Contacts of the helix formed by residues 426 - 435 (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 ASP 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A GLY 5.1 0.5 - - - +
312A ASN 4.6 1.9 - - - +
313A HIS* 3.3 27.3 - - - +
408A VAL* 4.2 4.4 - - + +
425A GLY* 1.3 69.2 - - - -
427A ALA* 1.3 64.5 + - - +
428A THR* 3.5 3.9 + - - -
429A THR* 2.7 42.3 + - - +
430A ASN* 3.1 25.3 + - - +
701A FAD 2.9 32.4 + - - +
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Residues in contact with ALA 427 (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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309A GLY 4.9 4.9 - - - +
310A ILE* 4.6 4.5 - - + -
373A VAL* 3.8 27.6 - - + -
374A GLY* 4.6 2.5 - - - +
406A PHE* 4.0 20.3 - - + +
425A GLY 4.3 0.4 - - - -
426A ASP* 1.3 68.4 - - - +
428A THR* 1.3 66.8 + - - +
430A ASN* 3.1 3.5 + - - +
431A LEU* 2.8 28.4 + - - +
701A FAD 2.8 29.1 + - + +
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Residues in contact with THR 428 (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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309A GLY 5.0 1.2 + - - -
310A ILE* 3.8 12.0 + - - +
313A HIS* 3.2 28.6 - - + +
315A ASP* 3.6 4.9 - - + -
316A GLY* 3.2 38.7 - - - +
319A LEU* 3.2 31.9 - - + +
426A ASP* 3.4 11.4 + - - -
427A ALA* 1.3 76.8 - - - +
429A THR* 1.3 64.2 + - - +
431A LEU* 3.1 7.5 + - - +
432A GLY 3.0 18.4 + - - -
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Residues in contact with THR 429 (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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313A HIS* 4.3 9.3 + - - -
319A LEU* 5.5 0.4 - - - -
426A ASP* 2.7 35.5 + - - +
427A ALA 3.3 0.2 - - - -
428A THR* 1.3 77.9 - - - +
430A ASN* 1.3 64.9 - - - +
432A GLY* 3.4 2.8 + - - -
433A LYS* 3.2 45.9 + - + +
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Residues in contact with ASN 430 (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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285A VAL* 3.6 16.7 - - - +
289A ILE* 3.8 11.7 - - + +
406A PHE* 3.8 19.3 - - + -
423A VAL* 3.6 22.7 + - + +
424A GLU 2.9 30.7 + - - +
425A GLY* 3.8 4.4 - - - -
426A ASP 3.1 21.5 + - - +
427A ALA 3.7 3.6 - - - +
429A THR* 1.3 79.2 - - - +
431A LEU* 1.3 65.2 + - - +
433A LYS* 3.5 9.2 + - - +
434A MET* 3.1 24.6 + - - +
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Residues in contact with LEU 431 (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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310A ILE* 3.9 28.3 - - + -
319A LEU* 4.4 11.9 - - + +
320A LEU* 4.4 23.3 - - + +
323A LEU* 3.9 25.8 - - + -
373A VAL* 4.3 15.5 - - + -
406A PHE* 4.0 28.7 - - + -
427A ALA 2.8 16.7 + - - +
428A THR* 3.1 8.3 + - - +
430A ASN* 1.3 76.0 - - - +
432A GLY* 1.3 60.0 + - - +
434A MET* 3.4 7.3 + - + +
435A MET* 3.0 38.4 + - + +
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Residues in contact with GLY 432 (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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319A LEU* 3.9 20.8 - - - +
428A THR 3.0 12.8 + - - -
429A THR* 3.8 4.0 - - - -
430A ASN 3.2 0.2 - - - -
431A LEU* 1.3 79.4 - - - +
433A LYS* 1.3 61.5 + - - +
434A MET 3.5 0.2 + - - -
435A MET* 3.6 13.7 + - - +
436A SER* 4.8 1.2 + - - -
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Residues in contact with LYS 433 (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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282A ASP* 5.1 11.3 + - - +
285A VAL* 5.4 5.4 - - + +
286A MET* 4.1 22.8 - - + +
289A ILE* 3.8 28.9 - - + -
429A THR* 3.2 34.0 + - - +
430A ASN* 3.9 7.7 + - - +
431A LEU 3.3 0.2 - - - -
432A GLY* 1.3 77.3 - - - +
434A MET* 1.3 60.7 + - - +
436A SER* 4.0 12.1 + - - -
437A LYS* 4.3 13.0 + - - -
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Residues in contact with MET 434 (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* 3.3 25.8 - - + +
292A ALA* 4.0 26.9 - - - -
293A ALA* 4.0 11.0 - - + -
296A ILE* 3.5 24.7 - - + -
323A LEU* 4.2 19.7 - - + -
406A PHE* 4.0 20.6 - - + -
430A ASN 3.1 14.7 + - - +
431A LEU* 4.0 8.3 - - + +
433A LYS* 1.3 78.5 - - - +
435A MET* 1.3 66.1 + - + +
436A SER 3.3 1.3 - - - -
437A LYS* 2.8 19.3 + - - +
438A ILE* 3.5 24.9 + - + +
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Residues in contact with MET 435 (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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319A LEU* 3.5 36.6 - - + +
322A GLU* 3.0 35.0 - - + +
323A LEU* 3.8 34.5 - - + +
326A ARG* 3.2 38.5 + - - +
431A LEU* 3.0 24.8 + - + +
432A GLY* 3.7 10.5 - - - +
433A LYS 3.5 0.8 - - - -
434A MET* 1.3 76.5 - - + +
436A SER* 1.3 63.5 + - - +
438A ILE* 3.1 16.1 + - - +
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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