Contacts of the strand formed by residues 182 - 188 (chain G) in PDB entry 1RFU
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 182 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145G ASP 3.4 2.8 + - - -
146G ILE* 3.3 39.6 - - + +
147G ILE 3.2 22.1 + - - -
180G PRO* 3.7 1.7 - - - +
181G ASP* 1.3 82.5 + - - +
183G VAL* 1.3 67.6 + - - +
184G VAL* 4.8 4.5 - - + -
204G SER 3.4 4.7 - - - +
205G GLN* 3.6 22.2 + - + +
241G LEU* 5.9 0.7 - - + -
245G THR* 5.4 4.5 - - + -
252G LEU* 3.7 31.0 - - + -
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Residues in contact with VAL 183 (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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147G ILE* 3.4 26.9 - - + -
172G MET* 3.3 29.1 - - + +
175G LEU* 3.6 26.7 - - + -
176G HIS* 3.7 28.3 - - + +
180G PRO* 3.8 10.8 - - + -
182G THR* 1.3 79.4 - - - +
184G VAL* 1.3 68.2 + - - +
185G ILE* 4.5 3.6 - - + -
202G LEU 4.0 0.6 - - - +
203G GLY* 3.4 0.2 - - - -
204G SER* 2.7 39.7 + - - +
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Residues in contact with VAL 184 (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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146G ILE* 5.7 0.2 - - + -
147G ILE 3.1 12.3 + - - +
148G THR* 3.5 3.4 - - - -
149G PRO* 2.9 29.3 - - - +
182G THR* 4.8 3.4 - - + -
183G VAL* 1.3 83.1 - - - +
185G ILE* 1.3 75.7 + - - +
186G THR* 3.4 1.4 + - - -
201G ALA* 5.5 2.9 - - + -
202G LEU 3.4 10.1 - - - +
203G GLY* 4.0 9.6 - - - -
221G MET* 5.8 2.7 - - + -
237G PHE* 3.9 31.6 - - + -
241G LEU* 4.5 15.9 - - + -
252G LEU* 4.5 9.4 - - + -
256G CYS* 4.5 18.6 - - - -
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Residues in contact with ILE 185 (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 PRO* 3.4 28.7 - - + -
151G GLN* 3.7 21.8 - - + +
154G ALA* 3.5 17.3 - - + -
168G ALA* 5.7 6.1 - - + +
171G VAL* 5.4 2.0 - - + -
172G MET* 4.2 21.5 - - + -
175G LEU* 4.3 12.3 - - + -
183G VAL* 4.5 0.2 - - + -
184G VAL* 1.3 74.0 - - - +
186G THR* 1.3 58.7 + - - +
187G SER 2.9 34.1 + - - +
188G SER* 4.7 4.9 - - - -
201G ALA* 3.3 3.5 - - - +
202G LEU* 2.8 41.4 + - + +
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Residues in contact with THR 186 (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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148G THR* 4.1 19.0 + - - +
149G PRO 3.2 10.8 + - - -
150G ASN* 4.3 4.9 + - - -
184G VAL* 4.3 5.6 - - + -
185G ILE* 1.3 71.1 - - - +
187G SER* 1.3 61.6 + - - +
201G ALA* 3.4 14.5 - - - +
223G MET* 3.5 3.1 - - - +
234G GLY* 5.6 2.5 - - - -
237G PHE* 3.3 41.3 - - + -
6402G ADP 2.8 61.6 + - - +
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Residues in contact with SER 187 (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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119G GLN* 2.9 25.1 + - - -
151G GLN* 3.1 8.3 + - - +
185G ILE* 2.9 10.9 + - - +
186G THR* 1.3 84.2 + - - +
188G SER* 1.3 66.8 + - - +
199G LEU* 4.1 18.2 - - - +
200G MET 3.0 15.0 - - - -
223G MET* 4.1 10.5 - - - -
6402G ADP 2.4 29.1 + - - -
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Residues in contact with SER 188 (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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119G GLN* 3.8 7.4 - - - +
151G GLN* 2.8 30.5 - - - -
162G ILE* 6.0 0.9 - - - -
185G ILE* 4.7 5.2 - - - -
187G SER* 1.3 79.7 - - - +
189G ASN* 1.3 59.8 + - - +
190G LEU* 3.3 32.5 + - - +
198G TYR 5.2 1.4 - - - +
199G LEU* 4.2 11.8 - - - +
200G MET* 3.0 26.2 + - - +
202G LEU* 5.8 0.7 - - - +
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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