Contacts of the helix formed by residues 384 - 397 (chain A) in PDB entry 4OWW
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 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A GLN* 3.6 8.9 + - - +
382A CYS 5.1 0.2 - - - -
383A THR* 1.3 86.4 + - - +
385A ASN* 1.3 60.0 + - - +
386A VAL* 3.8 6.6 + - - +
387A ALA* 3.2 25.3 + - - +
388A ALA* 3.0 27.0 + - - +
74C HIS* 5.8 7.9 - - - -
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Residues in contact with ASN 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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383A THR 5.5 1.0 + - - -
384A SER* 1.3 71.3 - - - +
386A VAL* 1.3 60.8 + - + +
388A ALA* 3.8 6.4 - - - +
389A SER* 2.9 31.7 + - - -
71C ALA* 5.9 8.7 - - + +
74C HIS* 6.1 5.4 + - - +
91C GLY* 4.9 9.5 - - - +
93C LEU* 6.1 1.7 - - - +
94C ILE* 4.3 14.2 - - + +
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A SER* 3.3 6.8 + - - +
385A ASN* 1.3 77.1 - - + +
387A ALA* 1.3 60.2 + - + +
389A SER* 3.4 2.0 + - - -
390A ASN* 2.9 46.4 + - - +
74C HIS* 5.2 4.5 - - - +
75C ALA* 3.5 39.7 - - + +
78C HIS* 5.3 7.2 - - + +
79C SER* 3.7 26.2 - - - +
83C PHE* 3.9 6.9 - - + -
94C ILE* 4.3 10.1 - - + -
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLN* 3.4 39.7 - - + +
344A SER* 6.0 0.4 - - - -
346A ARG* 5.8 0.8 - - + +
347A CYS* 4.4 4.0 - - - -
382A CYS* 4.1 8.9 - - + -
384A SER* 3.2 18.5 + - - +
386A VAL* 1.3 78.5 - - - +
388A ALA* 1.3 61.1 + - - +
390A ASN* 3.3 6.7 + - - +
391A ALA* 2.8 30.8 + - - +
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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
----------------------------------------------------------
379A LEU* 5.5 1.1 - - - +
382A CYS* 3.8 23.5 - - + +
384A SER 3.0 18.1 + - - +
385A ASN* 3.8 8.3 - - - +
387A ALA* 1.3 75.3 - - - +
389A SER* 1.3 62.3 + - - +
391A ALA* 3.2 3.2 + - - +
392A LYS* 3.0 43.3 + - - +
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Residues in contact with SER 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASN 2.9 18.4 + - - -
386A VAL 3.6 4.0 - - - -
388A ALA* 1.3 77.7 - - - +
390A ASN* 1.3 62.5 + - - +
392A LYS* 3.3 17.1 + - - +
393A LEU 3.2 16.5 + - - -
436A PHE* 4.1 3.1 - - - -
83C PHE* 4.2 4.4 - - - -
92C ASN* 5.5 0.6 + - - -
94C ILE* 3.2 29.3 + - - +
96C PRO* 3.1 33.5 - - - +
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Residues in contact with ASN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 5.7 1.0 - - - -
260A ASN* 3.9 25.6 + - - +
347A CYS* 3.6 19.5 - - - -
386A VAL* 2.9 36.5 + - - +
387A ALA* 3.8 4.6 - - - +
389A SER* 1.3 75.4 - - - +
391A ALA* 1.3 52.1 + - - +
393A LEU* 3.2 6.5 + - - +
394A ALA* 2.8 33.8 + - - +
79C SER* 4.9 2.6 + - - -
81C GLY* 5.9 1.6 - - - -
83C PHE* 3.8 9.6 - - - -
96C PRO* 3.6 24.6 - - - +
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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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346A ARG* 5.3 1.8 - - + -
347A CYS* 3.6 11.4 - - - -
350A ILE* 3.7 25.9 - - + +
379A LEU* 4.3 9.6 - - + +
382A CYS* 3.9 17.9 - - - -
387A ALA 2.8 18.8 + - - +
388A ALA 3.4 5.8 - - - +
389A SER 3.2 0.2 - - - -
390A ASN* 1.3 78.0 - - - +
