Contacts of the strand formed by residues 595 - 601 (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 GLN 595 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584O ASP* 4.8 3.8 - - - +
585O THR* 4.4 5.6 + - - -
593O GLY 3.1 5.0 + - - +
594O GLN* 1.3 73.0 - - - +
596O MET* 1.3 62.3 + - - +
597O ILE* 4.2 8.3 + - - +
629O ASP* 3.8 14.6 + - - +
632O LYS* 3.9 12.6 - - - +
639O PHE* 3.3 38.8 - - - +
640O VAL 3.2 20.9 - - - +
641O GLU* 4.4 3.8 - - + +
642O ILE* 4.9 0.7 - - - -
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Residues in contact with MET 596 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583O GLN* 4.5 1.1 - - + +
584O ASP* 3.5 14.6 - - - +
585O THR* 3.9 28.9 - - - +
594O GLN 3.9 0.6 + - - -
595O GLN* 1.3 74.7 - - - +
597O ILE* 1.3 71.3 + - - +
598O LEU* 4.0 15.5 - - + -
611O PHE* 4.2 17.9 - - + -
638O LEU 3.4 0.7 - - - +
639O PHE* 3.2 4.2 - - - -
640O VAL* 2.6 68.0 + - + +
642O ILE* 4.0 11.7 - - + -
658O PHE* 4.0 27.8 - - + -
673O PHE* 4.3 11.7 - - - -
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Residues in contact with ILE 597 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582O ARG* 3.8 1.6 - - - +
583O GLN* 3.5 4.0 - - - -
584O ASP* 3.1 44.2 + - + +
595O GLN* 4.2 8.5 - - - +
596O MET* 1.3 76.7 - - - +
598O LEU* 1.3 66.9 + - - +
599O THR* 4.1 3.2 + - - +
637O MET* 3.5 32.3 - - + -
638O LEU 3.1 5.8 - - - +
639O PHE* 3.3 39.7 - - + -
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Residues in contact with LEU 598 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580O VAL* 4.0 12.1 - - + -
582O ARG 3.1 3.1 - - - +
583O GLN* 3.2 32.3 - - + -
596O MET* 4.0 18.2 - - + -
597O ILE* 1.3 74.1 - - - +
599O THR* 1.3 62.4 + - - +
600O GLY 4.1 0.7 - - - -
603O PHE* 4.1 6.9 - - + -
609O VAL* 4.4 4.5 - - + -
636O ASN 3.6 0.5 - - - +
637O MET* 3.3 7.1 - - - +
638O LEU* 2.8 41.3 + - + +
640O VAL* 4.2 14.1 - - + -
658O PHE* 3.5 37.2 - - + -
660O VAL* 4.2 21.3 - - + -
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Residues in contact with THR 599 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580O VAL* 4.9 0.4 - - - -
581O GLU* 2.8 8.8 + - + +
582O ARG* 2.6 62.3 + - + +
597O ILE* 4.4 2.6 - - - +
598O LEU* 1.3 71.2 - - - +
600O GLY* 1.3 62.8 + - - +
603O PHE* 4.1 1.1 - - - -
636O ASN* 3.4 14.4 - - + +
637O MET* 3.5 28.0 - - + +
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Residues in contact with GLY 600 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579O MET 3.0 15.0 - - - -
581O GLU* 3.7 10.3 - - - -
599O THR* 1.3 76.4 - - - +
601O GLN* 1.3 68.8 + - - +
603O PHE* 3.3 15.0 - - - -
635O PRO 4.6 0.2 - - - +
636O ASN* 3.2 25.8 + - - +
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Residues in contact with GLN 601 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418O PRO* 4.0 21.3 - - - +
419O HIS* 5.7 2.1 - - - +
579O MET* 2.7 48.1 + - + +
581O GLU* 3.2 23.5 - - - +
600O GLY* 1.3 78.1 - - - +
602O ASN* 1.3 76.2 + - + +
603O PHE* 3.3 8.5 - - - -
635O PRO 4.9 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