Contacts of the strand formed by residues 392 - 403 (chain A) in PDB entry 2HU4
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 VAL 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASN 5.0 7.6 - - - +
361A TRP* 4.4 15.3 - - + -
377A ILE* 3.3 8.9 - - - +
378A TRP* 2.8 50.4 + - + -
390A PHE* 3.6 3.5 - - - -
391A SER* 1.3 91.5 - - - +
394A LYS* 1.3 73.7 + - - +
395A GLN* 4.8 3.8 - - + +
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Residues in contact with LYS 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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364A ARG* 5.0 4.0 - - - +
366A LYS* 4.1 2.0 - - - +
375A GLU* 3.0 39.6 + - - +
376A MET 3.4 9.6 - - - +
377A ILE* 4.2 12.8 - - + +
390A PHE* 3.8 27.7 - - + -
392A VAL* 1.3 83.0 - - - +
395A GLN* 1.3 64.2 + - - +
396A ASP* 4.0 16.7 + - - +
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Residues in contact with GLN 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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96A GLY* 3.7 4.0 - - - -
97A TRP* 2.8 65.6 - - + +
361A TRP* 5.1 2.8 - - + -
375A GLU* 3.4 3.4 - - - -
376A MET* 2.9 44.1 + - + +
392A VAL* 4.8 5.6 - - + +
394A LYS* 1.3 73.9 - - - +
396A ASP* 1.3 73.5 + - - +
397A ILE* 3.3 9.6 - - + +
446A PHE* 5.3 2.1 - - - -
453A THR* 3.5 13.8 + - - +
454A VAL 3.1 23.2 - - - +
455A GLY* 3.9 4.9 - - - +
458A TRP* 5.7 0.3 - - - -
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Residues in contact with ASP 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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366A LYS* 2.6 34.8 + - - +
374A PHE 4.3 3.1 - - - -
394A LYS* 4.0 16.2 + - - +
395A GLN* 1.3 73.9 - - - +
397A ILE* 1.3 65.5 + - - +
398A VAL 5.0 2.2 - - - +
399A ALA* 6.4 0.2 - - - -
455A GLY* 3.3 12.2 - - - -
456A TRP* 3.1 37.6 + - - +
458A TRP* 4.3 3.6 - - - -
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Residues in contact with ILE 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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97A TRP* 5.4 0.4 - - + -
374A PHE* 3.2 28.2 + - + +
376A MET* 3.8 22.0 - - + +
395A GLN* 3.3 32.8 - - + +
396A ASP* 1.3 78.3 - - - +
398A VAL* 1.3 80.2 + - + +
422A PHE* 4.2 11.0 - - + -
424A VAL* 4.6 2.7 - - + -
444A ILE* 3.9 7.4 - - + -
446A PHE* 3.7 40.2 - - + -
456A TRP 3.4 7.2 - - - +
458A TRP* 3.1 27.0 + - - -
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LYS* 2.9 24.7 - - - +
373A GLY* 3.9 8.5 - - - +
374A PHE* 2.9 30.6 + - + +
396A ASP* 5.8 1.6 - - - -
397A ILE* 1.3 97.9 - - + +
399A ALA* 1.3 72.4 + - - +
402A ASP* 4.0 20.2 - - + +
403A TRP 4.4 9.0 - - - +
404A SER* 4.8 1.8 - - - -
424A VAL* 5.3 0.7 - - + -
426A LEU* 4.3 8.5 - - + -
444A ILE* 3.9 16.6 - - + -
456A TRP 3.9 0.9 + - - -
457A SER* 3.9 3.8 - - - -
458A TRP 4.0 7.4 - - - +
459A PRO* 4.4 9.4 - - + -
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Residues in contact with ALA 399 (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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366A LYS* 4.1 4.9 - - - +
373A GLY* 3.2 8.0 - - - -
396A ASP* 6.0 1.1 - - - +
398A VAL* 1.3 77.9 - - - +
400A ILE* 1.3 62.4 + - - +
401A THR* 3.0 21.5 - - + +
402A ASP* 3.1 17.6 + - - +
456A TRP 4.8 0.4 + - - -
457A SER* 3.1 28.1 + - - +
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Residues in contact with ILE 400 (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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366A LYS* 3.5 43.2 - - + +
367A SER* 4.1 23.1 - - - +
372A SER* 3.5 16.8 - - - +
373A GLY* 4.1 4.9 - - - -
399A ALA* 1.3 71.8 - - - +
401A THR* 1.3 62.7 + - + +
402A ASP 3.1 2.7 + - - -
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Residues in contact with THR 401 (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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399A ALA* 3.5 12.8 - - + +
400A ILE* 1.3 81.3 - - + +
402A ASP* 1.3 73.9 + - - +
403A TRP* 5.7 2.9 + - - -
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Residues in contact with ASP 402 (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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372A SER* 3.5 4.4 - - - -
373A GLY* 2.8 28.6 + - - -
398A VAL* 4.0 5.6 - - + +
399A ALA* 3.1 15.7 + - - +
400A ILE 4.6 0.4 - - - -
401A THR* 1.3 103.8 + - - +
403A TRP* 1.3 66.9 + - - +
457A SER* 4.5 1.0 + - - -
459A PRO* 3.7 37.6 - - + +
461A GLY* 5.6 1.7 + - - -
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Residues in contact with TRP 403 (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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370A SER* 4.3 8.5 - - - -
371A ARG* 3.6 19.3 - - + -
372A SER* 3.7 18.2 - - - -
398A VAL* 4.4 3.7 - - - +
401A THR 5.7 2.3 + - - -
402A ASP* 1.3 78.8 + - - +
404A SER* 1.3 62.2 + - - +
426A LEU* 3.7 20.8 - - - +
427A ILE 3.5 21.5 - - - +
428A ARG* 3.6 30.7 - - - +
432A LYS* 3.4 52.9 - - + -
433A GLU* 3.6 22.4 + - + +
459A PRO* 5.4 0.2 - - - +
460A ASP* 5.1 5.2 + - - +
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 4.1 6.2 - - - +
371A ARG* 3.1 22.3 + - - +
373A GLY* 2.8 39.5 + - - -
374A PHE* 4.5 4.5 - - - -
398A VAL* 4.8 2.2 - - - -
402A ASP 3.6 1.0 + - - -
403A TRP* 1.3 74.9 - - - +
405A GLY* 1.3 61.2 + - - +
424A VAL* 4.4 14.1 - - - -
425A GLU 3.1 10.5 - - - -
426A LEU* 4.1 7.4 - - - -
427A ILE* 3.2 24.1 + - - +
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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