Contacts of the strand formed by residues 240 - 251 (chain d) in PDB entry 3J7Y
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 LYS 240 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617 ARG* 4.3 9.7 - - - +
219d ARG* 3.4 1.3 - - - -
220d GLN 2.8 39.2 + - - +
235d GLN* 4.1 13.3 + - - -
238d VAL* 3.9 24.9 + - + +
239d PRO* 1.3 76.9 - - - +
241d ASP* 1.3 66.6 + - - +
242d VAL* 3.7 8.9 - - + +
274d GLN* 3.5 35.2 - - + +
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Residues in contact with ASP 241 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189d LEU* 3.3 23.7 - - - +
217d HIS* 4.9 11.8 - - + -
218d THR 3.6 4.5 - - - +
219d ARG* 3.4 34.1 + - - +
239d PRO 4.4 3.8 - - - +
240d LYS* 1.3 80.3 - - - +
242d VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 242 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216d MET 3.8 0.5 - - - +
217d HIS* 3.5 11.8 - - - -
218d THR 2.8 34.0 + - - +
220d GLN* 3.1 36.8 - - + +
222d LEU* 5.9 5.2 - - + -
240d LYS* 3.7 19.3 - - + +
241d ASP* 1.3 77.3 - - - +
243d LEU* 1.3 74.5 + - - +
244d GLU* 3.9 10.4 - - + +
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Residues in contact with LEU 243 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215d ARG* 3.5 42.2 - - + +
216d MET 3.5 9.4 - - - +
217d HIS* 3.6 23.1 - - + +
242d VAL* 1.3 77.6 - - - +
244d GLU* 1.3 71.1 + - - +
245d TYR* 4.7 9.0 - - + -
264d LYS* 5.9 0.5 - - - +
268d PRO* 4.6 25.1 - - + -
270d ALA* 5.5 12.8 - - + -
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Residues in contact with GLU 244 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145d PHE* 3.0 28.4 - - + -
214d VAL 3.7 0.2 - - - +
215d ARG* 3.4 4.9 - - - +
216d MET* 2.8 63.3 + - + +
218d THR* 3.2 8.8 + - - +
220d GLN* 2.7 36.3 + - - +
242d VAL* 3.9 10.3 - - + +
243d LEU* 1.3 79.9 - - - +
245d TYR* 1.3 67.1 + - - +
246d VAL* 3.7 15.9 - - + -
264d LYS* 4.7 18.2 - - + +
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Residues in contact with TYR 245 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195d VAL* 4.9 15.3 - - + -
213d THR* 6.1 5.2 - - - -
214d VAL 3.5 6.3 - - - -
215d ARG* 4.0 34.9 + - + -
243d LEU* 4.7 10.3 - - + -
244d GLU* 1.3 77.9 - - - +
246d VAL* 1.3 62.5 + - - +
264d LYS* 3.5 4.7 - - - +
265d ILE* 2.8 67.4 + - + +
267d PRO* 3.7 16.6 - - + -
268d PRO* 3.9 26.9 - - + +
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Residues in contact with VAL 246 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145d PHE* 3.8 19.5 - - + -
214d VAL* 2.8 45.0 + - + +
216d MET* 4.1 9.0 - - - -
244d GLU* 3.7 27.1 - - + +
245d TYR* 1.3 72.9 - - - +
247d VAL* 1.3 61.5 + - - +
248d PHE* 3.5 28.1 - - + -
261d MET* 3.9 25.6 - - + -
263d THR 3.6 9.4 - - - +
264d LYS* 4.6 11.0 - - + +
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Residues in contact with VAL 247 (chain d).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211d GLN* 4.9 17.9 - - + +
212d ILE 3.3 17.3 - - - +
213d THR* 4.0 13.7 - - + +
246d VAL* 1.3 73.7 - - - +
248d PHE* 1.3 61.9 + - - +
249d GLU* 5.2 0.2 - - + -
261d MET* 3.6 3.8 - - - -
262d HIS* 2.8 37.3 + - + -
263d THR* 2.8 37.3 + - - +
265d ILE* 3.4 35.9 - - + -
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Residues in contact with PHE 248 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137d PHE* 4.1 15.5 - + + -
141d ALA* 3.2 48.5 - - + -
144d ILE* 4.8 10.8 - - + -
145d PHE* 5.2 0.4 - - + -
211d GLN* 3.4 4.7 - - - -
212d ILE* 2.8 43.6 + - + +
214d VAL* 4.3 12.3 - - + -
216d MET* 4.5 6.1 - - + -
246d VAL* 3.5 35.4 - - + -
247d VAL* 1.3 82.7 - - - +
249d GLU* 1.3 65.0 + - - +
259d TRP* 4.3 25.3 - - + -
260d ARG 3.3 10.3 - - - +
261d MET* 4.1 15.0 - - + -
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Residues in contact with GLU 249 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165d THR* 4.4 6.9 - - + +
209d TYR* 3.6 22.6 - - - +
210d GLY 3.2 21.1 - - - +
211d GLN* 3.0 26.7 - - + +
247d VAL* 5.2 0.7 - - + -
248d PHE* 1.3 77.9 - - - +
250d LYS* 1.3 60.9 + - - +
258d SER 3.2 2.1 - - - +
259d TRP* 3.4 6.1 - - - -
260d ARG* 2.8 38.2 + - - +
262d HIS* 3.6 47.4 + - + +
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Residues in contact with LYS 250 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129d ASP* 4.1 17.2 + - - +
209d TYR* 3.5 7.4 - - - -
210d GLY 3.1 26.4 + - - -
249d GLU* 1.3 76.6 - - - +
251d GLN* 1.3 73.3 + - - +
252d LEU* 3.5 23.7 - - + +
255d PRO 5.9 0.6 - - - -
257d GLY* 3.7 21.0 + - - +
258d SER* 3.4 22.9 - - - +
259d TRP* 3.4 52.3 - - + +
260d ARG* 6.3 1.3 - - - +
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Residues in contact with GLN 251 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207d ASN 3.7 3.8 - - - +
208d VAL 3.3 20.4 - - - +
209d TYR* 3.4 27.9 - - - +
250d LYS* 1.3 91.7 + - - +
252d LEU* 1.3 64.9 + - - +
255d PRO* 4.1 22.0 - - + +
257d GLY* 3.7 22.5 + - - -
258d SER 4.5 2.0 + - - +
260d ARG* 5.6 10.7 - - - +
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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