Contacts of the strand formed by residues 233 - 237 (chain I) in PDB entry 5G04
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 TYR 233 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218I SER* 3.4 28.9 + - - -
219I VAL 3.4 9.2 - - - -
220I VAL* 4.6 4.5 - - + +
232I SER* 1.3 74.9 - - - +
234I PHE* 1.3 59.2 + - - +
235I GLN* 2.8 36.8 + - + -
552I ILE 4.2 4.3 - - - -
553I CYS* 3.5 11.8 - - - -
554I ILE* 3.1 63.7 + - + +
556I LEU* 4.5 7.4 - - + -
575I LEU* 4.2 13.9 - - + -
584I HIS* 4.6 5.5 - - - +
586I LEU* 3.6 28.9 - - + -
601I LEU* 4.4 9.8 - - + +
603I ARG* 3.9 12.8 - - - +
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Residues in contact with PHE 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I GLY 4.7 10.8 - - - -
201I ILE* 4.2 20.4 - - + -
202I ALA* 5.6 6.7 - - + -
218I SER* 3.3 1.4 - - - -
219I VAL* 2.4 54.8 + - + +
221I THR* 3.3 32.5 - - + -
232I SER* 4.3 7.4 - - - -
233I TYR* 1.3 75.8 - - - +
235I GLN* 1.3 57.2 + - - +
236I LEU* 3.6 12.0 - - + +
551I ALA* 4.3 20.0 - - + -
552I ILE 3.9 2.7 - - - -
553I CYS* 4.0 22.7 - - + -
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Residues in contact with GLN 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216I SER* 3.7 20.1 + - - -
218I SER* 3.7 12.7 - - - +
233I TYR* 2.8 38.7 + - + +
234I PHE* 1.3 69.3 - - - +
236I LEU* 1.3 63.4 + - - +
551I ALA* 3.1 2.9 - - - -
552I ILE* 2.8 44.6 + - + +
584I HIS* 5.1 3.5 - - - +
603I ARG* 3.5 28.5 - - - +
604I HIS 3.6 19.0 + - - +
607I ILE* 3.6 34.2 - - + +
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Residues in contact with LEU 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I ILE* 4.1 17.3 - - + -
198I VAL* 3.8 29.6 - - + -
201I ILE* 4.7 5.6 - - + -
216I SER* 3.2 9.1 - - - -
217I LEU* 2.8 54.3 + - + +
219I VAL* 4.6 4.0 - - + -
234I PHE* 3.6 34.5 - - + +
235I GLN* 1.3 76.7 - - - +
237I GLU* 1.3 61.1 + - - +
238I THR* 5.1 0.7 - - + -
548I MET* 4.6 14.8 - - + +
550I GLN 3.4 10.8 - - - +
551I ALA* 4.2 8.5 - - + -
607I ILE* 4.8 0.4 - - - -
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Residues in contact with GLU 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I LYS 4.4 0.2 - - - +
235I GLN 4.1 0.4 + - - -
236I LEU* 1.3 72.4 - - - +
238I THR* 1.3 59.6 + - - +
239I ASN* 3.5 26.1 + - + +
547I SER 4.4 0.9 - - - +
548I MET* 3.7 21.3 - - - +
549I ASN 5.0 0.2 + - - -
550I GLN* 3.2 33.4 + - + +
552I ILE* 5.6 0.9 - - - +
606I ASP* 5.7 0.5 - - - +
607I ILE* 3.3 47.3 + - + +
608I SER* 5.3 5.1 + - - -
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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