.3 + - - +
375A ALA* 3.1 14.7 + - - +
539A LEU 4.7 9.2 + - - -
540A LEU* 5.9 1.4 - - - -
542A ALA 5.4 6.0 + - - -
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Residues in contact with ASP 372 (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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364A ARG* 3.1 30.2 + - - +
371A SER* 1.3 75.2 - - - +
373A LEU* 1.3 57.4 + - - +
375A ALA* 3.7 2.6 - - - +
376A GLU* 2.9 32.2 + - - +
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER* 3.3 8.4 + - - +
372A ASP* 1.3 76.4 - - - +
374A ALA* 1.3 59.9 + - - +
376A GLU* 3.1 6.3 + - + +
377A ALA* 2.9 27.0 + - - +
539A LEU* 3.5 31.4 - - + -
542A ALA* 5.8 6.7 - - + -
373B LEU* 5.8 0.2 - - + -
535B PHE* 4.0 15.0 - - + -
538B LYS* 3.9 41.5 - - + +
539B LEU* 4.2 13.7 - - + -
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA* 3.7 20.6 - - + -
371A SER* 3.2 17.6 + - - +
373A LEU* 1.3 76.4 - - - +
375A ALA* 1.3 60.1 + - - +
377A ALA* 3.1 4.9 + - - +
378A VAL* 2.9 33.5 + - - +
536A LEU* 4.3 15.1 - - + +
539A LEU* 3.6 24.3 - - + +
540A LEU* 5.7 2.0 - - - +
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 4.1 12.2 - - + +
364A ARG* 3.5 37.0 - - - +
370A ALA* 3.9 7.5 - - + +
371A SER 3.1 16.3 + - - +
372A ASP 3.7 4.3 - - - +
374A ALA* 1.3 77.9 - - - +
376A GLU* 1.3 57.8 + - - +
378A VAL* 3.3 4.5 + - - +
379A VAL* 3.0 33.3 + - + +
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Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 4.7 12.8 - - - +
372A ASP 2.9 17.5 + - - +
373A LEU* 3.1 13.4 + - + +
375A ALA* 1.3 73.5 - - - +
377A ALA* 1.3 66.3 + - - +
379A VAL* 3.2 13.6 + - - +
380A LEU* 2.9 62.4 + - + +
535B PHE* 5.2 0.9 - - + -
538B LYS* 3.4 38.1 + - + +
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Residues in contact with ALA 377 (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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373A LEU 2.9 9.5 + - - +
374A ALA 3.4 8.7 - - - +
376A GLU* 1.3 76.5 - - - +
378A VAL* 1.3 57.4 + - - +
380A LEU* 3.7 1.9 - - - +
381A HIS* 2.8 31.9 + - - +
531A PHE* 3.9 20.2 - - + -
535A PHE* 4.5 0.9 - - + -
536A LEU* 4.6 0.2 - - + -
539A LEU* 4.0 12.1 - - + -
1545A P6G 3.9 8.3 - - - +
535B PHE* 3.5 31.8 - - + -
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 3.8 22.7 - - + -
367A VAL* 4.9 6.5 - - + -
374A ALA* 2.9 20.8 + - + +
375A ALA* 3.5 8.7 - - - +
377A ALA* 1.3 75.6 - - - +
379A VAL* 1.3 65.1 + - - +
381A HIS* 3.2 2.2 + - - +
382A TYR* 3.0 28.9 + - + +
401A VAL* 3.9 31.6 - - + -
531A PHE* 3.9 18.2 - - + -
532A TRP* 3.8 25.1 - - + -
536A LEU* 4.4 5.6 - - + -
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Residues in contact with VAL 379 (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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356A ARG* 3.3 25.6 - - - +
359A PHE* 3.8 22.9 - - + -
360A LEU* 3.9 31.6 - - + -
363A VAL* 4.0 18.2 - - + -
375A ALA* 3.0 20.3 + - + +
376A GLU* 3.2 13.4 + - - +
378A VAL* 1.3 77.0 - - - +
380A LEU* 1.3 62.2 + - + +
382A TYR 3.7 0.2 - - - -
383A THR* 2.7 39.5 + - - +
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Residues in contact with LEU 380 (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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356A ARG* 4.9 0.7 - - - +
376A GLU* 2.9 45.7 + - + +
379A VAL* 1.3 84.5 - - + +
381A HIS* 1.3 63.7 + - - +
382A TYR 3.3 0.5 + - - -
383A THR 3.4 2.4 + - - +
385A TRP* 3.2 53.5 + - + -
1545A P6G 3.3 21.4 - - - +
527B GLN* 4.2 1.4 + - - -
530B ALA 5.6 0.2 - - - +
534B ARG* 4.2 15.5 - - + +
535B PHE* 3.7 42.0 - - + +
538B LYS* 5.4 3.1 - - + -
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Residues in contact with HIS 381 (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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377A ALA 2.8 17.7 + - - +
378A VAL* 3.5 5.4 - - - +
380A LEU* 1.3 78.9 - - - +
382A TYR* 1.3 85.1 + + + +
527A GLN* 5.5 1.1 - - + -
528A THR* 2.9 31.8 + - + -
531A PHE* 4.1 31.6 - + + -
1545A P6G 3.6 61.1 + - - +
527B GLN* 3.7 14.2 + - - -
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Residues in contact with TYR 382 (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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359A PHE* 4.0 18.6 - - + -
378A VAL* 3.0 23.3 + - + +
381A HIS* 1.3 94.7 - + + +
383A THR* 1.3 66.4 + - - +
393A HIS* 3.1 22.0 + - - -
397A ALA* 4.0 14.8 - - + +
400A ALA* 3.8 10.3 - - + -
401A VAL* 3.5 31.9 - - + -
404A ASP* 2.5 32.5 + - - +
528A THR* 3.2 9.6 - - + +
531A PHE* 4.9 2.2 - + - -
532A TRP* 2.8 39.8 + + - -
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Residues in contact with THR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 2.6 43.4 + - - +
359A PHE* 4.4 4.9 - - - -
379A VAL* 2.7 21.4 + - - +
380A LEU 3.4 0.8 + - - -
382A TYR* 1.3 77.0 - - - +
384A ASP* 1.3 69.6 + - - +
385A TRP* 3.3 44.6 - - + -
388A PRO* 4.2 4.5 - - + -
393A HIS* 4.4 1.8 - - - -
394A LEU* 5.9 1.6 - - - -
527B GLN* 3.1 27.7 + - - +
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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