Contacts of the helix formed by residues 246 - 261 (chain B) in PDB entry 2ABQ
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 GLY 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS* 5.9 0.7 - - - -
41B ASN* 4.5 5.7 - - - +
92B LYS* 5.6 0.4 - - - +
244B SER 2.6 6.9 + - - -
245B VAL* 1.3 74.9 - - - +
247B ALA* 1.3 60.2 + - - +
248B GLY 3.5 1.1 - - - -
249B ASP* 3.8 23.8 + - - +
250B SER* 3.0 24.8 + - - -
279B THR* 3.7 6.4 - - - +
285B PHE* 3.7 12.0 - - - -
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Residues in contact with ALA 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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244B SER* 3.2 17.9 + - - +
246B GLY* 1.3 75.3 - - - +
248B GLY* 1.3 67.0 + - - +
249B ASP 3.2 0.2 - - - -
250B SER* 3.0 13.7 + - - -
251B VAL* 3.2 17.4 + - - +
276B GLY* 3.7 18.8 - - - +
279B THR* 4.1 10.1 - - + -
280B ALA* 4.6 13.0 - - + -
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Residues in contact with GLY 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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38B LYS* 4.5 9.4 - - - +
161B ASP* 4.4 2.5 - - - -
179B LYS* 3.0 26.4 + - - -
246B GLY 3.5 0.2 - - - -
247B ALA* 1.3 79.5 - - - +
249B ASP* 1.3 62.4 + - - +
251B VAL* 2.8 26.5 - - - +
252B VAL* 3.3 7.6 + - - +
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Residues in contact with ASP 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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38B LYS* 2.6 60.2 + - - +
41B ASN* 2.8 43.9 + - + -
42B VAL* 3.3 24.2 - - + +
45B VAL* 5.0 2.0 - - + +
132B ALA* 5.2 0.7 - - - +
161B ASP* 3.8 2.6 - - - +
246B GLY* 3.8 13.3 + - - +
247B ALA 3.2 0.6 - - - -
248B GLY* 1.3 79.1 - - - +
250B SER* 1.3 55.1 + - - +
252B VAL* 3.6 2.8 + - - +
253B ALA* 3.1 22.5 + - - +
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Residues in contact with SER 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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45B VAL* 3.7 23.7 - - - +
246B GLY 3.0 12.8 + - - -
247B ALA 3.0 11.0 + - - -
249B ASP* 1.3 75.7 - - - +
251B VAL* 1.3 60.4 + - - +
252B VAL 3.1 1.3 - - - -
253B ALA* 3.7 1.1 - - - +
254B GLY 2.7 26.7 + - - -
275B ALA* 3.3 34.2 - - - +
276B GLY* 4.0 0.4 - - - -
279B THR* 2.7 20.4 + - - +
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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
----------------------------------------------------------
177B PHE* 6.1 0.9 - - + -
179B LYS* 3.2 36.3 - - + +
215B LEU* 4.8 8.5 - - + -
247B ALA 3.2 6.2 + - - +
248B GLY* 2.8 27.1 - - - +
250B SER* 1.3 76.2 - - - +
252B VAL* 1.3 58.3 + - - +
255B PHE* 2.9 26.4 + - - +
272B ALA* 3.1 34.1 + - + +
273B VAL* 4.6 4.9 - - + -
276B GLY* 3.5 22.9 - - - -
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Residues in contact with VAL 252 (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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42B VAL* 4.0 16.4 - - + -
130B VAL* 4.2 13.0 - - + -
159B ALA* 5.1 8.1 - - + -
160B VAL 5.9 1.1 - - - +
161B ASP* 4.2 25.6 - - + +
177B PHE* 4.8 14.1 - - + -
179B LYS* 4.7 6.7 - - + -
248B GLY 3.3 13.6 + - - +
249B ASP* 3.7 9.0 - - - +
250B SER 3.1 0.6 - - - -
251B VAL* 1.3 89.2 - - + +
253B ALA* 1.3 62.2 + - - +
255B PHE* 3.4 6.0 + - - +
256B LEU* 3.1 41.0 + - + +
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Residues in contact with ALA 253 (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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42B VAL* 3.8 15.7 - - + +
45B VAL* 3.9 19.5 - - + -
46B LEU* 3.4 32.1 - - + +
49B LEU* 4.1 2.2 - - + -
249B ASP 3.1 13.9 + - - +
250B SER 3.1 4.8 + - - +
252B VAL* 1.3 81.0 - - - +
254B GLY* 1.3 58.0 + - - +
256B LEU* 3.3 1.4 + - - -
257B ALA* 2.8 30.8 + - - +
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Residues in contact with GLY 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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49B LEU* 3.9 16.7 - - - +
