Contacts of the strand formed by residues 222 - 229 (chain J) in PDB entry 3Q2K
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 222 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I TYR* 3.8 19.7 - - + +
155I MET* 3.9 9.9 - - + -
234I MET* 3.6 20.1 - - + +
184J ALA* 5.0 0.7 - - - -
185J PHE* 4.9 0.4 - - - -
210J THR* 3.4 3.8 - - - -
211J ALA 2.9 26.3 + - - +
213J LEU* 4.1 6.5 - - + +
220J GLU* 3.6 6.1 - - - +
221J ASP* 1.3 93.5 + - - +
223J GLY* 1.3 62.8 + - - +
239J VAL 3.3 13.0 - - - +
240J THR* 3.0 23.3 + - - -
242J LEU* 3.5 10.7 - - - +
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Residues in contact with GLY 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I MET* 3.1 5.4 - - - +
234I MET* 4.0 8.5 - - - -
185J PHE* 3.8 15.4 - - - -
209J TYR 3.2 13.0 - - - -
210J THR* 3.8 3.4 - - - -
222J THR* 1.3 77.9 - - - +
224J VAL* 1.3 63.3 + - - -
239J VAL* 2.8 34.0 + - - +
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Residues in contact with VAL 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I MET* 3.3 19.5 - - + -
226I ALA* 4.1 11.2 - - + +
234I MET* 4.0 5.8 - - + -
235I GLY* 3.4 40.4 - - - +
236I SER* 4.0 7.6 - - - -
185J PHE* 3.9 4.8 - - - -
208J ALA* 3.1 4.3 - - - +
209J TYR* 2.8 35.1 + - + +
223J GLY* 1.3 81.4 - - - +
225J ALA* 1.3 72.5 + - - +
236J SER* 5.0 0.2 - - - -
237J ILE 3.4 5.8 - - - +
238J ASN* 3.5 20.2 - - - +
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Residues in contact with ALA 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J PHE* 4.8 1.3 - - + -
206J VAL* 4.9 0.7 - - + -
207J TYR 3.2 9.6 - - - +
208J ALA* 3.9 3.4 - - + -
224J VAL* 1.3 80.5 - - - +
226J ALA* 1.3 64.7 - - - +
227J LEU* 3.9 4.5 - - + +
236J SER* 3.2 5.5 - - - -
237J ILE* 3.0 47.9 + - + +
335J ILE* 3.7 32.1 - - + -
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Residues in contact with ALA 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I TYR* 4.9 4.5 - - + +
209I TYR* 3.6 20.9 - - + +
224I VAL* 4.1 19.3 - - + +
226I ALA* 4.2 20.5 - - + +
206J VAL* 3.3 5.2 - - - +
207J TYR* 2.7 37.4 + - + +
224J VAL* 4.2 0.6 - - - -
225J ALA* 1.3 75.6 - - - +
227J LEU* 1.3 61.2 - - - +
235J GLY 3.5 4.9 - - - -
236J SER* 4.6 0.4 - - - -
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Residues in contact with LEU 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209I TYR* 3.5 11.2 - - - -
224I VAL* 5.3 0.2 - - - +
156J VAL 5.5 0.2 - - - +
196J LEU* 3.9 39.7 - - + -
203J VAL* 4.5 10.1 - - + -
205J SER 3.7 4.9 - - - +
206J VAL* 3.4 28.0 - - + -
225J ALA* 3.9 11.2 - - + +
226J ALA* 1.3 80.1 - - - +
228J ARG* 1.3 61.8 + - - +
229J TRP* 4.0 20.2 - - + -
234J MET* 3.3 4.8 - - - +
235J GLY 2.8 26.5 + - - +
236J SER* 4.0 27.1 - - - +
237J ILE* 4.1 4.3 - - + +
331J LEU* 5.1 1.8 - - + -
335J ILE* 5.1 2.5 - - + -
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Residues in contact with ARG 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I TYR* 5.5 0.2 + - - -
209I TYR* 3.5 49.1 - - + +
210I THR 5.1 7.3 + - - +
339I ALA 5.8 1.8 + - - -
203J VAL* 3.7 2.1 - - - +
204J GLU* 2.7 58.4 + - - +
205J SER* 3.1 19.1 + - - +
227J LEU* 1.3 76.9 - - - +
229J TRP* 1.3 66.2 + - - +
232J GLY* 4.7 7.4 - - - +
233J ALA 3.4 10.1 - - - +
234J MET* 4.5 10.5 - - + -
344J ARG* 4.4 13.1 - - - +
204L GLU* 5.9 0.8 + - - -
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Residues in contact with TRP 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J VAL* 3.7 24.0 - - + -
196J LEU* 3.3 46.8 + - + -
200J VAL* 3.4 25.8 - - + +
201J GLY 3.1 32.3 + - - -
202J PRO 3.3 15.3 - - - -
203J VAL* 3.9 11.5 - - + +
204J GLU* 3.7 4.3 - - - +
227J LEU* 4.0 16.8 - - + -
228J ARG* 1.3 81.9 - - - +
230J ARG* 1.3 59.1 + - - +
231J HIS* 3.6 25.6 - + + +
232J GLY* 2.8 21.0 + - - -
233J ALA* 2.9 28.3 + - + +
234J MET* 3.8 21.8 - - - -
235J GLY 3.9 3.8 - - - -
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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