Contacts of the strand formed by residues 225 - 232 (chain G) in PDB entry 4GEK
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 225 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ASP* 2.7 30.4 + - - +
172A LYS* 3.7 30.5 - - + +
173A VAL* 4.1 12.1 - - + -
223G PHE* 3.2 1.7 - - - +
224G GLU* 1.3 96.8 + - + +
226G SER* 1.3 67.3 + - - +
240G ALA* 3.2 0.9 - - - +
241G LEU* 2.8 50.3 + - + +
243G ALA 5.1 1.3 - - - -
301G SO4 2.7 32.5 + - - -
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Residues in contact with SER 226 (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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170A ASP* 4.8 3.0 + - - +
173A VAL* 4.2 7.5 - - - +
215G LYS* 5.1 16.0 - - - +
218G LEU* 3.7 31.4 - - - +
219G HIS* 5.0 0.7 + - - -
223G PHE* 3.8 6.6 + - - +
225G HIS* 1.3 78.5 + - - +
227G GLU* 1.3 70.7 + - - +
238G LEU* 5.4 0.2 - - - -
239G VAL 3.2 12.8 - - - -
240G ALA* 3.6 10.8 - - - +
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Residues in contact with GLU 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.8 25.9 - - + +
170A ASP* 5.8 3.1 - - - +
173A VAL* 3.5 33.8 - - + +
177A LEU* 4.8 1.6 - - + -
212A GLU* 5.3 4.3 - - - +
231A GLN* 5.5 0.4 - - - +
215G LYS* 3.4 23.4 + - - +
226G SER* 1.3 80.8 - - - +
228G LEU* 1.3 93.6 + - - +
238G LEU* 3.2 7.5 - - - +
239G VAL* 2.9 38.4 + - + +
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Residues in contact with LEU 228 (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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177A LEU* 4.9 0.5 - - - +
228A LEU* 3.6 22.9 - - + -
231A GLN* 3.0 24.0 + - - +
166G PHE* 3.7 30.3 - - + -
211G VAL* 4.3 21.5 - - + -
215G LYS* 4.2 2.8 - - - +
227G GLU* 1.3 94.7 + - - +
229G TRP* 1.3 57.3 + - - +
230G PHE 3.6 16.4 - - - +
231G GLN* 3.5 23.1 - - + +
237G SER 3.4 17.0 - - - +
238G LEU* 4.0 12.3 - - + +
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Residues in contact with TRP 229 (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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176A LEU* 5.2 1.1 - - + -
177A LEU* 4.1 18.2 - - + -
180A MET* 4.3 5.2 - - + -
231A GLN* 3.9 9.9 - - - +
232A CYS* 3.5 1.2 - - - -
233A PHE* 2.8 59.3 + + - +
42G ILE* 5.3 2.2 - - + +
45G MET* 3.2 47.7 - - + +
46G ILE* 4.2 2.9 - - + -
49G LEU* 3.7 33.7 - - + -
161G VAL* 3.9 22.9 - - + -
227G GLU* 3.4 1.2 + - + -
228G LEU* 1.3 74.0 - - - +
230G PHE* 1.4 59.6 + - + +
237G SER* 2.9 51.1 + - - -
238G LEU 4.0 9.6 + - - -
239G VAL* 4.0 27.6 - - + -
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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
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41A ASN* 4.9 0.4 - - - -
230A PHE* 4.1 14.6 - + - -
231A GLN* 3.1 25.8 - - - -
232A CYS* 4.1 6.5 - - + -
37G PRO 4.3 1.6 - - - -
38G GLY* 3.7 34.1 - - - -
41G ASN* 3.7 25.8 - - + -
42G ILE* 3.5 23.6 - - + -
45G MET* 3.5 27.1 - - + -
228G LEU* 3.6 6.5 - - - +
229G TRP* 1.4 79.6 - - - +
231G GLN* 1.3 88.1 + - - +
232G CYS* 3.8 13.7 - - + -
235G PHE 4.9 0.4 - - - -
236G GLY* 3.2 4.1 - - - -
237G SER* 2.8 40.3 + - - +
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Residues in contact with GLN 231 (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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227A GLU* 5.3 0.5 - - - +
228A LEU* 3.0 36.2 + - - +
229A TRP* 3.9 5.2 - - - +
230A PHE* 3.1 15.6 - - - -
231A GLN* 2.9 38.0 + - + +
166G PHE* 4.6 8.7 - - + -
168G PHE* 3.8 21.2 - - - -
177G LEU* 4.6 0.8 - - - +
211G VAL* 5.0 2.8 - - - +
228G LEU* 3.5 23.6 - - + +
230G PHE* 1.3 81.2 - - - +
232G CYS* 1.3 64.5 + - - +
233G PHE 2.9 20.7 + - - +
235G PHE 3.3 16.6 - - - +
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Residues in contact with CYS 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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41A ASN* 5.6 4.0 - - - -
45A MET* 4.1 20.0 - - - -
229A TRP 3.5 3.6 - - - -
230A PHE* 4.2 6.3 - - + -
37G PRO* 3.6 33.9 - - - +
38G GLY* 4.5 2.5 - - - -
184G PHE* 5.9 1.6 - - - -
230G PHE* 3.8 19.2 - - + -
231G GLN* 1.3 76.9 - - - +
233G PHE* 1.4 85.3 + - - +
234G ASN 3.2 0.2 + - - -
235G PHE* 2.8 24.3 + - - +
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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