250B SER 2.7 15.9 + - - -
251B VAL 3.7 1.3 - - - -
253B ALA* 1.3 78.4 - - - +
255B PHE* 1.3 60.0 + - - +
258B ALA* 3.0 21.0 + - - +
271B PHE* 3.1 22.7 - - - -
272B ALA* 4.0 9.6 - - - -
275B ALA* 4.1 4.0 - - - -
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Residues in contact with PHE 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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157B PHE* 4.4 4.0 - + - -
177B PHE* 3.9 39.7 - + + -
213B SER* 4.4 0.9 - - - -
215B LEU* 5.7 2.2 - - + -
225B PHE* 3.9 24.9 - + - -
251B VAL 2.9 17.5 + - - +
252B VAL* 3.7 7.2 - - - +
254B GLY* 1.3 76.6 - - - +
256B LEU* 1.3 68.4 + - + +
258B ALA* 3.6 2.4 + - - +
259B LEU* 3.3 43.5 + - + +
265B LEU* 3.3 46.7 - - + -
268B ALA* 3.9 21.3 - - + +
269B VAL* 4.1 6.5 - - + -
272B ALA* 3.4 11.3 - - + +
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Residues in contact with LEU 256 (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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2B ILE* 4.4 17.7 - - + -
42B VAL* 4.9 5.2 - - + -
46B LEU* 4.4 3.6 - - + -
128B VAL* 4.0 22.9 - - + -
130B VAL* 3.3 33.9 - - + -
157B PHE* 4.2 23.8 - - + -
159B ALA* 4.7 7.4 - - + -
177B PHE* 6.0 0.4 - - + -
252B VAL* 3.1 28.1 + - + +
253B ALA 3.8 2.9 - - - +
255B PHE* 1.3 85.4 - - + +
257B ALA* 1.3 65.4 + - - +
259B LEU* 3.3 9.2 + - + +
260B GLN* 3.1 28.2 + - - +
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Residues in contact with ALA 257 (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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46B LEU* 4.1 6.5 - - + +
49B LEU* 4.0 16.8 - - + -
51B HIS* 3.3 31.8 + - + +
253B ALA 2.8 17.2 + - - +
254B GLY 3.7 3.8 - - - +
256B LEU* 1.3 76.0 - - - +
258B ALA* 1.3 62.0 + - - +
260B GLN* 3.2 16.0 + - - +
261B GLU* 3.2 20.5 + - - +
271B PHE* 4.1 7.4 - - + -
288B ARG* 4.5 0.9 - - - +
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Residues in contact with ALA 258 (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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254B GLY 3.0 17.1 + - - +
255B PHE 3.9 0.7 - - - +
257B ALA* 1.3 78.9 - - - +
259B LEU* 1.3 59.1 + - - +
261B GLU* 3.7 7.3 + - - -
263B LYS* 3.2 54.1 + - - +
268B ALA* 3.5 25.4 - - + -
271B PHE* 3.8 13.9 - - + -
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Residues in contact with LEU 259 (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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157B PHE* 4.2 17.7 - - + -
255B PHE* 3.3 40.4 + - + +
256B LEU* 3.3 10.3 + - + +
257B ALA 3.3 0.4 - - - -
258B ALA* 1.3 75.3 - - - +
260B GLN* 1.3 67.9 + - - +
261B GLU 3.2 0.4 - - - -
262B GLY* 3.2 12.5 + - - -
263B LYS 3.1 22.0 - - - +
264B SER 3.7 21.5 - - - +
265B LEU* 3.7 20.4 - - + +
268B ALA* 4.0 5.2 - - + -
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Residues in contact with GLN 260 (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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1B MSE 3.3 41.3 - - - +
2B ILE* 3.5 30.4 - - + +
51B HIS* 4.2 20.8 + - + +
52B GLU 5.7 0.8 + - - -
126B GLY 4.9 3.8 - - - +
128B VAL* 4.6 10.7 - - - +
256B LEU 3.1 22.9 + - - +
257B ALA* 3.2 11.0 + - - +
259B LEU* 1.3 81.5 - - - +
261B GLU* 1.3 56.8 + - - +
262B GLY 3.1 4.6 + - - -
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Residues in contact with GLU 261 (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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49B LEU 4.4 0.3 - - - +
51B HIS* 2.5 36.8 + - + -
257B ALA 3.2 13.3 + - - +
258B ALA* 4.1 4.6 - - - +
259B LEU 3.2 0.8 - - - -
260B GLN* 1.3 75.7 - - - +
262B GLY* 1.3 56.8 + - - +
263B LYS* 3.4 23.9 + - - +
271B PHE* 5.5 0.2 - - - -
288B ARG* 3.1 35.0 + - - -
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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