Contacts of the strand formed by residues 185 - 189 (chain G) in PDB entry 2JG7
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 185 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G THR* 3.4 29.2 - - + +
67G ARG* 5.0 0.4 - - - +
69G ALA 4.3 0.2 - - - -
70G TRP* 3.7 41.0 - - + +
73G TRP* 3.9 5.4 - - + -
157G GLY 3.0 11.0 + - - +
158G LEU* 3.3 9.6 - - + +
159G VAL* 2.7 33.4 + - - +
184G ASN* 1.3 78.7 - - - +
186G CYS* 1.3 57.3 + - - +
218G ILE* 3.5 38.6 - - + +
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Residues in contact with CYS 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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66G THR* 4.2 1.6 + - - -
158G LEU* 4.1 2.5 - - - -
159G VAL* 3.3 4.9 - - - -
161G ILE* 3.9 24.0 - - + -
172G TYR* 4.5 8.3 - - + +
176G ASN* 3.8 24.2 - - - +
179G ALA* 3.9 23.8 - - - -
180G LEU* 3.8 15.9 - - - -
185G VAL* 1.3 78.4 - - - +
187G LEU* 1.3 59.7 + - - +
217G ALA 4.0 3.1 - - - +
218G ILE 2.8 14.1 + - - +
219G CYS* 4.5 2.0 - - - -
220G SER* 2.9 28.2 + - - -
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Residues in contact with LEU 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G TYR* 4.0 9.9 - - + -
62G THR* 3.8 27.6 - - + -
63G VAL* 3.8 31.6 - - + +
66G THR* 4.7 3.6 - - - +
158G LEU* 3.8 18.8 - - + +
159G VAL 2.9 7.2 + - - +
160G GLY* 3.4 3.6 - - - -
161G ILE* 2.7 33.7 + - - +
186G CYS* 1.3 75.9 - - - +
188G TRP* 1.3 59.9 + - - +
220G SER* 3.4 5.6 - - - -
222G THR* 3.6 23.3 - - + +
232G MET* 3.8 24.9 - - + -
238G VAL* 6.0 2.0 - - + -
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Residues in contact with TRP 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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161G ILE* 3.3 12.6 - - - -
163G THR* 3.2 30.3 + - + +
168G PRO 3.4 26.2 - - - -
169G VAL* 5.3 0.2 - - - -
172G TYR* 3.3 63.3 - + + -
187G LEU* 1.3 76.5 - - - +
189G LYS* 1.3 74.5 + - - +
190G GLY* 3.6 4.5 + - - +
198G SER* 3.5 48.2 - - - -
201G VAL* 3.7 18.2 - - + -
202G THR* 3.7 13.7 - - - -
220G SER 2.8 15.3 + - - +
221G MET* 3.3 10.9 - - + +
222G THR 3.0 26.2 + - - +
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Residues in contact with LYS 189 (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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161G ILE 2.9 9.4 + - - +
162G ILE* 3.4 18.3 - - + -
163G THR 3.4 18.7 + - - -
187G LEU 4.1 0.6 + - - -
188G TRP* 1.3 73.1 - - - +
190G GLY* 1.3 77.2 + - - +
192G PRO* 4.3 0.4 - - - +
222G THR* 3.3 21.3 - - - +
224G GLY 2.9 30.9 + - - +
225G GLY 3.5 13.7 - - - +
228G ILE* 3.9 8.3 - - + -
229G GLY* 3.5 31.0 - - - +
232G MET* 3.9 18.8 - - - +
1510G NAD 2.8 38.1 + - - -
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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
------------------------------------------------------------
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