Contacts of the strand formed by residues 327 - 331 (chain L) in PDB entry 1QDU
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 PHE 327 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262K THR* 3.5 36.6 - - + -
265K PHE* 3.6 21.3 - - + -
266K THR* 4.1 14.1 - - + -
278K LYS* 3.6 30.5 - - + -
280K PHE* 3.9 20.9 - + - -
323L ASP 4.7 0.4 - - - -
324L GLU* 3.1 36.6 - - + +
325L ALA 3.2 13.4 - - - -
326L ASP* 1.3 78.1 - - - +
328L LEU* 1.3 62.5 + - - +
329L LEU 5.5 0.2 - - - +
392L PHE* 4.5 0.7 - - - -
393L THR* 2.9 26.5 + - - +
394L LEU* 2.8 16.9 - - - +
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Residues in contact with LEU 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278K LYS 3.2 9.3 + - - +
279K VAL* 3.8 23.5 - - + +
280K PHE* 2.8 30.3 + - - +
281K PHE* 5.5 1.1 - - + -
327L PHE* 1.3 82.2 - - - +
329L LEU* 1.3 69.2 + - - +
330L GLY 5.1 0.2 - - - +
366L ILE* 3.4 36.6 - - + -
367L LEU* 4.4 4.7 - - + -
370L LEU* 4.0 20.6 - - + -
389L PRO* 4.6 2.7 - - + -
390L THR 3.2 18.8 - - - +
392L PHE* 3.8 9.9 - - + -
394L LEU* 3.8 18.4 - - + -
398L LEU* 4.6 0.4 - - + -
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Residues in contact with LEU 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258K ILE* 4.0 22.4 - - + -
262K THR* 4.7 11.0 - - + +
280K PHE* 3.5 16.8 - - + +
282K ILE* 3.5 24.7 - - + -
327L PHE* 5.5 0.2 - - - +
328L LEU* 1.3 77.1 - - - +
330L GLY* 1.3 68.5 + - - +
331L MET* 4.1 25.8 - - + -
389L PRO* 3.2 6.1 - - - +
390L THR* 2.9 44.5 + - - +
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Residues in contact with GLY 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280K PHE 2.5 18.1 + - - -
281K PHE* 3.7 11.2 - - - -
282K ILE 3.1 24.6 + - - +
328L LEU 3.9 0.2 + - - -
329L LEU* 1.3 72.9 - - - +
331L MET* 1.3 62.0 + - - -
349L TYR* 3.0 26.0 + - - -
370L LEU* 4.8 2.0 - - - -
389L PRO* 4.5 6.7 - - - -
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Residues in contact with MET 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258K ILE* 3.4 30.3 - - + -
282K ILE* 4.0 24.2 - - + -
284K ALA 6.3 0.7 - - - +
286K GLN* 3.5 32.3 - - + +
329L LEU* 3.6 24.9 + - + -
330L GLY* 1.3 74.4 - - - +
332L ALA* 1.3 61.8 + - - +
333L THR* 3.8 15.3 - - + +
349L TYR* 3.6 8.0 + - - -
387L PRO* 3.6 2.4 - - - +
388L GLN* 3.0 46.0 + - + +
389L PRO* 4.5 0.7 - - - +
390L THR* 5.3 2.5 - - - +
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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