Contacts of the strand formed by residues 220 - 226 (chain G) in PDB entry 1P8J
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 220 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146G GLY* 6.0 3.8 - - - +
147G ILE 2.9 14.7 + - - +
148G VAL* 3.6 12.4 - - + -
149G VAL* 2.9 29.1 + - - +
165G GLY 4.6 7.5 + - - -
166G ASN* 3.3 14.2 + - - +
167G TYR 3.1 22.6 + - - -
168G ASP* 3.7 38.1 + - + +
169G PRO* 4.3 6.5 - - - +
203G ALA* 4.9 0.2 - - - -
218G ASN 5.3 1.8 - - - +
219G ALA* 1.3 76.0 - - - +
221G ILE* 1.3 58.4 + - - +
246G HIS* 6.1 0.2 - - - -
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Residues in contact with ILE 221 (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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149G VAL* 3.3 33.0 - - + +
151G ILE* 4.0 17.3 - - + -
156G ILE* 4.4 10.3 - - + -
163G LEU* 4.5 16.2 - - + +
166G ASN* 2.8 30.9 + - + +
167G TYR* 3.3 8.6 - - - +
168G ASP* 2.9 25.2 + - - -
199G ALA* 4.0 21.3 - - + +
202G VAL* 4.0 19.3 - - + -
203G ALA* 3.8 12.8 - - + -
219G ALA 3.9 0.6 + - - -
220G ARG* 1.3 73.8 - - - +
222G GLY* 1.3 64.4 + - - +
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Residues in contact with GLY 222 (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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149G VAL 2.8 10.5 + - - +
150G SER* 3.4 0.6 - - - -
151G ILE* 2.9 29.4 + - - +
156G ILE* 4.1 7.4 - - - +
167G TYR* 4.6 0.7 - - - -
168G ASP 3.9 1.3 - - - -
171G ALA* 3.5 22.9 - - - +
172G SER* 3.2 13.2 - - - -
221G ILE* 1.3 75.8 - - - +
223G GLY* 1.3 57.9 + - - -
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Residues in contact with GLY 223 (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 ILE* 3.4 10.5 - - - -
155G GLY 5.3 0.7 - - - -
156G ILE* 3.6 23.8 - - - +
171G ALA 3.4 0.8 + - - -
172G SER* 2.7 17.4 + - - -
173G PHE 3.0 21.3 + - - -
182G PRO* 3.2 10.3 - - - +
222G GLY* 1.3 74.0 - - - -
224G VAL* 1.3 64.6 + - - -
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Residues in contact with VAL 224 (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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150G SER* 3.5 9.0 - - - +
151G ILE 2.8 9.3 + - - -
152G LEU* 3.4 27.6 - - + -
153G ASP 3.0 27.4 + - - +
155G GLY 4.2 2.6 + - - -
173G PHE 3.1 10.3 - - - +
175G VAL* 3.7 16.8 - - + -
223G GLY* 1.3 74.6 - - - +
225G ARG* 1.3 59.5 + - - +
226G MET* 3.2 7.2 + - + +
239G SER* 3.6 26.9 - - - +
242G LEU* 3.3 33.9 - - + -
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Residues in contact with ARG 225 (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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153G ASP 3.7 4.3 - - - -
154G ASP 3.7 17.5 + - - +
155G GLY* 3.7 12.7 - - - +
173G PHE 2.9 7.7 + - - +
174G ASP* 2.9 42.9 + - + +
175G VAL 2.9 24.6 + - - -
176G ASN* 3.2 17.6 + - - +
177G ASP* 3.5 20.6 + - - -
182G PRO* 4.2 5.8 - - + +
183G GLN 3.5 24.4 + - - -
185G ARG* 3.8 21.3 - - - +
223G GLY 4.0 1.6 - - - -
224G VAL* 1.3 68.5 - - - +
226G MET* 1.3 59.0 + - - +
228G ASP* 2.8 42.6 + - + +
558H ASN* 4.2 2.8 - - - +
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Residues in contact with MET 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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152G LEU* 4.1 7.4 - - + -
153G ASP 2.8 8.6 + - - +
175G VAL* 4.2 3.6 - - + -
176G ASN* 3.2 23.2 + - - +
224G VAL* 3.6 18.2 - - + +
225G ARG* 1.3 75.2 - - - +
227G LEU* 1.3 81.0 + - + +
231G VAL* 3.6 16.0 - - + +
235G VAL* 3.7 18.4 - - + +
236G GLU* 4.2 15.7 - - + -
239G SER* 3.2 36.6 - - - +
254G TRP* 3.4 40.2 - - + -
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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