Contacts of the helix formed by residues 430 - 440 (chain A) in PDB entry 2EIT
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 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A THR* 3.6 11.9 - - - -
428A VAL* 3.6 2.3 - - - +
429A LYS* 1.3 103.8 + - + +
431A PHE* 1.3 60.3 + - - +
432A ALA* 3.4 12.0 + - - +
433A GLU* 2.9 25.7 + - - +
434A ALA* 2.9 26.3 + - - +
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Residues in contact with PHE 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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296A ILE* 3.8 22.2 - - + -
298A ASP* 3.8 13.5 - - + -
331A THR* 3.8 6.3 - - + +
430A ASP* 1.3 72.9 - - - +
432A ALA* 1.3 66.3 + - - +
434A ALA* 3.1 6.5 + - - +
435A LEU* 2.9 45.2 + - + +
449A VAL* 3.7 31.2 - - + -
456A HIS* 3.3 73.1 - + + +
459A TRP* 3.5 22.2 - + + -
460A ALA* 4.2 8.1 - - + -
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Residues in contact with ALA 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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430A ASP* 3.4 13.4 + - - +
431A PHE* 1.3 77.6 - - - +
433A GLU* 1.3 63.1 + - - +
435A LEU* 3.2 6.4 + - - +
436A GLU* 3.1 32.7 + - - +
459A TRP* 3.6 32.2 - - + -
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Residues in contact with GLU 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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409A PRO* 6.0 1.0 - - - +
427A ARG 5.1 1.2 - - - +
428A VAL* 3.8 18.4 - - + +
429A LYS* 2.8 39.1 + - + +
430A ASP* 2.9 21.1 + - - +
432A ALA* 1.3 76.9 - - - +
434A ALA* 1.3 63.5 + - - +
436A GLU* 3.2 19.5 + - - +
437A VAL* 2.9 31.0 + - + +
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Residues in contact with ALA 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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296A ILE* 3.6 34.5 - - + +
329A ILE* 3.7 22.6 - - + +
331A THR* 4.5 2.2 - - + -
428A VAL* 3.8 7.3 - - + +
430A ASP 2.9 14.4 + - - +
431A PHE* 3.3 13.2 - - - +
433A GLU* 1.3 76.2 - - - +
435A LEU* 1.3 56.6 + - - +
437A VAL* 3.4 1.7 + - - +
438A ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 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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296A ILE* 4.1 13.7 - - + -
431A PHE* 2.9 28.6 + - + +
432A ALA* 3.2 6.7 + - - +
434A ALA* 1.3 74.5 - - - +
436A GLU* 1.3 64.8 + - + +
438A ALA* 3.3 3.3 + - - +
439A ASN* 2.9 35.1 + - - +
459A TRP* 3.6 49.1 - - + +
460A ALA* 4.2 8.7 - - + -
463A GLU* 4.8 7.4 - - + +
464A PHE* 3.8 36.8 - - + +
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Residues in contact with GLU 436 (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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432A ALA* 3.1 25.1 + - - +
433A GLU* 3.2 21.5 + - - +
435A LEU* 1.3 76.1 - - + +
437A VAL* 1.3 65.5 + - + +
439A ASN* 3.3 6.0 + - - +
440A ASP* 3.0 26.2 + - - +
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Residues in contact with VAL 437 (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 ARG* 3.0 16.5 + - - +
329A ILE* 3.7 17.9 - - + -
409A PRO* 4.0 28.2 - - + +
426A ILE* 4.0 29.4 - - + -
428A VAL* 3.8 18.8 - - + -
433A GLU* 2.9 28.9 + - + +
434A ALA 3.9 2.9 - - - +
436A GLU* 1.3 77.7 - - + +
438A ALA* 1.3 63.7 + - - +
440A ASP* 3.2 17.1 + - - +
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Residues in contact with ALA 438 (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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296A ILE* 3.9 8.7 - - + -
327A ARG* 2.8 24.4 + - - +
329A ILE* 3.6 18.0 - - + +
434A ALA 2.8 21.4 + - - +
435A LEU* 3.3 5.1 + - - +
437A VAL* 1.3 74.4 - - - +
439A ASN* 1.3 60.2 + - - +
440A ASP 3.5 0.3 + - - -
441A THR* 4.2 4.5 + - - +
443A TYR 5.8 0.2 - - - +
464A PHE* 3.7 37.3 - - + -
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Residues in contact with ASN 439 (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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435A LEU* 2.9 27.1 + - - +
436A GLU* 3.9 4.9 - - - +
438A ALA* 1.3 74.8 - - - +
440A ASP* 1.3 57.9 + - - +
441A THR 2.9 12.0 + - - -
463A GLU* 2.8 23.3 + - - +
464A PHE* 3.7 8.2 - - - +
465A HIS* 2.8 38.4 + - + +
466A VAL* 5.6 0.2 - - - +
489A LYS* 2.9 23.9 + - - +
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Residues in contact with ASP 440 (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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409A PRO* 5.8 4.6 - - + +
410A LYS* 2.6 38.7 + - - +
415A GLN* 2.9 23.8 + - - +
436A GLU 3.0 17.5 + - - +
437A VAL* 3.2 11.9 + - - +
439A ASN* 1.3 74.5 - - - +
441A THR* 1.3 59.8 + - - +
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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