Contacts of the strand formed by residues 250 - 256 (chain G) in PDB entry 4A63
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 THR 250 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161G ILE 3.8 0.7 - - - +
162G GLN* 3.4 2.1 - - - -
163G ILE* 2.8 53.6 + - + +
175G ILE* 5.4 2.0 - - + -
240G TYR* 4.2 6.0 + - + -
241G GLU* 2.8 41.4 + - + +
242G PRO 3.3 1.2 - - - +
243G PRO* 3.2 21.9 - - - +
249G PHE* 1.3 70.3 - - - +
251G THR* 1.3 68.0 + - - +
252G ILE* 4.8 9.2 - - + -
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Residues in contact with THR 251 (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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1041F THR* 4.1 22.8 + - + +
1045F GLN* 4.6 7.6 - - + +
160G PRO* 4.0 14.4 - - + -
161G ILE 3.4 9.9 - - - +
162G GLN* 4.2 18.1 + - + +
249G PHE* 4.1 5.1 + - - +
250G THR* 1.3 77.4 - - - +
252G ILE* 1.3 64.7 + - - +
253G LEU* 4.0 24.9 - - + -
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Residues in contact with ILE 252 (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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159G CYS 3.7 0.9 - - - +
160G PRO* 3.7 0.5 - - - +
161G ILE* 3.0 32.7 + - - +
163G ILE* 3.8 29.4 - - + -
175G ILE* 3.8 31.4 - - + -
217G VAL* 4.1 21.5 - - + -
220G ASN* 5.9 1.1 - - - +
238G VAL* 3.9 17.0 - - + -
250G THR* 4.8 7.6 - - + -
251G THR* 1.3 78.0 - - - +
253G LEU* 1.3 63.7 + - - +
254G TYR* 3.5 37.9 + - + +
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Residues in contact with LEU 253 (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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1040F TYR* 3.8 25.8 - - + -
1041F THR* 3.8 32.9 + - + +
1044F SER* 4.2 6.1 - - - +
1045F GLN* 3.7 20.4 - - + +
158G THR* 3.9 20.2 - - + -
159G CYS 3.8 1.8 - - - -
160G PRO* 3.7 27.8 - - + -
217G VAL* 3.4 8.9 - - - +
218G GLU* 2.8 47.8 + - + +
251G THR* 4.0 9.2 - - + -
252G ILE* 1.3 72.2 - - - +
254G TYR* 1.3 58.1 + - - +
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Residues in contact with TYR 254 (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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157G LYS 3.6 0.2 - - - +
159G CYS* 2.8 36.8 + - - +
161G ILE* 3.6 35.9 - - + -
163G ILE* 6.3 0.2 - - + -
175G ILE* 4.1 13.9 + - - +
177G ALA* 3.6 32.1 + - + +
215G ILE* 3.5 19.7 - - + -
216G ARG 3.3 7.9 - - - -
217G VAL* 3.6 21.3 - - + +
236G VAL* 4.5 1.7 + - + -
238G VAL* 5.0 1.0 - - - +
252G ILE* 3.5 40.9 - - + +
253G LEU* 1.3 69.9 - - - +
255G ASN* 1.3 68.5 + - - +
256G PHE* 4.0 21.5 - + + -
275G ILE* 4.2 11.1 - - + +
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Residues in contact with ASN 255 (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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156G ALA 4.4 4.7 + - - -
157G LYS 3.4 21.0 + - - +
158G THR* 3.5 3.8 + - - +
214G LEU 3.4 2.8 - - - +
215G ILE* 3.4 4.3 - - - +
216G ARG* 3.0 39.9 + - + +
217G VAL 4.8 0.2 - - - +
218G GLU* 2.9 42.6 + - - +
254G TYR* 1.3 88.0 + - - +
256G PHE* 1.3 64.5 + - - +
257G MET* 2.8 28.6 - - + +
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Residues in contact with PHE 256 (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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151G LEU* 3.9 21.5 - - + -
153G CYS* 4.1 18.4 - - + -
154G GLN 4.6 0.9 + - - +
155G ILE* 3.6 5.7 - - - -
156G ALA 2.8 24.2 + - - +
157G LYS 4.5 1.6 + - - -
159G CYS* 4.2 11.0 - - + -
161G ILE* 4.9 5.6 - - + -
214G LEU* 3.4 11.9 - - + +
215G ILE* 3.8 35.4 - - + -
254G TYR* 4.0 27.4 - + + -
255G ASN* 1.3 73.4 - - - +
257G MET* 1.3 60.2 + - - +
258G CYS 3.4 6.9 + - - -
273G ILE* 3.8 31.0 - - + -
294G ILE* 3.5 36.7 - - + +
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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