Contacts of the strand formed by residues 229 - 233 (chain G) in PDB entry 5CAY
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 ARG 229 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G LYS* 3.1 34.4 + - + +
227G THR* 3.5 3.6 + - - +
228G MET* 1.3 78.6 - - + +
230G PHE* 1.3 70.7 + - - +
266G MET* 3.3 46.4 - - + +
267G MET 3.3 9.0 - - - +
268G GLU* 2.7 26.0 + - - +
278G ASN* 2.6 35.1 + - - +
279G GLY 3.7 10.3 + - - -
280G THR* 3.4 22.4 - - - +
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Residues in contact with PHE 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G CYS* 4.0 21.5 - - - -
45G ALA 3.8 7.0 - - - +
46G THR* 3.8 37.5 - - + -
47G LYS* 4.6 5.1 - - - +
93G LEU* 3.3 34.3 - - + -
225G TRP* 6.1 7.0 - + - -
227G THR* 3.5 32.3 - - + -
229G ARG* 1.3 92.2 - - - +
231G ARG* 1.3 63.9 + - - +
266G MET* 3.5 3.1 - - - -
267G MET* 2.8 49.6 + - + +
269G THR* 3.6 17.3 - - + -
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Residues in contact with ARG 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G CYS* 3.8 2.0 - - - -
45G ALA* 3.0 38.0 + - + +
47G LYS* 4.8 5.2 - - + -
60G ASP* 3.7 21.0 - - - +
61G ASN* 3.4 12.5 - - - +
62G ASP* 3.2 42.5 + - - +
64G TYR* 3.2 38.9 - - - +
230G PHE* 1.3 79.8 - - - +
232G TYR* 1.3 64.4 + - - +
233G CYS* 4.5 3.1 - - - -
263G CYS* 3.8 17.9 - - + -
264G THR* 2.8 43.3 + - - +
265G ARG* 4.0 4.4 - - - +
266G MET* 3.6 18.8 - - - +
267G MET* 5.5 0.9 - - - +
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Residues in contact with TYR 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G LEU* 3.8 25.6 - - + -
43G PHE 3.6 13.7 - - - -
44G CYS* 3.7 22.7 - - + -
82G VAL* 4.4 7.4 - - + -
85G GLN* 3.4 14.3 + - + -
86G ALA* 3.3 25.4 - - + -
89G ASP* 2.5 43.4 + - - +
230G PHE* 6.3 0.2 - - + -
231G ARG* 1.3 74.6 - - - +
233G CYS* 1.3 60.9 + - - +
240G LEU* 3.8 0.6 - - - +
263G CYS* 3.1 3.6 - - - +
264G THR* 2.7 52.5 + - + +
267G MET* 4.1 13.9 - - + +
494G LEU* 3.7 31.2 - - + -
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Residues in contact with CYS 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G LEU* 4.1 4.1 - - - +
43G PHE* 3.1 34.3 + - + +
45G ALA* 4.7 15.3 - - - -
231G ARG* 4.5 6.7 - - - -
232G TYR* 1.3 75.8 - - - +
234G ALA* 1.3 68.1 + - - +
235G PRO* 3.5 1.2 - - - +
240G LEU* 4.2 2.7 - - - -
262G THR* 3.7 8.3 - - + +
263G CYS* 2.0 46.7 - - - +
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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
------------------------------------------------------------
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