Contacts of the strand formed by residues 393 - 399 (chain A) in PDB entry 1QFM
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 GLU 393 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 4.2 10.3 + - + +
86A TYR* 2.7 39.6 + - - -
106A LEU* 4.1 5.0 - - - +
344A VAL* 3.8 4.3 - - - +
386A SER* 4.0 0.5 + - - +
387A GLY* 3.8 14.6 - - - -
391A ASP* 3.5 9.2 - - + +
392A THR* 1.3 89.6 + - - +
394A ILE* 1.3 69.0 + - - +
395A PHE* 4.0 11.9 - - + -
409A HIS* 2.8 33.6 + - - +
410A CYS 3.3 14.4 - - - +
411A ASP* 4.2 5.6 - - + +
412A LEU* 4.1 3.4 - - - +
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Residues in contact with ILE 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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344A VAL* 4.0 8.3 - - + -
350A VAL* 4.2 10.3 - - + -
361A LEU* 5.6 0.2 - - + -
375A PHE* 3.8 35.0 - - + -
385A TYR* 3.4 33.7 - - + +
386A SER 3.3 8.5 - - - +
393A GLU* 1.3 77.4 - - - +
395A PHE* 1.3 64.7 + - - +
396A TYR* 3.8 23.6 - - + -
409A HIS* 3.2 8.0 - - - -
410A CYS* 2.9 46.7 + - + +
412A LEU* 3.9 19.7 - - + -
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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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78A CYS* 3.8 10.5 - - + -
79A HIS* 3.4 46.7 - - + +
80A PHE* 5.0 1.3 - - - -
81A LYS 5.9 0.2 - - - -
86A TYR* 4.2 7.6 - + - -
106A LEU* 4.0 18.8 - - + -
385A TYR* 3.3 3.9 - - - -
386A SER* 2.9 42.4 + - - +
393A GLU* 4.0 17.7 - - + -
394A ILE* 1.3 75.8 - - - +
396A TYR* 1.3 65.7 + - - +
407A ILE* 4.4 2.9 - - + -
408A TYR 3.2 15.5 - - - +
409A HIS* 3.3 38.8 - + + -
422A PHE* 3.9 25.1 - + - -
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Residues in contact with TYR 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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78A CYS* 4.4 3.7 - - - +
361A LEU* 3.5 31.4 - - + -
375A PHE* 3.5 27.1 - + + +
376A PRO* 5.0 2.1 + - - +
377A LEU* 3.9 17.5 - - + -
382A VAL* 4.5 6.7 - - + -
384A GLY 3.2 12.1 - - - +
385A TYR* 4.4 7.2 - + + -
394A ILE* 3.8 31.9 - - + -
395A PHE* 1.3 79.4 - - - +
397A GLN* 1.3 62.6 + - - +
406A ILE 3.8 1.2 - - - +
407A ILE* 3.4 2.1 - - - -
408A TYR* 2.8 70.0 + + + +
409A HIS 4.9 1.6 - - - -
410A CYS* 5.0 3.6 - - + -
419A PRO* 3.5 21.4 - - + +
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Residues in contact with GLN 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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76A TYR 3.0 19.3 - - - +
77A SER* 3.5 8.5 - - - +
78A CYS* 3.4 29.6 - - - +
382A VAL* 3.2 7.8 - - - +
383A VAL* 2.8 46.6 + - + +
384A GLY* 2.8 24.7 + - - +
396A TYR* 1.3 76.0 - - - +
398A PHE* 1.3 64.8 + - - +
399A THR* 5.9 0.2 - - - -
404A PRO 5.2 5.4 - - - +
405A GLY* 5.6 1.7 - - - -
406A ILE 3.5 5.8 - - - +
407A ILE* 3.8 17.8 - - + +
783A SGM 5.7 0.6 - - - -
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Residues in contact with PHE 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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359A ASN 5.9 0.2 - - - -
377A LEU* 4.1 25.4 - - + -
378A GLU* 3.0 41.3 - - + -
379A VAL 3.3 22.7 - - - -
380A GLY* 3.4 20.0 - - - -
381A SER 3.2 16.4 - - - -
382A VAL* 4.6 1.1 - - + +
383A VAL* 4.8 0.2 - - - -
396A TYR 4.2 0.2 + - - -
397A GLN* 1.3 79.1 - - - +
399A THR* 1.3 72.7 + - - +
400A SER* 4.2 6.5 - - - -
403A SER* 4.2 10.5 - - - -
405A GLY* 2.9 24.5 - - - -
406A ILE* 2.8 29.2 + - + +
408A TYR* 4.0 20.6 - + + -
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Residues in contact with THR 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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380A GLY* 3.4 1.6 - - - -
381A SER* 2.9 42.1 + - - +
383A VAL* 4.0 20.9 - - + -
397A GLN* 5.9 0.2 - - - -
398A PHE* 1.3 82.3 - - - +
400A SER* 1.3 68.1 + - - +
403A SER 3.5 9.7 + - - -
404A PRO 4.0 5.9 + - - -
405A GLY* 4.2 7.9 - - - -
482A PRO 3.8 15.3 - - - +
483A ASN* 3.8 16.8 + - - +
484A TYR* 3.5 17.2 + - - +
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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