Contacts of the strand formed by residues 323 - 327 (chain A) in PDB entry 3DF0
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 GLU 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ARG* 3.4 28.9 + - - +
95A THR* 6.1 0.7 - - - +
267A THR* 3.4 16.6 + - - +
283A ARG* 3.7 25.3 + - + -
284A ILE 3.3 9.6 - - - +
285A ARG* 3.4 28.2 - - + +
292A GLU* 2.7 12.7 + - - +
321A ASP* 3.1 21.1 - - + +
322A GLY* 1.3 78.5 - - - +
324A PHE* 1.3 62.1 + - - +
716A CA 2.4 29.9 - - - -
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Residues in contact with PHE 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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257A LYS 5.9 0.2 - - - -
258A LEU* 4.7 1.3 - - + -
264A TYR* 4.0 25.1 - + - -
283A ARG* 3.2 7.6 - - - +
284A ILE* 2.9 60.1 + - + +
286A ASN* 4.5 2.7 - - + -
291A VAL 4.5 1.1 - - - -
292A GLU* 3.6 25.6 - - + +
293A TRP* 3.7 32.3 - + + +
298A ASN* 4.9 3.6 - - - -
299A ASP* 3.7 14.8 - - - +
322A GLY 3.2 22.4 - - - -
323A GLU* 1.3 78.2 - - - +
325A TRP* 1.3 82.7 + - - +
326A MET* 4.4 10.8 - - + -
335A TYR* 4.2 5.6 - - - -
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Residues in contact with TRP 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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268A GLY* 4.4 9.2 - - - -
270A GLU* 4.6 22.9 - - + -
281A LEU* 3.6 24.7 - - + -
282A ILE* 3.3 34.8 - - - -
283A ARG* 3.4 44.3 - - + +
293A TRP* 3.2 19.9 + - - -
297A TRP 3.9 9.1 + - - +
298A ASN* 4.1 0.2 - - - -
299A ASP* 4.4 8.3 + - - -
304A TRP* 3.6 32.0 - + + -
315A LEU* 3.5 34.5 + - + -
316A THR* 4.0 16.3 + - - +
317A GLU 5.1 1.4 - - - +
324A PHE* 1.3 80.5 - - - +
326A MET* 1.3 67.1 + - - +
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Residues in contact with MET 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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258A LEU* 4.3 7.6 - - + -
281A LEU* 3.7 6.7 - - - -
282A ILE* 3.1 39.5 + - + +
284A ILE* 4.4 9.4 - - + -
293A TRP* 3.5 53.6 - - + +
297A TRP* 4.2 9.6 - - - -
324A PHE* 4.4 4.3 - - + -
325A TRP* 1.3 79.0 - - - +
327A SER* 1.3 68.1 + - - +
330A ASP* 4.4 0.7 - - + -
331A PHE* 3.6 34.5 - - - +
334A HIS* 4.9 4.0 - - + +
335A TYR* 4.0 26.7 - - + -
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Residues in contact with SER 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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279A GLN* 5.3 4.5 - - - -
280A LYS* 3.5 15.7 - - - -
281A LEU* 4.5 3.1 - - - +
293A TRP* 5.5 0.6 - - - -
297A TRP* 4.3 22.5 - - - +
326A MET* 1.3 77.1 - - - +
328A PHE* 1.3 63.8 + - - +
329A SER* 3.3 13.8 + - - -
330A ASP* 2.7 42.0 + - - +
331A PHE* 3.0 22.3 + - - +
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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