Contacts of the strand formed by residues 386 - 392 (chain A) in PDB entry 1X11
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 THR 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ASN* 3.3 2.8 - - - -
336A TYR* 2.6 52.8 + - - +
385A MSE 1.3 77.7 - - - +
387A GLU* 1.3 71.5 + - - +
388A VAL* 3.8 13.2 - - + -
401A ASN* 4.0 20.9 - - - +
408A MSE 4.1 7.2 - - + +
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Residues in contact with GLU 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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334A ALA 3.6 5.6 - - - +
335A ASN* 3.2 19.7 - - - +
385A MSE 3.5 6.0 + - - +
386A THR* 1.3 77.1 - - - +
388A VAL* 1.3 62.9 + - - +
401A ASN* 4.1 3.8 - - - +
402A ALA* 3.3 26.8 + - + +
403A ASP* 4.6 1.6 + - + +
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Residues in contact with VAL 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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333A ALA* 3.7 4.5 - - - +
334A ALA* 2.7 59.8 + - + +
336A TYR* 4.1 12.1 - - + +
386A THR* 3.8 10.3 - - + +
387A GLU* 1.3 79.9 - - - +
389A ASP* 1.3 59.2 + - - +
390A LEU* 4.5 3.8 - - + -
399A VAL* 3.7 21.8 - - + -
400A LEU 2.8 19.7 - - - +
402A ALA* 3.7 5.4 - - - +
408A MSE 3.4 28.9 - - + -
463A PHE* 4.3 7.0 - - + -
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Residues in contact with ASP 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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331A ILE* 4.7 23.0 - - + +
332A PHE 3.4 9.9 - - - +
333A ALA* 4.4 8.5 - - - +
388A VAL* 1.3 75.1 - - - +
390A LEU* 1.3 65.1 + - - +
391A PHE 3.6 1.9 + - - -
400A LEU* 2.9 45.5 + - + +
402A ALA* 3.4 19.3 - - - +
405A GLN* 2.6 31.5 + - - +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A ILE 3.6 0.9 - - - +
331A ILE* 3.1 27.0 - - - +
332A PHE* 2.8 16.2 + - + +
334A ALA* 4.0 15.0 - - + -
388A VAL* 4.1 2.4 - - + -
389A ASP* 1.3 73.1 - - - +
391A PHE* 1.3 58.4 + - - +
392A ILE* 3.9 14.6 + - + +
397A ILE* 5.6 5.4 - - + -
398A LYS 3.5 2.0 - - - +
399A VAL* 3.7 34.1 - - + -
426A VAL* 4.9 2.5 - - + -
428A LEU* 5.2 7.2 - - + -
463A PHE* 3.7 35.0 - - + -
471A ILE* 3.8 35.4 - - + -
475A ILE* 5.3 1.1 - - + -
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Residues in contact with PHE 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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328A ASP 3.5 20.9 - - - -
329A GLY* 3.7 15.5 - - - -
330A ILE 3.6 3.4 - - - -
331A ILE* 4.0 18.6 - - + -
389A ASP 3.6 0.2 + - - -
390A LEU* 1.3 71.9 - - - +
392A ILE* 1.3 60.8 + - - +
393A LEU* 4.0 29.2 - - + -
396A ARG* 3.5 5.8 - - + +
397A ILE* 3.3 7.4 - - - +
398A LYS* 2.7 72.4 + - + +
400A LEU* 4.3 18.6 - - + -
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Residues in contact with ILE 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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326A LEU* 4.0 13.3 - - + +
329A GLY* 3.2 4.8 - - - -
330A ILE* 3.1 34.8 + - + +
332A PHE* 3.4 36.8 - - + -
390A LEU* 4.0 22.7 - - + +
391A PHE* 1.3 74.4 - - - +
393A LEU* 1.3 68.1 + - - +
396A ARG 3.8 1.6 - - - -
397A ILE* 3.6 10.5 - - + -
471A ILE* 4.4 10.5 - - + +
474A SER* 4.2 7.2 - - - +
475A ILE* 3.5 51.6 - - + +
478A ALA* 4.5 0.7 - - + -
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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