Contacts of the strand formed by residues 201 - 207 (chain G) in PDB entry 1I43
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 VAL 201 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G HIS* 4.1 13.0 - - + +
157G VAL* 3.4 38.1 - - + +
192G LEU* 6.4 0.2 - - + -
195G ALA 3.6 22.7 - - - +
196G LEU* 3.8 29.7 + - + +
199G LYS 3.3 1.6 + - - -
200G LYS* 1.3 78.6 - - - +
202G ASN* 1.3 63.8 + - - +
203G LEU 3.6 19.7 - - - +
204G PHE* 4.4 2.2 - - + +
229G LYS 4.9 2.9 - - - +
230G GLY 4.7 2.3 - - - +
231G ALA* 3.7 25.0 + - + +
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Residues in contact with ASN 202 (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 LEU 5.6 0.4 - - - +
150G VAL* 4.5 8.3 - - + -
151G PRO* 3.6 31.8 - - + +
154G GLY* 3.1 29.8 - - - -
155G HIS 2.9 20.9 + - - +
200G LYS* 3.4 17.3 + - - +
201G VAL* 1.3 76.0 + - - +
203G LEU* 1.3 64.9 + - + +
230G GLY 4.7 2.0 - - - +
231G ALA* 4.0 1.7 - - - -
232G LEU* 3.3 20.6 + - - +
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Residues in contact with LEU 203 (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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145G MET* 3.8 31.2 - - + -
146G LEU* 4.1 0.7 - - + -
149G LEU* 4.5 15.9 - - + -
150G VAL* 3.9 13.7 - - + -
155G HIS 3.8 1.6 + - - -
156G ILE* 3.3 45.8 - - + +
157G VAL 3.1 22.0 + - - -
201G VAL* 3.6 6.3 - - - +
202G ASN* 1.3 83.6 - - - +
204G PHE* 1.3 66.6 + - - +
205G PHE* 4.1 8.1 - - + -
232G LEU* 3.4 28.3 - - + +
234G CYS* 4.2 16.6 - - + +
254G LEU* 4.9 1.6 - - + -
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Residues in contact with PHE 204 (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 VAL* 3.0 50.0 - - + -
158G THR* 4.2 12.1 - - - -
159G THR* 4.4 7.9 - - + -
184G ILE* 4.5 7.0 - - + -
186G PRO 6.0 1.1 - - - -
192G LEU* 3.7 14.4 - - + -
201G VAL* 4.4 3.1 - - + +
203G LEU* 1.3 73.6 - - - +
205G PHE* 1.3 61.8 + - - +
206G THR* 3.5 30.1 - - + -
217G VAL* 4.5 5.2 - - + -
222G VAL* 3.3 43.1 - - + -
226G CYS* 3.8 16.4 - - - -
232G LEU 2.7 14.4 + - - +
233G VAL* 3.4 8.3 - - + -
234G CYS 3.0 25.5 + - - +
235G ILE* 5.1 0.2 - - + -
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Residues in contact with PHE 205 (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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142G SER* 4.8 8.1 - - - -
145G MET* 4.4 10.1 - - + -
146G LEU* 5.3 5.8 - - + -
156G ILE* 4.8 2.2 - - + -
157G VAL 2.8 9.1 + - - +
158G THR* 3.0 45.4 - - + +
162G CYS* 3.9 20.6 - - - -
166G THR* 4.1 20.6 - - + -
170G ILE* 5.1 2.9 - - + -
203G LEU* 3.9 18.3 + - + -
204G PHE* 1.3 75.5 - - - +
206G THR* 1.3 74.0 + - - +
207G GLU* 4.3 8.7 - - - -
234G CYS* 3.5 23.1 - - + -
236G ASP* 4.5 20.0 - - + -
256G LEU* 3.7 29.2 - - + -
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Residues in contact with THR 206 (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 THR* 3.0 33.5 + - - +
162G CYS* 5.5 2.5 - - - -
204G PHE* 3.5 31.2 - - + -
205G PHE* 1.3 84.9 - - - +
207G GLU* 1.3 76.8 + - - +
210G THR* 5.1 0.3 + - - -
217G VAL* 4.2 12.6 - - + +
234G CYS 3.1 4.8 + - - +
235G ILE* 3.0 28.3 - - + +
236G ASP* 2.8 22.2 + - - -
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Residues in contact with GLU 207 (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 THR* 5.7 0.7 - - - +
161G ASP 3.7 7.1 - - - +
162G CYS* 4.2 15.6 - - - -
163G TYR* 3.2 33.1 + - - +
166G THR* 5.6 0.2 + - - -
205G PHE* 4.3 7.6 - - - -
206G THR* 1.3 86.3 + - - +
208G SER* 1.3 64.2 + - - +
209G PRO 3.3 12.7 - - - +
210G THR* 3.7 20.9 + - - +
211G ASN* 4.0 8.9 + - - +
215G ARG 4.2 2.6 - - - +
217G VAL* 4.5 3.8 - - - +
236G ASP* 3.3 34.5 - - + +
239G PHE* 5.8 0.2 - - + -
500G PLP 3.7 20.6 + - + +
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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