Contacts of the strand formed by residues 390 - 403 (chain A) in PDB entry 4MJV
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 GLN 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A ILE* 5.2 7.0 - - + +
330A ASP* 5.6 1.0 - - - +
364A ARG* 5.6 0.5 + - - -
377A LEU* 3.6 26.7 - - + +
378A ARG 3.6 7.6 - - - +
379A ILE* 4.5 7.4 - - + -
388A LYS 3.4 6.7 + - - +
389A GLU* 1.3 72.7 - - - +
391A ILE* 1.3 59.8 + - - +
392A ARG 3.6 18.8 - - - +
394A LYS* 3.6 33.6 - - - +
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Residues in contact with ILE 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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359A ASP* 4.5 9.0 - - - +
378A ARG* 3.1 51.0 + - + +
380A LYS* 3.8 20.9 - - + +
389A GLU* 3.7 23.1 - - + +
390A GLN* 1.3 78.4 - - - +
392A ARG* 1.3 79.9 + - + +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LYS* 3.4 66.6 + - - +
361A TRP* 3.7 27.1 - - + -
376A ILE 4.7 0.2 - - - -
377A LEU* 3.7 2.3 - - - -
378A ARG* 3.3 33.5 + - + +
390A GLN* 3.6 13.0 - - - +
391A ILE* 1.3 96.4 + - + +
394A LYS* 1.3 66.2 + - - +
452A GLU* 4.4 20.6 + - - +
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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
----------------------------------------------------------
361A TRP* 5.0 1.1 - - - -
366A ILE* 5.6 1.4 - - - +
375A GLU* 2.4 33.5 + - - +
376A ILE 3.7 6.1 - - - -
377A LEU* 3.6 15.9 - - + +
390A GLN* 3.6 24.2 - - - +
392A ARG* 1.3 79.7 - - - +
395A GLN* 1.3 65.3 + - - +
396A VAL* 4.5 14.1 - - - +
455A ASP* 3.6 14.9 - - - +
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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 6.7 - - - -
97A PHE* 2.7 52.4 + - - +
361A TRP* 5.4 5.4 - - + -
375A GLU* 3.3 4.3 - - - +
376A ILE* 2.9 46.1 + - + +
394A LYS* 1.3 75.5 - - - +
396A VAL* 1.3 68.4 + - - +
397A VAL* 4.0 10.2 + - - +
446A MET* 3.9 14.1 - - - +
453A VAL* 3.2 34.6 + - - +
454A ALA 4.0 5.0 + - - +
455A ASP* 3.4 6.5 - - - +
458A TRP* 5.0 1.6 - - - -
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ILE* 4.2 12.6 - - + -
374A PHE 3.7 5.4 - - - +
375A GLU* 4.5 10.5 - - + -
394A LYS* 4.5 15.5 - - - +
395A GLN* 1.3 80.4 + - - +
397A VAL* 1.3 67.4 + - - +
398A VAL 3.6 23.8 - - - +
399A ASP* 4.2 6.3 - - + +
455A ASP* 3.2 33.6 - - + +
456A TRP 3.1 31.6 + - - +
458A TRP* 4.2 2.1 - - - -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PHE* 3.1 33.5 + - + +
375A GLU* 5.2 1.8 - - - -
376A ILE* 5.6 2.2 - - + -
395A GLN* 4.0 12.8 - - - +
396A VAL* 1.3 78.3 - - - +
398A VAL* 1.3 71.0 + - + +
422A PHE* 4.6 13.2 - - + -
424A VAL* 4.7 1.6 - - + -
444A ILE* 4.0 16.6 - - + +
446A MET* 3.5 36.1 - - + -
456A TRP 3.3 8.5 - - - -
458A TRP* 2.9 34.1 + - + -
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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 ILE* 3.6 1.7 - - - +
373A GLY* 3.2 9.9 - - - +
374A PHE* 2.7 51.8 + - + +
396A VAL* 3.6 7.0 - - - +
397A VAL* 1.3 90.0 - - + +
399A ASP* 1.3 71.8 + - - +
402A ASN* 4.0 19.5 - - + +
403A TRP 4.4 11.4 - - - +
404A SER* 4.8 1.6 - - - -
424A VAL* 4.7 3.8 - - + -
426A MET* 3.4 29.4 - - + -
457A SER* 3.6 5.4 - - - +
458A TRP 5.1 0.2 - - - +
459A HIS* 4.5 6.5 - - + -
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Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ILE* 4.4 1.6 - - - -
373A GLY* 3.4 5.4 - - - -
396A VAL* 4.2 10.7 - - + +
398A VAL* 1.3 75.1 - - - +
400A ASN* 1.3 57.6 + - - +
401A LEU* 2.8 50.2 + - - +
402A ASN* 2.9 32.4 + - - +
456A TRP 5.4 0.2 - - - +
457A SER* 3.0 33.8 + - - -
459A HIS* 4.2 3.6 + - - -
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Residues in contact with ASN 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 ILE* 3.3 33.0 - - + +
367A SER* 3.3 18.4 + - - +
372A SER* 3.0 38.5 + - - +
373A GLY* 3.7 4.7 - - - -
398A VAL 3.8 0.6 + - - -
399A ASP* 1.3 70.1 + - - +
401A LEU* 1.3 62.5 + - + +
402A ASN 3.1 7.4 + - - -
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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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372A SER* 5.8 0.2 - - - -
399A ASP* 2.8 16.9 + - - +
400A ASN* 1.3 79.6 - - + +
402A ASN* 1.3 67.8 + - - +
403A TRP* 5.8 1.9 + - - -
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Residues in contact with ASN 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* 3.3 7.3 - - - -
373A GLY 2.8 30.0 + - - -
398A VAL* 4.0 5.2 - - + -
399A ASP* 2.9 36.5 + - - +
400A ASN 3.1 0.8 - - - -
401A LEU* 1.3 87.4 + - - +
403A TRP* 1.3 64.1 + - - +
459A HIS* 3.3 50.1 + - + +
460A ASP 5.5 0.2 - - - +
461A GLY 5.7 0.8 - - - +
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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* 4.6 10.3 - - - -
371A ARG 3.5 18.4 - - - +
372A SER* 3.9 16.4 - - - -
373A GLY 4.6 0.2 - - - -
398A VAL* 4.4 4.5 - - - +
401A LEU 5.8 2.2 + - - -
402A ASN* 1.3 77.8 - - - +
404A SER* 1.3 60.7 + - - +
426A MET* 3.3 24.3 - - - +
427A ILE* 3.3 19.7 - - + +
428A ARG* 3.9 14.7 - - - +
432A GLU* 3.4 55.6 - - + +
433A GLU* 3.2 38.0 + - + +
460A ASP* 5.5 1.9 + - - +
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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
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365A THR* 3.7 6.6 - - - +
371A ARG* 2.8 13.1 + - - +
372A SER* 3.0 17.6 + - - +
373A GLY 2.8 31.6 + - - -
374A PHE* 4.3 11.7 - - - -
398A VAL* 4.8 2.5 - - - -
403A TRP* 1.3 72.6 - - - +
405A GLY* 1.3 64.7 + - - -
424A VAL* 4.6 5.8 - - - -
425A GLU 3.0 12.7 - - - +
426A MET* 4.3 2.7 - - - -
427A ILE* 3.0 31.0 + - - +
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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