Contacts of the strand formed by residues 238 - 243 (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 PHE 238 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G PRO* 6.4 1.8 - - + -
234G ALA* 3.4 12.0 - - - +
235G PRO* 3.1 28.5 + - + +
236G PRO 3.2 24.5 - - - -
237G GLY* 1.3 79.4 + - - +
239G ALA* 1.3 64.0 + - - +
499G LEU* 4.1 28.0 - - + -
500G ILE 3.3 22.2 - - - +
501G GLU* 3.5 36.1 - - + -
502G VAL* 4.2 5.3 - - - +
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Residues in contact with ALA 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234G ALA* 3.7 6.7 - - - +
238G PHE* 1.3 78.2 - - - +
240G LEU* 1.3 64.6 + - - +
241G LEU* 5.7 2.2 - - + -
260G ALA* 6.4 0.9 - - + -
261G ALA 5.4 2.2 - - - +
499G LEU* 3.7 7.7 - - - +
500G ILE* 3.0 47.9 + - + +
502G VAL* 5.0 7.9 - - + -
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Residues in contact with LEU 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G LEU* 4.4 6.5 - - + -
82G VAL* 4.3 17.5 - - + -
232G TYR 3.8 4.3 - - - +
234G ALA* 4.1 9.8 - - + +
239G ALA* 1.3 74.3 - - - +
241G LEU* 1.3 65.0 + - - +
260G ALA* 3.4 5.9 - - - +
261G ALA 3.2 32.6 + - - +
262G THR 3.6 10.1 - - - +
263G CYS* 3.5 39.5 - - - -
264G THR* 3.7 23.1 - - + +
497G TYR* 4.5 15.0 - - + -
498G LYS 3.7 3.6 - - - +
499G LEU* 3.8 22.0 - - + -
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Residues in contact with LEU 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G LEU* 3.7 29.2 - - + -
71G VAL* 5.1 3.4 - - + -
73G GLU* 3.8 28.9 - - + +
75G PHE* 4.0 12.3 - - + -
239G ALA* 3.8 2.4 + - + -
240G LEU* 1.3 81.4 - - - +
242G ARG* 1.3 63.4 + - - +
258G VAL* 4.2 7.4 - - + -
259G VAL 3.2 9.2 - - - +
260G ALA* 4.0 4.3 - - + -
497G TYR* 3.5 7.2 - - - -
498G LYS* 3.0 33.0 + - + +
500G ILE* 3.7 43.3 - - + -
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Residues in contact with ARG 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G GLU* 2.6 36.7 + - - +
75G PHE* 3.4 6.1 - - - -
241G LEU* 1.3 78.3 - - - +
243G CYS* 1.3 73.2 + - - +
244G ASN* 3.1 36.5 + - - +
258G VAL* 3.5 3.1 - - - -
259G VAL* 2.8 42.6 + - + +
260G ALA* 5.9 0.4 - - - -
261G ALA* 6.3 1.1 - - + +
265G ARG* 3.6 12.3 - - - +
496G ASP* 2.9 44.9 + - - +
497G TYR* 3.6 33.6 + - + -
604G NAG 5.0 0.6 - - - -
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Residues in contact with CYS 243 (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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75G PHE* 3.4 21.5 - - + -
242G ARG* 1.3 80.9 + - - +
244G ASN* 1.3 56.9 + - - +
245G ASP* 3.2 25.2 + - - +
248G TYR* 3.8 31.6 - - + +
252G GLU* 5.0 2.7 - - - -
255G CYS* 2.1 48.7 - - - -
496G ASP* 2.9 22.1 + - + +
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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