Contacts of the strand formed by residues 235 - 241 (chain A) in PDB entry 2DPM
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 TYR 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PRO* 3.8 19.5 - - + -
35A THR* 3.7 23.5 + - - -
36A TYR* 4.3 6.7 - - + -
188A GLY* 3.6 28.3 - - - -
189A ASP 2.9 19.2 + - - +
190A PHE* 3.3 13.9 - - + -
191A VAL 3.0 23.9 + - - -
233A GLY 5.0 2.9 - - - -
234A ALA* 1.3 75.3 - - - +
236A VAL* 1.3 62.3 + - - +
281A ASN* 3.5 5.6 - - - +
282A TYR* 3.7 31.6 - + + -
284A LYS* 6.5 0.9 - - + -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 4.5 0.4 - - - -
191A VAL* 3.4 13.7 - - + +
193A PHE* 4.3 6.7 - - + -
226A PHE* 3.3 43.3 - - + +
229A LEU* 4.0 36.1 - - + -
230A SER* 4.6 1.1 - - - +
234A ALA* 4.4 4.7 - - + +
235A TYR* 1.3 79.7 - - - +
237A MET* 1.3 58.5 - - - +
280A THR* 3.3 21.1 - - - -
281A ASN* 2.9 27.6 + - + +
282A TYR* 3.6 5.6 - - - -
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Residues in contact with MET 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.9 22.0 - - - +
31A LEU* 3.6 33.4 - - + +
32A ILE* 3.7 27.6 - - + +
190A PHE* 3.7 16.8 - - + -
191A VAL 2.9 5.9 + - - +
192A TYR* 3.4 24.9 - - + -
193A PHE* 2.7 34.2 + - - -
226A PHE* 4.3 1.1 - - - -
236A VAL* 1.3 75.4 - - - +
238A LEU* 1.3 59.8 + - - +
278A ILE* 3.7 24.2 - - + -
279A VAL 3.2 6.1 - - - +
280A THR* 4.3 4.5 - - + -
282A TYR* 3.7 6.7 - - - +
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TYR* 4.7 0.7 - - - -
193A PHE* 3.2 23.3 - - + +
195A PRO* 4.5 1.3 - - + -
222A LEU* 3.8 25.1 - - + -
226A PHE* 3.9 14.4 - - + -
237A MET* 1.3 76.9 - - - +
239A SER* 1.3 76.9 - - - +
240A ASN* 4.0 14.1 - - + +
246A VAL* 5.5 0.2 - - + -
250A TYR* 3.1 43.5 - - + +
277A ILE 3.9 0.3 - - - +
278A ILE* 3.2 6.6 - - - -
279A VAL* 2.8 50.2 + - + +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 3.9 4.2 - - - -
24A LEU* 4.5 3.1 - - - +
28A ILE* 5.3 0.2 - - - +
192A TYR* 2.8 27.9 + - - -
193A PHE 2.9 8.2 + - - -
194A ASP* 3.5 20.0 - - - -
195A PRO* 3.4 22.2 - - - +
197A TYR* 3.5 16.2 - - - -
238A LEU* 1.3 75.0 - - - +
240A ASN* 1.3 66.3 + - - +
276A GLU* 5.0 0.9 - - - -
277A ILE 3.5 6.5 - - - -
278A ILE* 4.2 13.2 - - - +
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Residues in contact with ASN 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PRO* 4.2 10.5 - - - +
197A TYR* 3.4 19.7 - - - -
198A ILE* 3.0 28.2 + - - +
219A GLN* 3.2 27.1 + - - +
222A LEU* 5.6 0.2 - - - +
238A LEU* 4.0 16.7 + - + +
239A SER* 1.3 77.1 + - - +
241A SER* 1.3 76.1 + - - +
246A VAL* 4.1 22.4 - - + +
250A TYR* 5.4 4.8 + - - -
276A GLU* 3.4 7.6 - - - +
277A ILE* 3.1 30.7 + - + +
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A TYR* 3.6 18.8 - - - -
198A ILE* 2.7 30.4 + - - +
200A LEU* 4.2 11.0 - - - -
240A ASN* 1.3 87.6 + - - +
242A SER* 1.3 59.8 + - - +
243A SER* 3.1 21.3 + - - -
246A VAL* 3.4 13.7 - - - +
275A SER 4.8 2.2 - - - -
276A GLU* 4.6 3.6 - - - -
277A ILE* 3.5 11.2 - - - +
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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