Contacts of the strand formed by residues 374 - 378 (chain O) in PDB entry 4R2G
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 HIS 374 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256O SER* 4.6 0.4 - - - -
257O THR 2.8 25.5 + - - -
258O GLN* 2.3 25.2 + - + +
259O LEU* 3.7 32.0 + - + +
261O LEU* 4.0 20.3 - - + +
294O ILE* 4.1 22.2 - - + +
373O MET* 1.3 66.3 - - - +
375O SER* 1.3 61.3 + - - +
376O PHE* 3.2 39.9 - + - -
385O CYS* 2.9 45.0 + - + +
387O SER* 4.3 12.0 + - - -
390O LEU* 6.4 0.2 - - + -
416O LEU* 5.5 3.8 - - + -
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Residues in contact with SER 375 (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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256O SER* 3.4 2.9 - - - -
257O THR* 2.8 40.3 + - - +
370O GLU* 2.6 43.0 + - - +
373O MET 3.0 1.6 + - - -
374O HIS* 1.3 74.0 + - - +
376O PHE* 1.3 64.6 + - - +
383O PHE 3.5 11.4 - - - -
384O TYR* 4.2 13.5 - - - +
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Residues in contact with PHE 376 (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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255O VAL 3.9 9.0 - - - +
256O SER* 4.1 15.3 - - - -
261O LEU* 4.2 13.9 - - + -
294O ILE* 5.5 0.2 - - + -
296O CYS* 3.2 31.0 - - + -
331O CYS* 4.0 1.1 - - - -
374O HIS* 3.2 35.2 - + - -
375O SER* 1.3 75.5 - - - +
377O ASN* 1.3 71.5 + - - +
378O CYS* 3.9 13.0 - - + -
382O PHE* 3.7 7.1 - - - +
383O PHE* 2.9 58.6 + + + +
385O CYS* 3.3 24.9 - - - -
445O CYS* 5.4 1.8 - - + -
447O SER* 6.0 2.2 - - - -
511O NAG 5.0 4.5 - - + -
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Residues in contact with ASN 377 (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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112O TRP* 4.4 11.4 - - + -
116O LEU* 4.1 6.4 - - - +
210O PHE* 3.8 21.4 - - + +
255O VAL* 4.1 9.3 + - + +
376O PHE* 1.3 81.0 - - - +
378O CYS* 1.3 61.5 + - - +
379O GLY 4.1 1.4 + - - -
380O GLY* 3.0 32.9 + - - -
381O GLU 3.8 7.6 + - - -
382O PHE* 3.1 42.6 - - + -
511O NAG 3.7 26.6 + - - +
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Residues in contact with CYS 378 (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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296O CYS* 4.6 4.3 - - - -
376O PHE* 3.9 9.1 + - + -
377O ASN* 1.3 77.0 + - - +
379O GLY* 1.3 64.1 + - - +
380O GLY 3.1 1.3 + - - -
381O GLU* 3.2 24.9 + - - +
383O PHE* 3.6 22.4 - - + -
443O ILE* 3.7 16.1 - - - +
444O ARG 4.0 2.7 - - - -
445O CYS* 2.0 66.0 - - + -
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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