Contacts of the helix formed by residues 407 - 415 (chain G) in PDB entry 2W3S
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 ARG 407 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405G ASP* 3.1 42.7 + - - +
406G PHE* 1.3 78.8 - - - +
408G GLU* 1.3 63.5 + - - +
409G ASP* 3.2 31.6 + - - +
410G THR* 2.5 29.7 + - - +
411G ILE* 3.7 6.9 + - - +
447G VAL* 4.0 9.4 - - - -
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Residues in contact with GLU 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407G ARG* 1.3 75.1 - - - +
409G ASP* 1.3 58.0 + - - +
411G ILE* 3.4 3.8 + - - +
412G ALA* 2.7 38.3 + - - +
444G LEU* 3.1 31.7 - - + +
447G VAL* 3.8 26.3 - - + +
448G ARG* 3.4 25.1 + - + +
442H ARG* 2.4 33.5 + - - -
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Residues in contact with ASP 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407G ARG* 3.2 28.1 + - - +
408G GLU* 1.3 77.9 + - - +
410G THR* 1.3 57.9 + - - +
412G ALA* 3.3 7.8 - - - +
413G ALA* 2.8 36.6 + - - +
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Residues in contact with THR 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377G ILE* 4.8 3.1 - - + -
400G ALA 5.5 3.4 - - - +
401G LEU* 5.3 4.5 - - + -
404G GLN* 3.5 43.3 - - + +
405G ASP* 2.8 19.9 + - + +
407G ARG* 2.5 26.3 + - - +
409G ASP* 1.3 78.3 - - - +
411G ILE* 1.3 68.8 + - - +
413G ALA* 3.1 5.7 + - - +
414G ALA* 3.1 23.0 + - + +
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Residues in contact with ILE 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368G LEU* 6.5 0.7 - - + -
370G LEU* 5.5 0.7 - - + -
377G ILE* 5.3 3.6 - - + -
397G PHE* 4.0 4.3 - - + -
401G LEU* 3.5 42.6 - - + -
406G PHE* 5.3 8.7 - - + -
407G ARG 3.9 9.9 - - - +
408G GLU 3.4 5.8 + - - +
410G THR* 1.3 81.6 - - - +
412G ALA* 1.3 65.6 - - - +
414G ALA* 2.9 12.6 + - - +
415G LEU* 3.0 21.4 + - + +
443G ALA* 3.6 30.3 - - + -
444G LEU* 3.7 20.0 - - + +
446G TYR* 6.6 0.2 - - + -
447G VAL* 3.4 26.5 - - + -
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Residues in contact with ALA 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408G GLU* 2.7 22.3 + - - +
409G ASP* 3.3 10.5 - - - +
411G ILE* 1.3 75.6 - - - +
413G ALA* 1.3 63.2 + - - +
414G ALA 3.1 0.3 + - - -
415G LEU* 3.2 29.2 + - - +
416G PRO* 4.1 2.8 - - - +
444G LEU* 4.1 6.9 - - + +
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Residues in contact with ALA 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409G ASP 2.8 20.4 + - - +
410G THR* 3.6 4.9 - - - +
412G ALA* 1.3 72.8 - - - +
414G ALA* 1.3 58.9 + - + +
415G LEU 3.4 0.6 + - - -
416G PRO* 3.8 10.2 - - - +
417G LEU* 5.4 0.2 - - - +
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Residues in contact with ALA 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397G PHE* 3.0 30.1 - - + -
400G ALA* 4.0 19.5 - - + +
401G LEU* 4.3 4.9 - - + -
410G THR 3.1 12.5 + - - +
411G ILE 2.9 2.6 + - - -
413G ALA* 1.3 76.9 - - - +
415G LEU* 1.3 64.0 + - - +
416G PRO* 3.5 2.9 - - - -
417G LEU* 3.1 31.2 - - + +
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Residues in contact with LEU 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397G PHE* 3.8 13.7 - - + -
411G ILE* 3.0 33.0 + - + +
412G ALA* 3.2 23.8 + - + +
414G ALA* 1.3 72.3 - - - +
416G PRO* 1.4 61.9 - - + +
417G LEU 2.7 16.9 + - - -
418G LEU* 3.1 14.2 + - + +
440G GLN* 2.9 53.4 + - + +
443G ALA* 4.1 3.6 - - + -
444G LEU* 3.9 24.5 - - + -
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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