Contacts of the strand formed by residues 236 - 246 (chain O) in PDB entry 2AXT
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 GLU 236 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47O THR 5.1 0.3 - - - +
48O LEU* 3.1 34.7 - - + +
230O VAL* 5.6 0.2 - - - +
231O ASP* 3.3 27.5 + - + +
234O THR* 2.7 38.6 + - - +
235O GLY* 1.3 77.8 - - - +
237O ILE* 1.3 62.6 + - - +
266O TYR* 3.1 35.9 + - + +
267O ALA 3.4 6.7 - - - +
268O SER* 4.4 3.7 - - - -
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Residues in contact with ILE 237 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O LEU* 4.0 0.9 - - - -
56O TYR* 5.4 2.2 - - + -
66O ILE* 6.4 0.7 - - + -
162O ILE* 3.9 23.3 - - + -
168O PHE* 4.1 17.7 - - + -
227O VAL* 3.8 26.5 - - + -
229O LYS 3.3 9.9 - - - +
230O VAL* 4.1 17.7 - - + -
235O GLY 5.3 0.7 - - - -
236O GLU* 1.3 79.9 - - - +
238O ALA* 1.3 63.4 + - - +
265O PHE* 4.2 8.7 - - + -
266O TYR* 3.7 4.2 - - - -
267O ALA* 3.0 48.6 + - + +
269O ILE* 4.3 24.2 - - + -
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Residues in contact with ALA 238 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O PRO 5.2 4.0 - - - +
47O THR* 5.7 0.2 - - - -
48O LEU* 3.7 27.8 - - + +
227O VAL* 3.5 5.9 - - - +
228O ALA* 2.7 29.0 + - - -
229O LYS* 2.9 19.2 + - + -
237O ILE* 1.3 75.0 - - - +
239O GLY* 1.3 53.7 + - - +
264O VAL* 6.1 1.6 - - + -
265O PHE* 3.3 19.3 - - - +
266O TYR* 4.7 6.1 - - + -
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Residues in contact with GLY 239 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226O ASN 3.6 10.5 - - - -
228O ALA* 3.7 13.9 - - - -
238O ALA* 1.3 78.6 - - - +
240O THR* 1.3 64.7 + - - +
264O VAL* 3.1 13.8 - - - +
265O PHE* 3.0 33.3 + - - -
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Residues in contact with THR 240 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O SER 4.1 0.2 - - - +
226O ASN* 3.0 38.8 + - - +
228O ALA* 5.2 7.6 - - + -
239O GLY* 1.3 77.5 - - - +
241O PHE* 1.3 62.9 + - - +
263O GLY 3.5 13.0 - - - +
264O VAL* 4.3 4.9 - - + +
265O PHE* 3.5 5.5 - - - -
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Residues in contact with PHE 241 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O LEU* 3.5 24.9 - - + -
72O GLN 3.5 12.6 - - - -
73O PRO* 4.2 1.1 - - + -
146O PHE* 3.7 26.0 - + - -
223O ILE* 4.2 8.5 - - + -
224O SER 3.6 11.4 - - - +
225O LEU* 4.2 12.6 - - + -
240O THR* 1.3 77.8 - - - +
242O GLU* 1.3 72.0 + - - +
243O SER* 4.1 6.3 - - - -
261O ILE* 3.5 28.7 - - + -
262O GLN* 3.6 3.5 - - - +
263O GLY* 3.2 48.6 + - - +
264O VAL 3.2 29.2 - - - -
265O PHE* 4.4 1.1 - - + -
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Residues in contact with GLU 242 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O ILE* 3.2 4.1 - - - -
224O SER* 3.2 34.8 + - - +
241O PHE* 1.3 77.6 - - - +
243O SER* 1.3 64.2 + - - +
260O LYS* 3.8 33.7 + - + +
261O ILE 3.2 10.1 - - - +
262O GLN* 3.3 27.0 - - + +
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Residues in contact with SER 243 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O PHE* 4.0 11.8 - - - -
147O THR 5.7 0.2 - - - -
148O VAL* 5.8 0.9 - - - -
172O PHE* 4.3 11.8 - - - -
222O GLN 2.9 11.0 - - - -
223O ILE* 3.2 25.6 - - - -
241O PHE* 4.1 2.7 - - - -
242O GLU* 1.3 73.5 - - - +
244O GLU* 1.3 61.7 + - - +
245O GLN* 4.8 1.9 + - - -
260O LYS* 3.3 5.1 - - - +
261O ILE* 2.7 52.2 + - - +
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Residues in contact with GLU 244 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O PHE* 3.5 20.9 - - + -
172O PHE* 4.4 0.5 - - - -
221O GLY* 3.6 2.3 - - - -
222O GLN* 2.9 33.5 + - + +
243O SER* 1.3 77.4 - - - +
245O GLN* 1.3 66.3 + - - +
258O GLU* 3.2 22.4 - - - +
259O VAL 3.2 19.3 - - - +
260O LYS* 3.7 20.1 + - + -
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Residues in contact with GLN 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144O LEU* 4.5 4.2 - - + +
145O LEU 3.0 34.9 + - - +
146O PHE* 3.7 12.9 - - - +
147O THR 3.4 25.3 + - - +
172O PHE* 4.2 5.2 - - + -
174O VAL* 3.9 27.8 - - + +
220O LYS 5.0 2.5 - - - -
221O GLY* 4.6 4.9 - - - -
243O SER* 4.8 1.7 + - - -
244O GLU* 1.3 78.9 - - - +
246O LEU* 1.3 78.7 + - - +
258O GLU* 3.9 3.3 - - - +
259O VAL* 2.9 34.4 + - + +
261O ILE* 4.1 16.0 - - + +
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Residues in contact with LEU 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144O LEU* 4.2 2.6 - - - +
145O LEU 4.7 1.6 + - - -
174O VAL* 4.5 10.8 - - + +
219O THR* 4.3 31.1 + - + +
220O LYS 5.5 2.8 + - - +
245O GLN* 1.3 98.2 + - - +
247O SER* 1.3 67.4 + - - +
256O PRO* 4.0 25.6 - - + +
257O HIS 3.6 16.6 - - - +
258O GLU* 3.9 22.0 - - + -
259O VAL* 4.8 2.7 - - - -
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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