Contacts of the strand formed by residues 322 - 328 (chain E) in PDB entry 2ONK
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 PRO 322 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E PHE 3.8 12.3 - - - +
111E ALA* 4.0 3.1 - - + -
112E LYS* 3.7 12.1 + - - -
312E GLN* 3.3 42.2 - - + +
315E LEU* 4.0 7.6 - - + -
316E ARG* 3.1 41.7 + - + +
320E GLN 3.2 9.6 - - - +
321E GLU* 1.3 90.8 - - + +
323E LEU* 1.3 61.1 + - - +
324E VAL* 3.5 10.0 + - + +
263J GLU* 5.8 0.3 - - - +
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Residues in contact with LEU 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E MET* 3.1 42.6 - - + +
110E PHE* 3.2 12.8 + - - +
111E ALA* 3.6 17.8 - - - +
112E LYS* 3.8 27.1 - - + +
284E VAL* 4.6 9.4 - - + -
312E GLN* 4.6 1.9 + - - -
322E PRO* 1.3 70.5 - - - +
324E VAL* 1.3 61.4 + - - +
325E PRO 3.1 19.1 - - - +
326E PRO* 3.3 7.4 - - - +
327E ARG* 3.7 43.3 - - + +
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Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E GLN* 3.4 37.0 - - - +
316E ARG* 4.1 13.2 - - - +
322E PRO* 3.5 12.0 + - + +
323E LEU* 1.3 75.2 - - - +
325E PRO* 1.3 72.7 - - + +
326E PRO* 5.0 0.2 - - + -
262J ALA* 3.7 5.9 - - - +
263J GLU* 3.1 56.1 + - + +
266J SER* 4.5 7.4 - - - +
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Residues in contact with PRO 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323E LEU* 3.1 15.5 - - - +
324E VAL* 1.3 86.6 - - + +
326E PRO* 1.3 83.4 - - + +
327E ARG* 3.9 9.1 + - + +
340E GLU* 5.2 14.1 - - + +
262J ALA* 3.9 12.8 - - + +
266J SER* 3.6 32.8 - - - +
279J THR* 6.0 0.4 - - + -
280J GLY 5.9 0.7 - - - +
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Residues in contact with PRO 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ILE* 4.2 0.7 - - + -
109E MET 3.4 15.3 - - - +
110E PHE* 5.4 0.4 - - - -
307E ILE* 3.9 28.9 - - + +
312E GLN* 4.3 14.4 - - - +
323E LEU* 3.3 8.2 - - + +
325E PRO* 1.3 101.3 - - + +
327E ARG* 1.3 64.5 + - - +
338E MET 3.1 28.0 - - - +
339E VAL* 3.6 15.5 - - + +
340E GLU* 4.1 8.8 + - - +
342E SER* 5.5 0.2 - - - -
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Residues in contact with ARG 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E TYR* 6.1 1.4 - - - -
108E ILE* 2.9 9.9 - - - +
109E MET* 2.7 59.1 + - + +
259E PRO* 5.9 4.6 - - - +
284E VAL* 5.1 9.1 - - - +
323E LEU* 3.7 37.1 - - + +
325E PRO* 3.9 4.4 + - + +
326E PRO* 1.3 81.9 - - - +
328E ALA* 1.3 58.5 + - - +
339E VAL* 3.1 9.4 - - - -
340E GLU 3.8 4.0 - - - -
342E SER* 2.7 30.1 + - - +
259J PRO* 5.9 5.5 - - - +
327J ARG* 5.8 4.4 - - - +
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Residues in contact with ALA 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E THR 3.2 11.2 - - - +
108E ILE* 4.3 1.8 - - + -
109E MET* 4.7 3.6 - - - -
327E ARG* 1.3 78.6 - - - +
329E ASP* 1.3 57.8 + - - +
330E THR 3.0 23.6 - - - +
332E VAL* 4.3 12.1 - - + +
339E VAL* 3.5 15.3 - - + +
340E GLU 4.0 3.6 + - - -
341E VAL* 3.1 31.1 - - + +
342E SER* 3.4 10.8 + - - +
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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