Contacts of the helix formed by residues 402 - 410 (chain E) in PDB entry 2Y1M
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 THR 402 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390E ASP* 2.9 34.3 + - - +
391E VAL* 3.7 22.9 - - + -
401E CYS* 1.3 72.2 - - - +
403E SER* 1.3 61.9 + - - +
404E CYS 2.9 2.0 - - - -
405E LEU* 2.5 31.2 + - + +
406E THR* 2.9 18.7 + - - -
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Residues in contact with SER 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E ASN* 4.3 9.1 + - - -
401E CYS* 3.9 10.1 - - - -
402E THR* 1.3 80.4 + - - +
404E CYS* 1.3 57.8 + - - +
406E THR* 4.4 4.0 + - - -
407E SER* 3.3 28.9 + - - -
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Residues in contact with CYS 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E ILE* 3.0 36.9 - - + +
384E CYS* 3.2 20.0 - - - -
400E MET* 5.5 0.2 - - - -
401E CYS* 3.7 8.3 + - - +
402E THR 2.9 0.4 - - - -
403E SER* 1.3 79.4 - - - +
405E LEU* 1.3 64.3 + - - +
407E SER* 4.2 3.4 - - - -
408E TRP* 3.3 20.4 + - - +
417E PRO* 4.5 0.5 - - - +
1436E ZN 2.4 33.9 - - - -
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Residues in contact with LEU 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E VAL* 4.3 18.4 - - + -
393E ILE* 4.4 8.3 - - + -
400E MET* 4.1 14.6 - - + -
401E CYS 3.4 6.0 + - - +
402E THR* 2.5 32.8 + - + +
404E CYS* 1.3 73.9 - - - +
406E THR* 1.3 58.7 + - + +
408E TRP* 3.2 5.1 + - + +
409E GLN* 3.0 55.2 + - + +
417E PRO* 4.0 25.1 - - + -
423E ILE* 5.2 6.1 - - + -
426E THR* 4.3 23.3 - - + +
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Residues in contact with THR 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E THR* 2.9 15.7 + - - -
403E SER* 4.4 3.8 + - - -
405E LEU* 1.3 74.8 - - + +
407E SER* 1.3 56.5 + - - +
408E TRP 3.0 5.4 - - - -
409E GLN* 3.0 25.1 + - + +
410E GLU* 2.8 42.0 + - + +
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Residues in contact with SER 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E SER* 3.3 22.1 + - - -
404E CYS* 4.3 2.7 - - - -
405E LEU 3.4 0.6 - - - -
406E THR* 1.3 77.6 + - - +
408E TRP* 1.3 56.7 + - - +
410E GLU* 3.7 21.4 + - - +
411E SER* 2.9 18.8 + - - -
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Residues in contact with TRP 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E ILE* 5.9 1.1 - - + -
404E CYS 3.3 18.0 + - - +
405E LEU 3.2 4.8 + - - +
406E THR 3.0 0.6 - - - -
407E SER* 1.3 76.1 - - - +
409E GLN* 1.3 74.8 + - + +
410E GLU 3.2 1.3 - - - -
411E SER* 3.3 15.1 + - - -
413E GLY* 3.2 45.2 + - - -
414E GLN 3.6 9.2 - - - -
415E GLY 3.0 21.3 + - - -
416E CYS 4.2 8.5 - - - -
417E PRO* 3.4 33.2 - - + +
420E ARG* 3.2 44.4 - - + -
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Residues in contact with GLN 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E LEU* 3.0 48.3 + - + +
406E THR* 3.0 31.4 + - + +
408E TRP* 1.3 82.3 - - + +
410E GLU* 1.3 65.3 + - + +
412E GLU* 3.6 10.2 + - - -
413E GLY 4.3 6.1 + - - +
415E GLY 5.8 1.3 - - - +
423E ILE* 4.8 17.9 - - + +
426E THR* 5.9 1.0 - - - +
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Residues in contact with GLU 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E THR* 2.8 23.8 + - + +
407E SER* 3.7 21.0 + - - +
408E TRP 3.2 0.2 - - - -
409E GLN* 1.3 74.6 - - + +
411E SER* 1.3 56.0 + - - +
412E GLU* 2.8 17.3 + - - +
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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