Contacts of the strand formed by residues 174 - 181 (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 ALA 174 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G GLY 3.6 4.9 + - - +
173G THR* 1.3 76.0 - - - +
175G ILE* 1.3 64.6 + - - +
237G VAL* 3.4 26.0 - - + -
238G VAL 3.5 9.9 - - - +
239G PRO* 4.5 2.2 - - + -
240G TYR 4.0 0.2 - - - +
277G LEU* 3.4 5.9 - - - +
278G GLU* 2.8 42.0 + - + +
279G MET 5.6 1.8 - - - +
280G ARG* 6.3 0.4 - - - -
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Residues in contact with ILE 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G PHE* 4.6 4.9 - - + -
163G ILE* 3.9 18.6 - - + -
174G ALA* 1.3 74.6 - - - +
176G ARG* 1.3 58.7 + - - +
236G VAL 3.9 1.4 - - - +
237G VAL* 3.4 4.0 - - - -
238G VAL* 2.9 39.6 + - + +
239G PRO 5.1 2.0 - - - +
240G TYR* 3.9 33.2 - - + -
250G THR* 5.4 3.6 - - + -
252G ILE* 3.8 30.3 - - + -
254G TYR* 4.1 5.6 + - - +
275G ILE* 3.5 31.6 - - + -
276G THR 3.4 4.7 - - - +
277G LEU* 3.7 17.0 - - + -
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Residues in contact with ARG 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G ALA 4.1 0.4 - - - -
175G ILE* 1.3 73.8 - - - +
177G ALA* 1.3 64.1 + - - +
178G MET* 4.4 16.9 - - - +
226G VAL* 4.0 16.6 - - - +
235G SER* 2.8 45.4 + - - -
236G VAL 3.6 4.5 - - - +
237G VAL* 3.4 30.2 - - + +
274G ILE 3.4 1.8 - - - +
275G ILE* 3.2 8.5 - - - +
276G THR* 2.9 44.0 + - - +
278G GLU* 2.9 37.8 + - - +
282G GLY* 5.8 1.6 - - - -
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Residues in contact with ALA 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G ARG* 1.3 74.0 - - - +
178G MET* 1.3 59.8 + - - +
215G ILE* 4.0 19.5 - - + +
235G SER* 3.5 3.7 - - - -
236G VAL* 3.1 32.5 + - + +
254G TYR* 3.6 36.8 - - + +
273G ILE* 4.9 0.7 - - + -
274G ILE 3.3 6.1 - - - -
275G ILE* 3.8 13.9 - - + -
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Residues in contact with MET 178 (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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116G PRO* 3.9 33.7 - - + -
176G ARG* 4.4 15.5 - - - +
177G ALA* 1.3 73.0 - - - +
179G PRO* 1.3 74.6 - - + +
180G VAL* 3.9 4.2 + - + -
215G ILE* 3.9 3.8 - - - +
233G ARG* 3.7 31.9 - - + +
234G GLN 3.6 11.7 - - - +
235G SER* 3.8 22.0 - - - +
272G LEU 3.8 0.3 - - - +
273G ILE* 3.7 0.7 - - - -
274G ILE* 3.0 41.2 + - + +
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Residues in contact with PRO 179 (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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177G ALA 4.6 1.1 - - - +
178G MET* 1.3 89.4 - - + +
180G VAL* 1.3 65.4 + - - +
191G VAL* 3.6 37.8 + - + +
214G LEU* 3.7 30.7 - - + +
215G ILE* 3.6 19.9 - - + +
233G ARG* 4.5 5.2 + - - -
234G GLN 3.5 18.6 - - - +
235G SER* 5.1 0.2 - - - -
271G ILE* 4.0 10.1 - - + -
272G LEU 3.3 6.5 - - - +
273G ILE* 4.6 0.7 - - + -
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Residues in contact with VAL 180 (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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116G PRO* 4.0 28.3 - - + +
118G ASN* 6.3 0.7 - - - +
178G MET* 4.2 8.5 - - + -
179G PRO* 1.3 79.7 - - - +
181G TYR* 1.4 72.0 + - - +
187G VAL* 3.9 19.1 - - + +
191G VAL* 3.7 8.3 - - - -
233G ARG* 4.1 14.8 - - - +
271G ILE* 3.3 2.6 - - - -
272G LEU* 2.7 40.4 + - + +
274G ILE* 3.6 31.6 - - + -
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Residues in contact with TYR 181 (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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180G VAL* 1.4 86.2 - - - +
182G LYS* 1.3 63.0 + - - +
183G LYS 3.6 0.7 - - - -
186G HIS* 3.4 38.8 - - + +
187G VAL* 3.7 12.9 - - - +
189G ASP* 3.3 32.1 + - + -
190G VAL 3.9 7.4 + - - -
191G VAL* 3.5 24.7 - - + +
192G LYS 4.8 1.7 + - - -
265G GLY 3.3 5.0 + - - -
266G MET* 3.3 27.1 + - + +
269G ARG* 3.0 51.8 + - + -
270G PRO 3.6 9.2 - - - +
271G ILE* 3.4 23.6 - - + -
272G LEU* 5.3 1.3 - - - +
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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