Contacts of the strand formed by residues 326 - 330 (chain B) in PDB entry 2P2F
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 THR 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ARG* 3.9 12.2 - - - +
93B THR* 2.6 41.3 + - + +
94B ALA 3.6 1.3 - - - +
96B ILE* 3.9 30.3 - - + -
295B TYR* 3.4 7.0 + - - -
298B GLY 6.0 0.7 - - - -
299B ASP 3.8 8.5 - - - +
300B ILE* 4.3 16.9 - - + +
301B TYR* 3.0 29.3 + - - +
325B ALA* 1.3 72.8 - - - +
327B THR* 1.3 63.0 + - - +
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Residues in contact with THR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ALA 3.0 16.6 + - - +
95B ILE* 3.3 17.6 - - + -
96B ILE 3.1 21.9 + - - -
301B TYR* 3.5 19.7 - - - -
316B LEU* 2.7 33.5 + - + +
317B LEU* 5.0 3.8 - - + -
320B PRO* 3.9 15.5 - - + -
321B LEU* 4.3 13.9 - - + -
325B ALA 3.8 0.6 - - - -
326B THR* 1.3 76.2 - - - +
328B LEU* 1.3 65.2 + - - +
329B MET* 3.9 1.1 + - + -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 3.5 20.2 - - + +
98B GLU* 4.3 11.4 - - + -
300B ILE* 5.0 3.6 - - + -
301B TYR 2.8 18.0 + - - +
302B TRP* 3.2 39.1 - - + +
303B CYS 4.5 0.3 + - - -
316B LEU* 3.5 16.4 - - - +
327B THR* 1.3 75.7 + - - +
329B MET* 1.3 78.7 + - - +
330B PHE* 3.8 8.1 - - + +
345B VAL* 3.9 8.1 - - + -
349B HIS* 3.7 30.3 - - + -
351B VAL* 3.8 26.0 - - + -
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Residues in contact with MET 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 4.1 14.8 - - + -
96B ILE 2.8 12.7 + - - +
97B TRP* 3.2 14.7 - - + -
98B GLU 3.0 23.9 + - - -
141B MET* 3.6 22.7 - - + -
142B VAL 3.4 45.1 - - - +
143B PRO* 3.8 4.7 - - + -
145B ALA* 5.0 0.9 - - + -
146B ALA* 4.3 13.7 - - + +
307B VAL* 4.9 6.1 - - + -
316B LEU* 3.5 29.8 - - + -
317B LEU* 4.0 16.4 - - + -
327B THR* 3.9 2.5 + - + -
328B LEU* 1.3 73.2 - - - +
330B PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 3.5 20.0 - - + -
99B GLY 3.8 4.3 - - - -
141B MET* 3.5 27.3 - - + +
302B TRP* 3.6 38.0 - + + +
304B THR* 5.7 3.4 - - + -
328B LEU* 3.8 6.5 + - + +
329B MET* 1.3 74.6 - - - +
331B GLU* 1.3 67.7 + - - +
332B GLY* 3.2 43.9 + - - +
333B VAL 3.3 25.4 - - - -
334B PRO* 4.0 6.3 - - + -
341B ARG* 3.5 44.0 - - + -
342B MET* 6.0 0.2 - - - -
345B VAL* 4.2 6.1 - - + -
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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