Contacts of the strand formed by residues 234 - 240 (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 MET 234 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209G TYR* 3.8 20.4 - - + +
210G THR* 3.6 29.8 - - - +
211G ALA* 3.3 27.4 - - + -
213G LEU* 3.6 13.2 - - + -
222G THR* 3.5 33.9 - - + +
223G GLY* 4.3 0.9 - - - -
224G VAL* 4.1 13.9 - - + -
154H TYR 3.0 8.6 + - - +
155H MET* 3.2 10.5 - - + +
156H VAL 3.1 20.8 + - - -
227H LEU 3.3 13.0 - - - +
228H ARG* 4.1 13.2 - - + -
229H TRP* 3.9 6.6 - - - -
232H GLY 3.6 3.5 + - - +
233H ALA* 1.3 77.6 - - - +
235H GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 235 (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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224G VAL* 3.5 20.5 - - - +
155H MET* 4.3 2.5 - - - -
156H VAL 3.0 14.1 - - - -
226H ALA* 3.4 4.5 - - - -
227H LEU* 2.8 37.9 + - - -
229H TRP* 3.9 5.0 - - - -
234H MET* 1.3 77.4 - - - +
236H SER* 1.3 61.8 + - - -
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Residues in contact with SER 236 (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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224G VAL* 4.1 4.0 - - - -
236G SER* 3.3 19.0 + - - -
238G ASN* 2.6 24.4 + - - -
156H VAL 3.2 5.4 + - - +
157H THR* 2.9 18.3 - - - +
158H VAL* 3.0 24.3 + - - +
224H VAL* 4.7 0.7 - - - -
225H ALA 3.1 12.8 - - - -
227H LEU* 3.8 7.5 - - - +
235H GLY* 1.3 75.0 - - - -
237H ILE* 1.3 62.6 + - - +
238H ASN* 3.2 12.9 + - - -
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Residues in contact with ILE 237 (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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158H VAL* 3.4 31.4 - - + +
185H PHE* 4.0 10.4 - - + -
189H ALA 4.9 0.9 - - - +
192H TYR* 4.2 5.8 - - + +
193H VAL* 3.9 37.7 - - + +
196H LEU* 4.5 8.5 - - + -
223H GLY 4.0 0.5 - - - +
224H VAL* 3.4 4.0 - - - +
225H ALA* 2.9 50.7 + - + +
227H LEU* 4.1 15.0 - - + -
236H SER* 1.3 75.5 - - - +
238H ASN* 1.3 66.6 + - - +
239H VAL* 3.8 20.2 - - + -
335H ILE* 4.7 3.6 - - + -
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Residues in contact with ASN 238 (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* 4.0 8.3 - - - +
157G THR* 4.0 10.8 + - - +
235G GLY 4.3 1.0 - - - -
236G SER* 2.9 25.7 + - - -
157H THR* 4.5 4.0 - - - +
158H VAL 2.9 10.3 + - - -
159H ASN* 3.1 24.9 + - - +
160H VAL 2.8 26.2 + - - +
161H PHE* 3.8 15.2 - - + -
223H GLY 3.6 4.0 - - - -
224H VAL* 3.2 17.7 - - - +
236H SER* 3.2 21.4 + - - -
237H ILE* 1.3 75.1 - - - +
239H VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 239 (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* 3.6 4.9 - - - +
160H VAL* 3.4 10.3 - - + +
161H PHE* 5.1 0.2 - - - -
184H ALA* 3.7 35.4 - - + +
185H PHE* 3.8 33.7 - - + +
189H ALA* 4.0 17.3 - - + -
222H THR* 3.2 1.2 - - - -
223H GLY 2.6 41.2 + - - +
237H ILE* 3.8 13.7 - - + -
238H ASN* 1.3 81.5 - - - +
240H THR* 1.3 64.6 + - - +
241H MET* 3.9 13.0 - - + -
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Residues in contact with THR 240 (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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154G TYR* 4.7 2.6 - - + +
155G MET* 4.4 8.7 - - + -
255G LEU* 3.8 23.3 - - + -
160H VAL 3.1 8.7 + - - +
161H PHE* 4.2 7.1 - - + -
162H TRP 3.1 24.8 + - - +
221H ASP 3.3 5.2 - - - -
222H THR* 3.0 27.8 + - - +
239H VAL* 1.3 75.3 - - - +
241H MET* 1.3 64.6 + - - +
242H LEU* 3.1 21.6 + - + +
243H THR* 3.6 20.9 - - - +
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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