Contacts of the helix formed by residues 244 - 255 (chain B) in PDB entry 3A7H
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 SER 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A THR 4.1 7.0 - - - -
47A GLN 3.3 13.0 - - - -
48A LYS* 3.8 16.2 - - - +
118B GLU* 2.6 34.3 + - - -
243B TYR* 1.3 77.1 - - - +
245B LYS* 1.3 63.5 + - - +
246B PRO* 3.6 11.0 - - - +
247B LEU* 3.4 13.5 + - - +
248B LYS* 3.3 18.0 + - - +
273B PHE* 4.3 3.6 - - - -
277B ASN* 5.0 2.6 + - - -
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Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN* 3.0 51.9 + - + +
243B TYR 3.7 0.9 + - - -
244B SER* 1.3 69.4 - - - +
246B PRO* 1.3 75.6 - - + +
248B LYS* 3.1 14.6 + - + +
249B GLU* 2.8 50.5 + - + +
272B LYS* 6.2 0.7 - - - +
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Residues in contact with PRO 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A THR 4.0 8.1 - - - +
47A GLN* 4.4 2.0 - - + -
244B SER* 3.5 14.8 - - - +
245B LYS* 1.3 94.1 - - + +
247B LEU* 1.3 56.2 + - - +
249B GLU* 3.4 10.0 + - + +
250B PHE* 2.9 28.6 + - - +
271B HIS* 3.4 8.1 - - + -
272B LYS* 3.7 35.9 - - + +
273B PHE* 3.5 23.7 - - + +
276B ARG* 3.9 14.8 - - - +
277B ASN* 5.4 1.8 - - - +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU* 4.0 14.1 - - + -
121B ILE* 4.4 12.6 - - + -
125B LEU* 4.9 3.1 - - + -
209B ALA* 5.0 4.3 - - + +
213B ALA* 4.4 9.2 - - + -
239B LEU* 3.5 25.8 - - + -
243B TYR* 3.7 22.2 - - + -
244B SER* 3.4 15.3 + - - +
245B LYS 3.2 1.0 - - - -
246B PRO* 1.3 77.7 - - - +
248B LYS* 1.3 63.1 + - - +
250B PHE* 3.1 8.1 + - + +
251B VAL* 3.1 27.9 + - + +
273B PHE* 3.6 43.0 - - + -
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Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 6.0 2.2 - - - +
238B THR* 6.2 0.3 - - - -
239B LEU* 3.6 40.3 + - + +
240B GLU* 5.0 1.0 - - - +
241B GLY 3.0 33.2 + - - +
243B TYR* 3.2 28.4 + - + +
244B SER 3.3 6.7 + - - +
245B LYS* 3.1 17.8 + - + +
247B LEU* 1.3 78.1 - - - +
249B GLU* 1.3 58.3 + - + +
251B VAL* 3.3 4.7 + - - +
252B GLU* 2.9 29.8 + - - +
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B LYS* 2.8 44.9 + - + +
246B PRO* 3.8 8.5 - - + +
248B LYS* 1.3 76.7 - - + +
250B PHE* 1.3 58.5 + - - +
252B GLU* 3.2 15.6 + - - +
253B ALA* 2.8 31.5 + - - +
271B HIS* 4.1 12.1 + - + +
272B LYS* 4.1 18.0 + - - +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 4.0 24.7 - - + -
129B LEU* 4.0 12.1 - - + -
205B LEU* 3.8 25.1 - - + -
209B ALA* 4.3 14.8 - - + -
246B PRO 2.9 14.3 + - - +
247B LEU* 3.1 12.8 + - + +
249B GLU* 1.3 75.8 - - - +
251B VAL* 1.3 67.3 + - + +
253B ALA* 3.2 10.8 + - - +
254B CYS* 3.2 29.1 + - - -
268B LEU* 3.9 18.2 - - + -
271B HIS* 3.7 31.6 - + + +
273B PHE* 4.1 10.3 - + + -
274B ILE* 4.0 23.3 - - + -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLY* 4.3 3.1 - - - +
209B ALA* 3.9 25.4 - - + -
210B ILE* 3.7 24.2 - - + +
237B PRO 4.5 3.6 - - - +
238B THR* 4.5 1.1 - - - -
239B LEU* 4.1 30.3 - - + +
247B LEU* 3.1 15.9 + - + +
248B LYS 3.5 7.9 - - - +
249B GLU 3.3 0.2 - - - -
250B PHE* 1.3 76.5 - - - +
252B GLU* 1.3 65.9 + - - +
254B CYS* 3.1 5.9 + - - +
255B LEU* 2.9 48.8 + - + +
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Residues in contact with GLU 252 (chain B).
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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237B PRO 5.7 1.8 - - - -
238B THR* 4.8 18.8 - - + -
248B LYS 2.9 14.6 + - - +
249B GLU* 3.3 19.1 - - - +
251B VAL* 1.3 80.6 - - - +
253B ALA* 1.3 65.1 + - - +
255B LEU* 3.2 20.6 + - - +
256B ASN* 4.0 4.2 + - - +
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Residues in contact with ALA 253 (chain B).
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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249B GLU 2.8 20.8 + - - +
250B PHE* 3.7 7.4 - - - +
251B VAL 3.2 0.2 - - - -
252B GLU* 1.3 74.6 - - - +
254B CYS* 1.3 60.8 + - - +
256B ASN* 4.3 5.9 + - - +
261B PHE 4.5 1.2 - - - +
262B ARG* 4.0 7.1 - - - +
263B PRO* 3.4 34.6 - - + +
268B LEU* 4.4 7.9 - - + -
271B HIS* 4.9 7.0 - - + +
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Residues in contact with CYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 3.4 29.8 - - - +
203B TRP* 3.8 5.2 - - - -
205B LEU* 4.0 4.3 - - - -
206B GLY* 3.5 21.3 - - - -
250B PHE* 3.2 31.4 + - - +
251B VAL 3.1 4.8 + - - +
253B ALA* 1.3 79.4 - - - +
255B LEU* 1.3 59.8 + - - +
256B ASN 3.1 0.7 + - - -
262B ARG* 3.1 29.3 + - - -
268B LEU* 3.9 27.6 - - - -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B TRP* 3.3 51.4 - - + +
206B GLY* 3.9 8.3 - - - +
207B ILE* 3.8 15.5 - - + +
210B ILE* 3.7 15.7 - - + -
236B PRO* 3.0 25.7 - - + +
237B PRO* 3.4 37.4 - - + +
251B VAL* 2.9 34.2 + - + +
252B GLU* 3.2 9.5 + - - +
254B CYS* 1.3 73.9 - - - +
256B ASN* 1.3 59.6 + - - +
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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