Contacts of the strand formed by residues 409 - 414 (chain O) in PDB entry 2O93
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 409 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403O SER 3.7 5.6 - - - +
404O GLN* 3.9 17.5 - - - +
407O SER 5.1 1.1 - - - +
408O TYR* 1.3 78.3 - - - +
410O LEU* 1.3 59.0 + - - +
411O ARG* 2.9 44.9 + - + +
445O LEU* 3.7 0.6 - - - -
446O HIS* 2.7 57.2 + - + +
560O LEU* 3.8 2.3 - - - +
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Residues in contact with LEU 410 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403O SER* 3.1 13.4 + - - +
409O GLU* 1.3 69.1 - - - +
411O ARG* 1.3 60.7 + - - +
443O VAL* 3.8 21.1 - - + -
444O GLN 3.0 25.8 - - - +
445O LEU* 3.5 15.3 - - + -
456O LEU* 5.0 4.0 - - + -
503O LEU* 5.1 1.6 - - + -
546O PHE* 4.4 3.4 - - + -
547O ARG* 4.1 10.5 - - - +
548O VAL* 4.1 12.8 - - + +
560O LEU* 3.4 50.9 - - + +
561O GLN* 3.7 9.6 - - - +
562O THR* 2.6 39.8 + - - +
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Residues in contact with ARG 411 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409O GLU* 2.9 46.6 + - + +
410O LEU* 1.3 74.2 - - - +
412O ILE* 1.3 67.3 + - - +
413O GLU* 3.3 27.4 + - - +
443O VAL* 3.5 8.1 - - - +
444O GLN 3.0 30.6 + - - +
446O HIS* 3.0 35.8 + - - +
562O THR* 4.7 2.9 - - - -
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Residues in contact with ILE 412 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411O ARG* 1.3 78.8 - - - +
413O GLU* 1.3 69.1 + - - +
414O VAL* 3.1 25.2 - - - +
415O GLN* 3.6 33.8 - - - +
416O PRO* 4.6 4.0 - - + -
441O PRO* 5.6 1.1 - - + -
442O VAL 3.3 7.9 - - - +
443O VAL* 3.6 12.8 - - + -
546O PHE* 3.4 27.8 - - + -
562O THR* 3.4 39.2 - - + +
563O ALA 4.5 4.9 - - - +
564O SER* 4.9 2.2 - - - -
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Residues in contact with GLU 413 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411O ARG* 3.3 23.4 + - - +
412O ILE* 1.3 74.0 - - - +
414O VAL* 1.3 64.1 + - + +
415O GLN* 4.3 0.7 + - - +
442O VAL* 2.8 35.5 + - + +
444O GLN* 3.2 38.6 - - + +
446O HIS* 3.3 17.2 + - - -
510O ARG* 4.2 13.6 + - - +
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Residues in contact with VAL 414 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412O ILE* 3.1 16.7 - - - +
413O GLU* 1.3 83.9 - - + +
415O GLN* 1.3 63.7 + - - +
435O ALA* 3.6 26.2 - - + -
436O PRO* 5.5 0.4 - - + -
437O THR* 4.2 18.6 - - + +
440O HIS 4.4 2.9 - - - +
441O PRO* 3.7 3.0 - - - +
442O VAL* 3.2 47.9 + - + +
510O ARG* 5.6 2.7 - - - +
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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