Contacts of the strand formed by residues 394 - 401 (chain A) in PDB entry 3HN8
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 ASP 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A LYS* 3.4 31.6 - - + +
385A TYR* 3.4 3.2 - - - -
386A ASP* 2.6 41.7 + - + +
388A ASP* 3.6 1.9 + - - -
392A ARG* 3.2 5.4 - - - +
393A HIS* 1.3 71.7 - - - +
395A LEU* 1.3 61.6 + - - +
396A ILE* 4.1 0.2 - - - +
601A CA 2.8 22.4 - - - -
606A CA 2.8 22.5 - - - -
476B GLU* 3.2 9.3 - - - +
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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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327A LYS* 3.4 19.8 + - - -
383A SER* 4.7 0.9 - - - -
384A VAL 3.1 20.6 - - - +
385A TYR* 3.4 35.2 - - + +
393A HIS 3.7 2.4 + - - -
394A ASP* 1.3 70.6 - - - +
396A ILE* 1.3 60.6 + - - +
397A GLY* 3.5 21.3 - - - +
398A GLN* 4.3 15.5 - - + +
423A GLY 4.1 9.0 - - - +
424A GLY* 5.5 0.2 - - - -
425A SER* 3.2 49.1 - - - +
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.8 18.6 - - + -
325A PRO* 3.4 31.9 - - + +
327A LYS* 4.2 20.8 + - + +
333A SER* 4.2 9.4 - - - +
335A PRO* 4.0 15.7 - - + -
384A VAL* 2.7 31.4 + - + +
385A TYR 3.6 21.1 - - - +
386A ASP* 3.7 16.6 - - + +
394A ASP 3.4 0.9 + - - +
395A LEU* 1.3 76.3 - - - +
397A GLY* 1.3 57.6 + - - +
420A ILE* 4.5 4.1 - - + +
422A GLU* 3.5 23.7 - - - +
423A GLY 5.3 0.3 + - - -
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Residues in contact with GLY 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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384A VAL 2.7 33.5 + - - +
395A LEU* 3.5 9.8 - - - +
396A ILE* 1.3 83.3 - - - +
398A GLN* 1.3 65.4 + - - +
420A ILE* 3.5 18.4 - - - +
421A LEU 3.5 11.4 - - - -
422A GLU* 4.5 0.9 - - - -
423A GLY 5.4 0.7 - - - -
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Residues in contact with GLN 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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381A HIS* 3.6 17.8 + - + +
382A PHE 3.1 8.3 - - - +
383A SER* 3.4 23.6 + - - +
384A VAL* 5.5 0.4 - - - -
385A TYR* 5.5 2.2 + - - -
395A LEU* 4.3 9.9 - - + +
397A GLY* 1.3 81.0 - - - +
399A VAL* 1.3 66.7 + - - +
420A ILE* 3.7 1.0 - - - +
421A LEU* 2.7 40.0 + - + +
425A SER* 3.6 24.0 + - - -
429A ASP* 3.0 24.1 + - - +
432A GLU* 3.1 15.0 - - - +
455A ASN* 5.7 0.8 - - - +
564A GLN* 3.3 14.6 - - - +
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Residues in contact with VAL 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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301A ILE* 4.1 10.8 - - + -
303A PHE* 4.6 9.9 - - + -
381A HIS* 3.5 5.1 - - - -
382A PHE* 2.9 69.7 + - + +
384A VAL* 5.5 2.0 - - + -
398A GLN* 1.3 81.6 - - - +
400A VAL* 1.3 67.6 + - - +
401A LEU* 5.1 1.8 - - + -
418A ARG* 4.6 11.7 - - + +
419A ASP 3.8 8.7 - - - +
420A ILE* 3.7 31.9 - - + +
421A LEU* 4.5 5.2 - - - -
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Residues in contact with VAL 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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342A LEU* 5.5 0.2 - - + -
379A LYS* 4.2 16.2 - - + -
380A LEU 3.7 10.1 - - - +
381A HIS* 4.0 10.3 - - + +
399A VAL* 1.3 79.2 - - - +
401A LEU* 1.3 70.7 + - - +
402A ASP 3.7 2.3 + - - -
418A ARG* 5.1 5.7 + - - +
421A LEU* 4.7 5.0 - - + +
432A GLU* 3.6 45.1 - - + +
454A SER* 4.2 13.5 - - - +
562A TRP* 3.9 44.0 + - + +
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Residues in contact with LEU 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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303A PHE* 3.5 39.3 - - + -
305A LEU* 4.4 8.3 - - + -
316A VAL* 5.9 0.7 - - + -
379A LYS* 3.6 8.3 - - - +
380A LEU* 3.0 62.1 + - + -
382A PHE* 4.2 11.2 - - + -
399A VAL* 4.1 3.5 + - + -
400A VAL* 1.3 76.5 - - - +
402A ASP* 1.3 67.8 + - - +
404A LEU* 3.7 7.7 - - + +
407A LEU* 3.6 28.5 - - + -
418A ARG* 3.9 20.6 - - + +
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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