Contacts of the strand formed by residues 234 - 240 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209O TYR* 3.7 20.9 - - + +
210O THR* 3.7 32.3 - - - +
211O ALA* 3.5 27.4 - - + -
213O LEU* 3.7 25.1 - - + -
222O THR* 3.7 21.3 - - + +
223O GLY* 4.1 3.1 - - - -
224O VAL* 4.2 14.6 - - + +
154P TYR 3.3 6.4 + - - +
155P MET* 3.4 11.6 - - + +
156P VAL 3.3 17.2 + - - -
227P LEU 3.1 11.9 - - - +
228P ARG* 4.4 10.5 - - + -
229P TRP* 3.8 5.9 - - - -
232P GLY 3.5 5.1 + - - +
233P ALA* 1.3 78.0 - - - +
235P GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O VAL* 3.6 18.5 - - - +
155P MET* 4.4 0.4 - - - -
156P VAL 2.9 16.4 - - - -
226P ALA* 3.4 3.3 - - - -
227P LEU* 2.9 33.4 + - - +
229P TRP* 3.7 8.4 - - - -
234P MET* 1.3 76.5 - - - +
236P SER* 1.3 62.4 + - - -
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Residues in contact with SER 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O VAL* 3.9 4.9 - - - -
236O SER* 3.3 18.5 + - - -
238O ASN* 2.6 30.7 + - - -
156P VAL 3.0 5.8 + - - +
157P THR* 3.4 5.0 - - - +
158P VAL* 3.0 24.1 + - - +
196P LEU* 5.2 0.7 - - - +
224P VAL* 4.8 0.2 - - - -
225P ALA 3.2 11.4 - - - -
226P ALA* 4.5 1.1 - - - -
227P LEU* 4.2 5.5 - - - +
235P GLY* 1.3 75.9 - - - -
237P ILE* 1.3 61.5 + - - +
238P ASN* 3.2 16.8 + - - -
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Residues in contact with ILE 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158P VAL* 3.3 35.4 - - + +
160P VAL* 5.3 0.4 - - + -
185P PHE* 4.0 11.1 - - + -
189P ALA 5.3 0.2 - - - +
192P TYR* 4.1 5.4 - - + +
193P VAL* 4.1 25.6 - - + +
196P LEU* 3.9 33.7 - - + -
223P GLY 4.1 0.3 - - - +
224P VAL* 3.4 4.3 - - - +
225P ALA* 3.0 51.1 + - + +
227P LEU* 4.3 3.6 - - + -
236P SER* 1.3 74.5 - - - +
238P ASN* 1.3 64.0 + - - +
239P VAL* 4.1 17.3 - - + -
335P ILE* 5.0 2.2 - - + -
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Residues in contact with ASN 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155O MET* 3.9 15.9 - - + -
157O THR* 3.4 14.0 + - - +
236O SER* 2.5 32.3 + - - -
157P THR* 4.0 4.0 - - - +
158P VAL 3.0 9.1 + - - -
159P ASN* 3.1 24.5 + - - +
160P VAL 2.9 26.9 + - - +
161P PHE* 3.6 5.6 - - + -
223P GLY 3.7 4.3 - - - -
224P VAL* 3.6 12.6 - - - +
236P SER* 3.2 20.6 + - - -
237P ILE* 1.3 73.5 - - - +
239P VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155O MET* 3.3 9.0 - - - +
160P VAL* 3.2 12.1 - - + +
184P ALA* 3.8 21.1 - - + +
185P PHE* 3.6 33.9 - - + -
189P ALA* 4.1 17.5 - - + -
222P THR* 3.5 0.6 - - - -
223P GLY 2.8 41.3 + - - +
237P ILE* 4.1 12.6 - - + -
238P ASN* 1.3 79.9 - - - +
240P THR* 1.3 64.2 + - - +
241P MET* 3.7 23.8 - - + -
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Residues in contact with THR 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154O TYR* 4.7 2.7 - - + +
155O MET* 4.3 8.3 - - + -
255O LEU* 3.9 23.3 - - + -
160P VAL 2.9 8.4 + - - +
161P PHE* 4.4 3.1 - - + -
162P TRP 2.8 30.5 + - - -
221P ASP 3.5 5.2 - - - -
222P THR* 2.9 29.2 + - - +
239P VAL* 1.3 76.4 - - - +
241P MET* 1.3 67.1 + - - +
242P LEU* 3.1 17.9 + - + +
243P THR* 3.3 22.7 - - - +
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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