Contacts of the helix formed by residues 385 - 398 (chain A) in PDB entry 4U0L
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 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TRP* 3.7 12.3 + - - -
383A ALA* 3.4 2.5 - - - +
384A ASP* 1.3 80.3 - - - +
386A LYS* 1.3 60.0 + - - +
387A SER* 3.0 23.0 + - - -
388A GLU* 3.2 17.1 + - - +
389A ALA* 2.9 28.2 + - - +
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Residues in contact with LYS 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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5A TRP* 3.4 34.4 - - + -
385A SER* 1.3 73.1 - - - +
387A SER* 1.3 60.7 - - - +
389A ALA* 3.4 6.8 + - - +
390A LEU* 3.0 28.1 + - - +
404A SER* 3.7 18.6 - - - +
405A GLU* 3.5 34.9 + - - +
407A ILE* 3.2 32.5 + - + +
408A VAL* 4.6 6.5 - - - +
409A LEU 4.9 0.9 - - - +
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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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385A SER* 3.0 17.4 + - - -
386A LYS* 1.3 80.9 - - - +
388A GLU* 1.3 59.7 + - - +
390A LEU* 3.5 4.9 + - - +
391A LYS* 3.1 38.0 + - - +
404A SER* 4.1 15.7 + - - -
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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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383A ALA* 3.9 11.9 - - + -
384A ASP* 4.6 7.2 - - + +
385A SER* 3.2 23.2 + - - +
387A SER* 1.3 76.9 + - - +
389A ALA* 1.3 61.2 + - - +
390A LEU 3.2 1.3 - - - -
391A LYS* 2.3 42.3 + - - +
392A LYS* 2.9 45.6 + - + +
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Residues in contact with ALA 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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5A TRP* 4.1 9.9 - - + -
7A PHE* 4.0 13.9 - - + -
380A ALA* 3.6 25.8 - - - +
383A ALA* 3.5 11.8 - - + +
385A SER 2.9 19.6 + - - +
386A LYS* 3.4 8.0 + - - +
388A GLU* 1.3 75.8 - - - +
390A LEU* 1.3 58.9 + - - +
392A LYS 3.4 0.5 + - - -
393A ILE* 3.0 30.0 + - - +
407A ILE* 4.1 8.1 - - + -
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Residues in contact with LEU 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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10A TYR* 3.5 35.2 - - + -
386A LYS 3.0 17.6 + - - +
387A SER* 3.5 7.2 - - - +
389A ALA* 1.3 73.8 - - - +
391A LYS* 1.3 62.8 + - + +
393A ILE* 3.3 3.9 + - - +
394A ASN* 2.8 48.2 + - - +
399A ASN* 5.3 2.2 - - - +
401A VAL* 3.7 12.3 - - + +
402A THR* 3.5 31.9 - - - +
404A SER* 3.9 16.4 - - - +
407A ILE* 3.6 12.7 - - + +
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Residues in contact with LYS 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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387A SER* 3.1 22.7 + - - +
388A GLU* 2.3 41.8 + - - +
390A LEU* 1.3 81.8 - - + +
392A LYS* 1.3 63.3 + - + +
394A ASN* 3.4 7.7 + - - +
395A MET* 3.3 20.9 + - - +
399A ASN* 6.1 0.4 - - - +
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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
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376A ILE* 3.3 9.8 - - - +
379A SER* 3.8 31.3 + - - +
380A ALA* 3.7 23.1 - - + +
383A ALA* 4.9 5.7 - - + +
388A GLU* 2.9 33.1 + - + +
389A ALA 3.8 0.2 - - - +
391A LYS* 1.3 75.8 - - + +
393A ILE* 1.3 65.6 + - - +
395A MET* 3.1 41.2 + - - +
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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
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7A PHE* 3.8 36.8 - - + -
10A TYR* 3.6 33.4 - - + -
11A TYR* 3.6 23.8 - - + +
376A ILE* 4.5 4.0 - - - -
377A LEU* 3.8 20.9 - - + +
380A ALA* 3.6 11.8 - - + +
389A ALA 3.0 16.8 + - - +
390A LEU* 3.4 13.5 - - - +
392A LYS* 1.3 77.2 - - - +
394A ASN* 1.3 60.0 + - - +
395A MET 3.0 0.2 - - - -
396A ALA* 2.9 24.4 + - - +
397A PHE* 3.4 13.1 + - + -
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Residues in contact with ASN 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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10A TYR* 2.6 37.1 + - - -
390A LEU* 2.8 26.8 + - - +
391A LYS* 3.7 8.4 - - - +
392A LYS 3.2 0.2 - - - -
393A ILE* 1.3 75.1 - - - +
395A MET* 1.3 58.8 + - - +
396A ALA 3.1 0.2 - - - -
397A PHE 4.3 0.7 - - - +
398A GLY* 2.7 44.7 + - - +
399A ASN* 3.2 26.9 + - + +
401A VAL* 2.9 27.2 + - - +
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Residues in contact with MET 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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293A GLN* 3.0 18.4 + - - +
372A ARG* 3.8 27.8 - - - +
376A ILE* 4.0 22.1 - - + +
379A SER* 5.7 1.1 - - - -
391A LYS 3.3 11.3 + - - +
392A LYS* 3.2 37.5 - - - +
393A ILE 3.0 1.0 - - - -
394A ASN* 1.3 77.7 - - - +
396A ALA* 1.3 57.0 + - - +
398A GLY* 4.5 0.9 + - - -
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Residues in contact with ALA 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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289A TRP* 3.4 19.4 - - + -
292A ALA* 3.7 2.8 - - - +
293A GLN* 2.8 22.4 + - - +
373A LEU* 3.7 29.6 - - + -
376A ILE* 3.8 15.2 - - + +
377A LEU* 4.6 2.2 - - + -
393A ILE 2.9 11.9 + - - +
395A MET* 1.3 81.7 - - - +
397A PHE* 1.3 72.3 + - + +
398A GLY 3.6 0.4 - - - -
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Residues in contact with PHE 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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10A TYR* 3.6 29.4 - + - +
11A TYR* 3.4 37.9 - + - -
18A LEU* 3.7 22.7 - - + +
124A PHE* 4.5 0.9 - - - -
285A PHE* 3.5 29.6 - - + -
286A MET* 5.6 0.2 - - - -
288A ALA* 4.6 5.9 - - + +
289A TRP* 4.0 18.8 - - + +
292A ALA* 3.7 12.3 - - - +
326A MET* 3.8 16.4 - - + -
373A LEU* 5.0 4.0 - - + -
377A LEU* 4.1 4.9 - - + -
393A ILE* 3.4 21.7 + - + -
396A ALA* 1.3 86.6 - - + +
398A GLY* 1.3 64.6 + - - +
400A ARG* 3.8 18.7 + - - +
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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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10A TYR* 4.6 0.3 + - - -
124A PHE* 3.7 20.9 - - - -
292A ALA* 3.9 3.8 - - - +
394A ASN* 2.7 40.1 + - - +
395A MET 4.5 0.6 - - - -
396A ALA 3.6 1.8 - - - -
397A PHE* 1.3 76.9 - - - +
399A ASN* 1.3 60.7 + - - -
400A ARG* 2.9 9.0 + - - +
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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