392A LYS* 1.3 56.5 + - - +
394A ALA* 3.3 2.7 + - - +
395A LEU* 2.9 28.8 + - - +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 5.6 7.2 - - + -
388A ALA* 3.0 33.9 + - - +
389A SER* 3.6 11.5 - - - +
390A ASN 3.2 0.4 - - - -
391A ALA* 1.3 73.8 - - + +
393A LEU* 1.3 67.0 + - - +
395A LEU* 3.2 7.1 + - - +
396A PHE* 3.0 29.1 + - - -
432A THR* 3.1 25.7 + - - +
433A LEU* 3.9 20.0 - - + -
436A PHE* 3.8 26.5 - - + -
91C GLY 3.0 18.6 + - - -
92C ASN* 2.8 29.5 + - - +
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Residues in contact with LEU 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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256A ARG* 5.2 4.5 - - + -
259A GLN* 3.4 39.9 - - - +
260A ASN* 5.8 1.3 - - - +
389A SER 3.2 10.3 + - - +
390A ASN* 3.5 9.4 - - - +
392A LYS* 1.3 76.4 - - - +
394A ALA* 1.3 58.6 + - - +
396A PHE* 3.0 3.8 + - + -
397A TYR* 2.8 52.5 + - + +
400A LEU* 4.2 7.2 - - + -
436A PHE* 3.5 12.2 - - + -
440A ILE* 4.0 29.8 - - + -
444A PHE* 4.2 8.5 - - + -
96C PRO* 3.8 18.8 - - + +
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 4.4 9.8 - - - +
347A CYS* 4.3 15.0 - - + +
350A ILE* 4.1 11.1 - - + +
351A ARG* 3.1 50.7 + - + +
354A CYS* 5.0 0.2 - - - -
390A ASN 2.8 21.0 + - - +
391A ALA* 3.4 9.2 - - - +
393A LEU* 1.3 75.8 - - - +
395A LEU* 1.3 62.7 + - - +
397A TYR* 3.3 4.7 + - - +
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Residues in contact with LEU 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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350A ILE* 3.8 9.8 - - + +
351A ARG* 4.9 1.2 + - - -
354A CYS* 3.9 25.4 - - - -
375A ILE* 3.9 33.2 - - + -
379A LEU* 4.4 5.6 - - + -
391A ALA 2.9 17.3 + - - +
392A LYS* 3.2 6.0 + - - +
394A ALA* 1.3 76.5 - - - +
396A PHE* 1.3 61.4 + - + +
397A TYR 3.6 0.3 + - - -
398A ASP 4.9 0.7 + - - -
399A TRP* 4.2 8.1 + - - -
411A ASN 4.4 5.4 - - - +
414A PRO* 4.1 2.0 - - + -
415A ALA* 3.6 42.4 + - + +
418A VAL* 4.9 0.9 - - + -
433A LEU* 4.2 31.4 - - + -
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Residues in contact with PHE 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 LYS 3.0 23.6 + - - +
393A LEU* 3.9 3.4 - - + +
395A LEU* 1.3 77.4 - - + +
397A TYR* 1.3 55.1 + - - +
398A ASP 3.2 2.5 - - - -
399A TRP* 2.8 71.0 + + + +
400A LEU* 3.6 12.9 + - + +
415A ALA* 3.7 19.1 - - + -
419A MET* 4.0 20.9 - - + -
433A LEU* 3.6 45.8 - - + -
436A PHE* 3.5 28.0 - + + -
437A MET* 4.0 15.7 - - + -
440A ILE* 5.8 2.2 - - + -
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Residues in contact with TYR 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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252A ARG* 3.5 47.6 + - + -
253A ASP* 4.8 6.1 - - - -
255A VAL* 3.4 14.6 - - - +
256A ARG* 3.1 38.7 + - + -
259A GLN* 3.0 28.5 + - - -
292A LEU* 4.8 5.6 - - + -
351A ARG* 3.9 12.6 - - - +
393A LEU* 2.8 36.6 + - + +
394A ALA* 3.3 13.7 + - - +
395A LEU 3.4 0.4 - - - -
396A PHE* 1.3 76.5 - - - +
398A ASP* 1.3 59.7 + - - +
399A TRP 3.6 0.3 + - - -
400A LEU* 3.7 20.8 + - + +
401A PHE* 4.8 1.0 + - - -
444A PHE* 3.6 15.8 - + - -
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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