Contacts of the strand formed by residues 222 - 229 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G TYR 3.5 19.3 - - - +
155G MET* 3.5 23.1 - - + -
234G MET* 3.6 10.5 - - + +
184H ALA* 5.2 0.2 - - - -
185H PHE* 4.7 1.1 - - - -
210H THR* 3.3 5.5 - - - -
211H ALA 3.0 26.9 + - - +
213H LEU* 3.8 10.4 - - + +
220H GLU* 3.5 7.2 - - - +
221H ASP* 1.3 96.8 + - - +
223H GLY* 1.3 63.5 + - - +
239H VAL 3.2 5.8 - - - +
240H THR* 3.0 21.4 + - - +
242H LEU* 3.2 11.8 - - - +
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Residues in contact with GLY 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G MET* 3.4 5.5 - - - +
234G MET* 4.3 2.5 - - - -
185H PHE* 3.6 17.7 - - - -
209H TYR 3.2 11.4 - - - -
210H THR* 4.1 0.4 - - - -
222H THR* 1.3 80.6 - - - +
224H VAL* 1.3 66.1 - - - -
238H ASN* 3.6 0.3 - - - -
239H VAL 2.6 43.3 + - - +
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Residues in contact with VAL 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G MET* 4.2 4.7 - - + -
226G ALA* 4.3 13.4 - - + +
227G LEU 4.6 1.6 - - - +
234G MET* 3.4 16.6 - - + -
235G GLY* 3.2 47.1 - - - +
236G SER* 3.6 9.9 - - - -
185H PHE* 3.9 4.4 - - - -
207H TYR 4.0 0.2 - - - +
208H ALA* 3.1 5.5 - - - +
209H TYR* 2.9 33.4 + - + +
223H GLY* 1.3 77.4 - - - +
225H ALA* 1.3 65.5 + - - +
236H SER* 4.7 0.7 - - - -
237H ILE 3.4 5.4 - - - +
238H ASN* 3.2 20.9 - - - +
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Residues in contact with ALA 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H PHE* 4.5 1.3 - - + -
206H VAL* 4.7 0.4 - - + -
207H TYR 3.1 9.2 - - - +
208H ALA* 4.1 3.6 - - + -
224H VAL* 1.3 79.7 - - - +
226H ALA* 1.3 62.3 + - - +
227H LEU* 3.8 13.0 - - + +
236H SER* 3.1 5.8 - - - -
237H ILE* 2.9 49.1 + - + +
335H ILE* 3.9 24.5 - - + -
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Residues in contact with ALA 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G TYR* 4.8 9.2 - - + +
209G TYR* 3.7 22.0 - - + -
224G VAL* 4.2 14.4 - - + +
226G ALA* 4.1 23.1 - - + +
206H VAL* 3.2 7.3 - - - +
207H TYR 2.7 32.9 + - - +
224H VAL 4.3 0.2 - - - -
225H ALA* 1.3 75.9 - - - +
227H LEU* 1.3 59.0 + - - +
235H GLY 3.4 8.5 - - - +
236H SER* 4.4 1.6 - - - +
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Residues in contact with LEU 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209G TYR* 3.8 8.2 - - - -
196H LEU* 3.6 33.4 - - + -
203H VAL* 5.0 5.2 - - + -
205H SER 3.7 5.4 - - - +
206H VAL* 3.6 24.0 - - + -
225H ALA* 3.8 20.2 - - + +
226H ALA* 1.3 81.1 - - - +
228H ARG* 1.3 61.4 + - - +
229H TRP* 3.8 27.6 - - + -
234H MET* 3.3 7.3 - - - +
235H GLY 2.8 30.9 + - - +
236H SER* 3.8 25.6 - - - +
237H ILE* 4.0 6.3 - - + +
331H LEU* 4.6 3.6 - - + -
335H ILE* 5.0 0.9 - - + -
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Residues in contact with ARG 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C GLU* 5.6 4.0 + - - -
209G TYR* 3.5 46.2 - - + +
210G THR 5.4 5.6 + - - -
339G ALA 5.7 3.0 + - - -
203H VAL* 3.6 2.9 - - - +
204H GLU* 2.8 61.0 + - - +
205H SER* 3.1 18.0 + - - +
227H LEU* 1.3 76.2 - - - +
229H TRP* 1.3 64.2 + - - +
232H GLY* 4.8 6.3 - - - +
233H ALA 3.6 9.0 - - - +
234H MET* 4.1 12.6 - - + -
344H ARG* 4.2 15.2 - - - +
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Residues in contact with TRP 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H VAL* 3.7 28.5 - - + -
196H LEU* 3.1 45.7 + - + -
200H VAL* 3.7 19.5 - - + +
201H GLY* 3.1 27.4 + - - -
202H PRO 3.2 14.8 - - - +
203H VAL* 3.4 12.8 - - + +
204H GLU* 3.7 6.5 - - - +
227H LEU* 3.8 25.1 - - + -
228H ARG* 1.3 84.7 - - - +
230H ARG* 1.3 59.4 + - - +
231H HIS* 3.3 23.8 - + + +
232H GLY* 3.0 17.2 + - - -
233H ALA* 3.0 28.0 + - + +
234H MET 3.9 20.6 - - - -
235H GLY* 3.9 4.3 - - - -
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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