Contacts of the strand formed by residues 402 - 407 (chain A) in PDB entry 1T9A
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 GLY 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A ASP 3.0 10.7 + - - -
369A LEU* 3.4 5.8 - - - +
370A ILE 2.9 24.8 + - - -
392A ALA* 3.2 27.2 + - - +
396A ALA* 3.9 2.7 - - - -
401A GLY* 1.3 74.4 - - - -
403A ILE* 1.3 67.1 + - - +
420A GLN* 3.4 8.5 - - - -
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Residues in contact with ILE 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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295A LEU* 5.5 0.2 - - - +
370A ILE* 3.4 23.3 - - + +
377A PHE* 4.0 17.0 - - + -
388A PHE* 4.4 18.2 - - + -
389A ALA* 5.2 3.8 - - + -
392A ALA* 4.6 7.2 - - + -
402A GLY* 1.3 80.2 - - - +
404A ILE* 1.3 72.1 + - - +
417A VAL* 4.0 25.6 - - + -
418A GLN 4.3 7.4 - - - +
419A THR* 3.7 22.9 - - + -
420A GLN* 2.8 44.5 + - - +
421A ILE 3.3 6.2 + - - -
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Residues in contact with ILE 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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292A ALA* 3.5 41.7 - - + +
295A LEU* 4.1 15.7 - - + -
296A ILE* 3.7 19.5 - - + -
369A LEU* 4.0 20.6 - - + -
370A ILE 2.9 9.6 + - - +
371A ILE* 4.4 6.7 - - + -
372A ALA* 2.8 29.8 + - - +
403A ILE* 1.3 78.3 - - - +
405A HIS* 1.3 63.7 + - - +
406A PHE* 3.6 27.1 - - + -
421A ILE* 3.3 15.7 - - + +
423A VAL* 4.3 5.2 - - + -
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Residues in contact with HIS 405 (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 ALA* 3.5 21.8 - - + -
375A ALA 2.9 24.8 + - - -
376A ARG* 5.1 1.1 - - - -
377A PHE* 3.8 19.1 - + - -
403A ILE* 4.9 0.2 - - + -
404A ILE* 1.3 76.8 - - - +
406A PHE* 1.3 70.6 + - - +
407A GLU* 3.3 28.8 + - + +
412A ASN* 3.4 27.0 + - + -
413A ILE* 4.5 7.7 - - - +
414A ASN 4.9 0.8 + - - -
419A THR* 4.1 22.7 + - + +
421A ILE 2.8 13.1 + - - +
422A ALA* 3.5 5.5 - - + +
423A VAL 2.8 25.7 + - - -
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Residues in contact with PHE 406 (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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289A ILE* 5.4 0.9 - - + -
292A ALA* 4.6 0.2 - - + -
296A ILE* 5.5 0.2 - - + -
371A ILE* 3.9 15.7 - - + -
372A ALA 2.8 20.6 + - - +
373A VAL* 4.2 13.0 - - + -
374A GLY* 3.2 21.7 + - - -
404A ILE* 3.6 22.7 - - + -
405A HIS* 1.3 73.8 + - - +
407A GLU* 1.3 58.4 + - - +
423A VAL* 3.4 36.8 - - + +
425A GLY 4.9 0.4 - - - -
427A ALA* 4.0 24.0 - - + -
430A ASN* 3.8 27.4 - - + -
431A LEU* 4.0 15.7 - - + -
434A MET* 4.0 31.0 - - + -
701A FAD 3.6 8.7 + - - -
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Residues in contact with GLU 407 (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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375A ALA 4.0 1.4 + - - +
405A HIS* 3.3 31.6 + - + +
406A PHE* 1.3 74.3 - - - +
408A VAL* 1.3 62.7 + - - +
409A SER* 2.8 39.9 + - - +
412A ASN* 3.8 8.5 - - + -
413A ILE* 3.7 21.7 - - + +
423A VAL 3.2 5.5 + - - -
424A GLU* 3.4 8.1 - - - +
425A GLY 3.1 22.0 + - - -
701A FAD 2.5 57.0 + - - +
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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