Contacts of the strand formed by residues 389 - 397 (chain A) in PDB entry 4M5X
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 ALA 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A ILE* 4.0 18.2 - - + -
333A GLN 3.1 16.8 - - - +
334A CYS* 3.7 11.0 - - - -
335A LYS* 3.8 7.2 - - - +
372A GLN* 3.6 6.2 - - - +
373A LEU* 2.9 34.2 + - + -
379A TYR* 4.2 16.4 - - + -
387A GLN 3.6 0.6 + - - +
388A GLU* 1.3 77.4 - - - +
390A GLU* 1.3 64.8 + - - +
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Residues in contact with GLU 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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331A TYR* 3.9 7.8 - - + +
332A ILE* 3.3 3.0 - - - +
333A GLN* 2.7 59.6 + - + +
335A LYS* 3.9 16.3 - - + -
370A VAL* 3.6 21.5 - - + +
371A GLU 3.5 4.0 - - - -
372A GLN* 3.5 28.4 + - - +
389A ALA* 1.3 77.9 - - - +
391A LYS* 1.3 60.0 + - - +
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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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330A SER* 5.3 8.3 - - - +
331A TYR* 3.3 14.4 - - - +
332A ILE* 4.1 15.9 - - + -
370A VAL* 3.7 1.1 - - - -
371A GLU* 2.7 68.5 + - + +
373A LEU* 4.0 28.3 - - + -
389A ALA 4.3 0.2 - - - -
390A GLU* 1.3 75.3 - - - +
392A GLY* 1.3 64.2 + - - +
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Residues in contact with GLY 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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330A SER* 3.5 2.8 + - - -
331A TYR* 3.0 50.7 + - - +
369A ALA 4.4 9.6 - - - -
391A LYS* 1.3 79.5 - - - +
393A VAL* 1.3 68.6 + - - +
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Residues in contact with VAL 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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328A MET* 4.2 19.1 - - + -
329A VAL 3.3 11.4 - - - +
330A SER* 4.1 15.9 - - - +
331A TYR* 3.7 1.9 - - - -
345A GLU* 5.3 2.7 - - - +
367A TYR* 3.5 47.5 + - + +
368A VAL* 3.6 27.3 + - + +
369A ALA 5.1 0.2 + - - -
392A GLY* 1.3 78.7 - - - +
394A LYS* 1.3 67.7 + - - +
395A PHE* 5.8 0.4 - - + -
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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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328A MET* 3.3 5.9 - - - -
329A VAL* 2.9 48.5 + - + +
331A TYR* 3.9 28.7 + - + -
340A ARG* 4.7 11.0 - - - +
368A VAL* 4.9 4.5 - - + -
393A VAL* 1.3 78.8 - - - +
395A PHE* 1.3 67.1 + - - +
436A PHE 5.0 2.5 - - - +
438A GLN* 4.0 28.7 - - + +
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Residues in contact with PHE 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 4.1 1.6 - - - -
328A MET* 3.8 21.1 - - + +
347A TYR* 3.6 21.3 - + - -
350A ILE* 3.6 33.0 - - + -
364A PHE* 3.8 24.9 - + - -
367A TYR* 3.9 21.3 - + - -
368A VAL* 3.8 25.1 - - + -
393A VAL* 5.8 0.4 - - + -
394A LYS* 1.3 73.4 - - - +
396A LEU* 1.3 57.6 + - - +
397A THR 4.3 1.8 - - - +
398A LEU* 3.9 10.8 - - + -
436A PHE* 3.5 27.7 + - + +
437A LEU* 3.5 15.9 - - + -
438A GLN* 2.7 34.1 + - - +
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Residues in contact with LEU 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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327A LYS* 2.9 27.4 + - + +
328A MET 3.8 20.4 - - - +
329A VAL* 3.8 24.7 - - + +
344A ARG* 5.2 7.0 - - + -
394A LYS 3.5 0.6 + - - -
395A PHE* 1.3 74.1 - - - +
397A THR* 1.3 70.7 + - + +
437A LEU* 4.2 11.7 - - - +
438A GLN* 3.8 37.8 + - + +
439A LYS 4.7 6.5 + - - +
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Residues in contact with THR 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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325A ARG 4.8 0.7 + - - -
326A GLY* 3.5 5.4 - - - -
327A LYS* 2.7 54.3 + - + +
347A TYR* 2.6 24.1 + - - -
395A PHE* 3.7 2.3 - - - -
396A LEU* 1.3 86.7 - - + +
398A LEU* 1.3 61.8 + - - +
437A LEU* 4.5 4.9 - - - -
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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