Contacts of the helix formed by residues 410 - 416 (chain A) in PDB entry 3FGU
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ILE* 4.7 0.4 - - - -
226A VAL 3.1 18.3 - - - +
409A ASP* 1.3 88.0 + - - +
411A SER* 1.3 59.5 + - - -
412A VAL 3.3 0.2 + - - -
413A TYR 3.6 0.5 + - - -
414A LYS* 2.9 33.5 + - - +
600A ANP 3.2 19.1 - - - -
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Residues in contact with SER 411 (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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226A VAL 3.5 1.0 + - - -
227A GLY* 3.9 1.1 - - - -
410A GLY* 1.3 71.7 - - - -
412A VAL* 1.3 60.1 + - - +
414A LYS* 4.4 4.9 - - - -
415A LEU* 2.8 44.3 + - - +
600A ANP 2.2 82.5 + - - -
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Residues in contact with VAL 412 (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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226A VAL* 3.1 20.1 + - + +
227A GLY 3.5 23.1 - - - +
293A ILE 4.7 1.6 - - - +
294A GLY 4.7 1.3 - - - -
295A GLY* 3.8 20.4 - - - +
298A MET* 4.0 18.2 - - + -
332A THR* 4.3 3.8 - - + -
411A SER* 1.3 74.3 - - - +
413A TYR* 1.3 67.4 + - - +
416A HIS* 3.1 32.6 + - + +
419A PHE* 3.9 27.1 - - + +
600A ANP 3.9 20.0 - - + +
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Residues in contact with TYR 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A MET* 4.4 7.6 - - + -
226A VAL* 3.3 17.4 + - + +
408A VAL* 3.3 43.6 - - + +
409A ASP 4.6 0.4 - - - +
410A GLY 4.0 4.7 - - - +
412A VAL* 1.3 80.4 - - - +
414A LYS* 1.3 69.2 + - + +
416A HIS 4.2 4.5 - - - +
419A PHE* 4.0 22.2 - + - -
420A LYS* 3.5 40.8 + - + +
423A PHE* 4.1 14.6 - + - -
424A HIS* 2.6 34.2 + - - -
438A PHE* 3.5 16.0 - + - +
439A ILE 5.5 0.2 + - - -
440A GLU* 3.8 26.2 - - + -
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Residues in contact with LYS 414 (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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408A VAL 4.3 4.3 - - - -
409A ASP* 2.6 32.2 + - - +
410A GLY 2.9 20.9 + - - +
411A SER* 4.3 2.9 - - - +
413A TYR* 1.3 84.9 - - + +
415A LEU* 1.3 71.5 + - + +
416A HIS 4.5 1.4 - - - +
420A LYS* 4.3 12.0 + - - -
440A GLU* 3.5 44.5 - - + +
441A SER 2.7 28.9 + - - -
442A GLU* 5.0 0.8 - - - +
443A GLU 5.3 2.4 - - - +
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Residues in contact with LEU 415 (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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336A SER* 4.1 7.2 - - - -
411A SER* 2.8 29.5 + - - +
414A LYS* 1.3 85.6 - - + +
416A HIS* 1.3 65.0 + - - +
417A PRO* 3.4 6.6 - - - +
600A ANP 3.5 36.7 + - + +
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Residues in contact with HIS 416 (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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298A MET* 4.9 7.2 - - - -
335A VAL* 4.0 8.8 + - + +
336A SER* 3.4 29.5 + - - +
339A GLU* 2.8 36.7 + - - +
375A SER* 3.5 17.8 + - - -
411A SER 3.8 1.4 + - - -
412A VAL* 3.1 23.8 + - + +
413A TYR 4.2 9.7 - - - +
414A LYS 4.5 1.6 - - - +
415A LEU* 1.3 78.2 + - - +
417A PRO* 1.4 70.5 - - + +
418A SER* 3.2 30.4 + - - -
419A PHE* 3.1 30.8 + - + +
420A LYS* 4.9 5.5 + - - +
421A GLU* 5.1 0.9 - - - +
422A ARG* 4.7 0.7 - - - -
600A ANP 4.8 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