Contacts of the helix formed by residues 410 - 415 (chain E) in PDB entry 3TMH
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 410 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389E GLY 5.0 0.2 - - - -
407E GLN* 2.6 30.9 + - - -
408E LYS 2.6 4.7 + - - -
409E GLY* 1.3 84.5 - - - +
411E PRO* 1.3 75.2 - - - +
412E ALA 3.4 2.5 - - - -
413E ASP 3.1 11.3 + - - -
414E LEU* 3.1 11.6 + - - +
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Residues in contact with PRO 411 (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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381E LEU* 4.1 9.1 - - + +
382E ALA 3.9 24.9 - - - +
384E GLY* 4.1 9.6 - - - +
386E ASN* 6.3 0.4 - - + -
387E GLY 3.9 13.9 - - - +
388E TYR* 3.3 26.9 - - + +
389E GLY* 4.5 2.5 - - - +
407E GLN* 5.0 2.5 - - - +
409E GLY 4.6 0.4 - - - +
410E GLY* 1.3 80.2 - - - +
412E ALA* 1.3 68.3 + - - +
413E ASP 3.1 0.3 + - - -
414E LEU* 3.3 7.2 + - + +
415E ALA* 3.2 22.7 + - - +
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Residues in contact with ALA 412 (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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381E LEU* 4.0 12.6 - - + -
388E TYR 3.1 7.5 + - - +
389E GLY 3.6 18.6 - - - +
390E PHE* 3.8 21.1 - - + -
406E VAL* 3.7 13.2 - - + -
410E GLY 3.4 0.6 - - - -
411E PRO* 1.3 79.5 - - - +
413E ASP* 1.3 62.6 + - - +
415E ALA* 3.4 2.4 + - - +
416E GLY 3.3 4.3 + - - -
417E LEU* 3.1 36.1 + - + +
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Residues in contact with ASP 413 (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 VAL* 3.3 16.4 - - + +
407E GLN 3.2 20.9 - - - +
408E LYS* 3.7 9.9 - - - +
409E GLY* 3.0 21.7 + - - +
410E GLY 3.1 5.2 + - - +
411E PRO 3.1 0.8 - - - -
412E ALA* 1.3 80.8 - - - +
414E LEU* 1.3 62.2 + - - +
416E GLY* 3.1 19.2 + - - -
417E LEU 4.4 7.7 - - - +
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Residues in contact with LEU 414 (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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409E GLY* 3.4 32.1 - - - +
410E GLY 3.1 13.1 + - - +
411E PRO* 4.1 5.4 - - + +
413E ASP* 1.3 76.6 - - - +
415E ALA* 1.3 59.2 + - - +
416E GLY* 3.1 6.5 + - - -
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Residues in contact with ALA 415 (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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377E LYS* 5.5 2.6 - - - +
379E CYS* 3.4 33.6 - - + +
380E ARG 4.1 9.0 - - - +
381E LEU* 3.8 22.2 - - + -
411E PRO 3.2 16.1 + - - +
412E ALA 3.9 1.8 - - - +
414E LEU* 1.3 77.0 - - - +
416E GLY* 1.3 58.9 + - - +
417E LEU 3.5 2.0 - - - -
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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