Contacts of the helix formed by residues 323 - 329 (chain A) in PDB entry 4QNW
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 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.6 7.9 - - - +
30A THR* 3.7 23.7 - - - +
322A PHE* 1.3 74.1 - - - +
324A ARG* 1.3 66.2 + - - -
326A PHE* 3.1 5.2 + - - +
327A ILE* 3.1 22.8 + - - +
401A FMN 2.9 27.8 + - - -
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Residues in contact with ARG 324 (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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297A GLY* 4.1 12.5 - - - +
323A GLY* 1.3 72.7 - - - +
325A TYR* 1.3 63.0 + - - +
327A ILE* 3.2 20.6 + - - +
328A SER* 3.2 13.3 + - - -
345A TYR* 3.3 50.6 + - + +
350A PHE* 3.5 32.0 - - + -
401A FMN 2.7 73.1 + - + +
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Residues in contact with TYR 325 (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 TYR 3.7 24.7 - - - -
299A ASP* 3.7 20.9 + - + +
322A PHE* 4.4 8.0 - + + +
323A GLY 3.3 2.0 - - - +
324A ARG* 1.3 80.6 - - - +
326A PHE* 1.3 57.9 + - - +
328A SER* 3.7 2.0 - - - -
329A THR* 2.8 36.8 + - - +
332A LEU* 3.5 19.3 - - + -
342A LEU* 3.8 31.6 - - + -
343A GLN 3.5 27.1 - - - -
344A LYS* 4.7 3.3 - - - -
345A TYR* 3.6 33.8 + + - -
401A FMN 4.9 2.8 + - - -
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Residues in contact with PHE 326 (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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25A MET 4.7 0.4 - - - -
26A ILE* 3.6 12.8 - - - -
27A MET* 3.5 49.1 - - + -
48A TYR* 5.0 0.2 - - - -
52A ARG* 2.8 61.7 + - + -
58A THR* 4.3 6.3 - - + -
322A PHE* 3.5 17.8 - - + +
323A GLY 3.1 4.6 + - - +
325A TYR* 1.3 74.2 - - - +
327A ILE* 1.3 62.3 + - - +
329A THR 3.8 12.6 + - - +
330A PRO 3.8 12.8 - - - -
332A LEU* 3.8 30.9 - - + +
333A PRO* 3.7 25.6 - - + -
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Residues in contact with ILE 327 (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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27A MET* 6.3 0.4 - - + -
30A THR* 4.2 15.5 - - + +
32A ARG* 3.5 38.4 - - - +
48A TYR* 3.6 18.6 - - - +
52A ARG* 2.8 23.7 + - - -
323A GLY 3.1 15.8 + - - +
324A ARG* 3.2 13.0 + - - +
326A PHE* 1.3 76.8 - - - +
328A SER* 1.3 58.8 + - - +
349A SER* 3.8 22.0 - - - +
350A PHE* 4.1 21.5 - - + -
362A TYR* 3.3 16.1 - - + -
401A FMN 4.1 15.5 - - + -
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Residues in contact with SER 328 (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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324A ARG 3.2 5.9 + - - -
325A TYR* 3.4 8.5 + - - -
327A ILE* 1.3 78.5 - - - +
329A THR* 1.3 63.0 + - - +
330A PRO* 3.6 4.8 - - - +
343A GLN* 2.7 44.1 + - - +
344A LYS 3.9 4.3 - - - -
345A TYR* 3.8 23.0 - - - +
362A TYR* 3.4 34.7 - - - +
363A PRO 4.5 3.1 - - - +
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Residues in contact with THR 329 (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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325A TYR* 2.8 20.2 + - - +
326A PHE* 3.8 8.0 - - - -
327A ILE 3.4 1.0 - - - -
328A SER* 1.3 83.9 + - - +
330A PRO* 1.4 66.5 - - - +
331A ASP* 3.8 0.2 - - - +
332A LEU* 3.0 33.4 + - - +
335A ARG* 3.4 39.9 - - - +
342A LEU* 4.0 12.0 - - + +
343A GLN* 3.0 23.6 + - - +
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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