Contacts of the strand formed by residues 401 - 406 (chain A) in PDB entry 2OZO
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 LEU 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A GLU* 5.6 0.3 - - - +
328A LYS* 5.7 0.7 + - - -
330A LEU* 4.9 5.2 - - + -
387A ALA* 4.0 30.3 - - + +
390A MET* 4.0 35.0 + - + +
391A HIS* 3.4 24.3 + - - +
393A LEU 5.3 1.4 + - - -
399A VAL 3.8 1.2 + - - +
400A ARG* 1.3 75.7 - - - +
402A ILE* 1.3 64.8 + - - +
403A GLY* 3.8 16.2 - - - +
404A VAL* 6.0 0.7 - - + -
412A LEU* 3.5 37.5 - - + -
413A VAL 3.1 19.7 - - - +
414A MET* 4.6 5.8 - - + +
480A PHE* 5.1 4.9 - - + -
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Residues in contact with ILE 402 (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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322A PRO* 3.4 36.8 - - + -
323A GLU* 4.8 12.7 - - - +
328A LYS* 5.7 1.2 - - - +
329A LYS 4.4 0.2 - - - +
332A LEU* 4.0 11.7 - - + +
357A TYR* 4.0 33.2 - - + -
359A MET* 5.6 1.6 - - - -
364A ILE* 4.4 8.5 - - + -
366A VAL* 4.3 12.8 - - + -
391A HIS* 2.9 18.9 - - - -
400A ARG* 4.8 1.3 - - + -
401A LEU* 1.3 76.1 - - - +
403A GLY* 1.3 59.7 + - - +
413A VAL* 2.9 17.7 + - + +
414A MET* 4.1 15.5 - - - -
415A GLU* 4.0 16.6 - - + -
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Residues in contact with GLY 403 (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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330A LEU* 3.5 12.6 - - - -
332A LEU* 3.6 14.5 - - - +
391A HIS* 4.1 5.4 - - - -
401A LEU* 3.4 12.5 - - - +
402A ILE* 1.3 83.8 - - - +
404A VAL* 1.3 60.7 + - - -
413A VAL* 2.9 31.3 + - - +
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Residues in contact with VAL 404 (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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330A LEU* 2.8 37.3 + - + +
331A PHE* 3.3 33.3 - - + -
332A LEU* 2.7 31.9 + - - +
387A ALA* 5.4 6.5 - - + -
401A LEU* 5.8 0.9 - - + -
403A GLY* 1.3 76.1 - - - -
405A CYS* 1.3 62.7 + - - +
410A LEU* 3.7 25.8 - - + -
411A MET 3.1 16.6 - - - +
412A LEU* 5.1 10.3 - - + -
413A VAL 4.7 0.4 - - - +
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Residues in contact with CYS 405 (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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331A PHE* 5.3 1.1 - - - -
332A LEU* 4.0 17.7 - - + +
333A LYS 4.4 0.4 - - - -
334A ARG* 3.6 44.2 - - - -
337A LEU* 4.6 13.0 - - + -
404A VAL* 1.3 80.9 - - - +
406A GLN* 1.3 67.1 + - - +
409A ALA 3.4 1.9 - - - +
410A LEU* 3.8 0.5 - - - -
411A MET* 2.8 51.0 + - + +
413A VAL* 4.8 5.8 - - + +
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Residues in contact with GLN 406 (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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331A PHE* 5.3 16.4 - - + -
332A LEU 5.1 1.2 + - - -
334A ARG* 5.5 0.9 - - - +
374A GLY* 5.9 1.2 - - - -
404A VAL* 4.8 0.2 - - - +
405A CYS* 1.3 75.9 - - - +
407A ALA* 1.3 64.5 + - - +
409A ALA 3.4 10.0 - - - +
410A LEU* 3.9 31.3 + - + +
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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