Contacts of the helix formed by residues 341 - 349 (chain C) in PDB entry 2GD4
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 VAL 341 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C GLN* 2.5 14.6 + - - +
336C GLN* 4.8 9.9 - - + +
339C GLY* 3.6 15.9 - - - +
340C LEU* 1.3 77.9 - - - +
342C ASP* 1.3 74.1 + - - +
343C LEU 3.3 1.6 - - - -
344C PHE* 3.0 16.6 + - - +
345C SER* 3.5 13.8 + - - -
180I GLU* 5.1 11.7 - - - +
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Residues in contact with ASP 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ASP* 3.5 23.6 - - - +
98C THR* 3.2 22.7 + - - +
101C GLN* 2.8 26.2 + - - +
341C VAL* 1.3 76.7 - - - +
343C LEU* 1.3 56.5 + - - +
344C PHE 2.7 17.7 + - - -
345C SER* 2.9 15.8 + - - +
348C ALA* 3.3 31.3 - - - +
349C SER* 3.7 6.8 - - - +
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PHE* 3.3 30.1 - - + -
90C THR* 3.5 23.1 - - + +
98C THR* 4.1 15.3 + - + +
101C GLN* 4.7 1.2 + - - -
102C LEU* 3.5 12.6 - - + -
340C LEU* 3.2 43.2 - - + +
341C VAL 3.3 1.6 - - - +
342C ASP* 1.3 76.6 - - - +
344C PHE* 1.3 69.7 + - + +
349C SER* 5.5 2.0 - - - +
351C LEU* 4.2 11.3 - - + +
363C TYR* 4.1 3.6 - - - -
364C VAL* 3.3 31.4 + - + +
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Residues in contact with PHE 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PHE* 3.6 19.1 - + - -
332C LYS* 3.9 39.9 - - + +
335C LEU* 4.3 5.6 - - + -
336C GLN* 3.8 31.2 - - + +
340C LEU* 3.6 34.8 - - + -
341C VAL 3.0 6.9 + - - +
342C ASP 2.7 5.1 + - - -
343C LEU* 1.3 101.8 - - + +
345C SER* 1.3 56.9 + - - +
346C PRO* 3.5 9.4 - - - +
363C TYR* 3.6 12.4 - - - -
364C VAL* 3.3 39.9 - - + +
365C SER 5.4 0.2 - - - -
367C ALA* 5.4 1.6 - - + -
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Residues in contact with SER 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C VAL* 3.5 15.6 + - - -
342C ASP* 2.9 9.4 + - - +
344C PHE* 1.3 77.7 - - - +
346C PRO* 1.3 68.9 - - - +
347C ALA* 3.8 10.2 + - - +
348C ALA* 2.9 40.2 + - - +
349C SER* 3.3 2.8 + - - -
363C TYR* 4.2 2.9 - - - +
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Residues in contact with PRO 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C PHE 3.5 8.5 - - - +
345C SER* 1.3 84.8 - - - +
347C ALA* 1.3 64.8 + - - +
348C ALA 3.0 1.0 + - - -
349C SER* 3.8 8.9 + - - -
361C ASP* 4.0 24.3 - - + +
363C TYR* 3.4 50.2 - - + -
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Residues in contact with ALA 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C SER* 3.3 8.7 - - - +
346C PRO* 1.3 80.3 - - + +
348C ALA* 1.3 61.6 + - + +
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Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C ASP* 3.3 34.2 - - - +
345C SER* 2.9 19.1 + - - +
346C PRO 3.0 0.2 + - - -
347C ALA* 1.3 82.9 - - + +
349C SER* 1.3 62.1 + - - +
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Residues in contact with SER 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ASP* 5.7 1.4 - - - +
98C THR* 3.0 13.9 + - - -
342C ASP* 3.7 10.5 - - - +
343C LEU* 5.5 1.3 - - - -
345C SER 3.8 8.5 - - - -
346C PRO* 3.8 7.1 + - - -
348C ALA* 1.3 77.6 - - - +
350C ALA* 1.3 79.2 + - - +
351C LEU* 3.8 4.4 + - - -
361C ASP* 3.7 13.2 + - - -
362C LEU 3.5 23.9 + - - -
363C TYR* 4.5 9.0 - - - -
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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