Contacts of the helix formed by residues 246 - 260 (chain B) in PDB entry 2AX1
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 ALA 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ALA 4.7 4.0 + - - -
81B LYS* 6.5 0.2 - - - -
82B LEU* 4.9 17.9 - - + +
245B LEU* 1.3 77.1 - - - +
247B PRO* 1.3 76.2 - - + +
248B GLU* 4.5 2.5 - - + +
249B ALA* 3.1 16.0 + - + +
250B ARG* 3.0 21.1 + - - +
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Residues in contact with PRO 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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245B LEU 3.9 2.7 - - - +
246B ALA* 1.3 86.5 - - + +
248B GLU* 1.3 64.4 + - + +
250B ARG* 3.3 9.3 + - + +
251B GLN* 3.1 24.1 + - - +
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Residues in contact with GLU 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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82B LEU* 4.1 19.7 - - + +
123B TRP* 3.3 21.4 + - + -
127B LEU* 3.3 36.3 - - + +
246B ALA* 3.3 2.1 - - + +
247B PRO* 1.3 81.4 - - + +
249B ALA* 1.3 58.5 + - - +
251B GLN* 3.5 1.5 + - - -
252B ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 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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80B ALA 5.9 1.1 - - - +
81B LYS 6.0 0.7 - - - -
82B LEU* 3.4 31.0 - - + +
174B ALA* 4.5 9.4 - - - +
245B LEU* 4.2 13.0 - - + -
246B ALA* 3.1 23.4 + - + +
248B GLU* 1.3 76.9 - - - +
250B ARG* 1.3 66.1 + - - +
252B ALA* 3.2 4.0 + - - +
253B ILE* 2.9 33.9 + - + +
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Residues in contact with ARG 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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241B GLN* 2.9 75.8 + - - +
243B CYS 3.2 20.4 + - - -
244B ASP* 4.5 2.0 - - - +
245B LEU* 3.4 31.6 + - + +
246B ALA 3.0 11.4 + - - +
247B PRO* 3.6 11.1 - - + +
249B ALA* 1.3 76.9 - - - +
251B GLN* 1.3 61.4 + - - +
253B ILE* 4.7 0.2 - - - -
254B LYS* 3.2 8.8 + - - +
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Residues in contact with GLN 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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126B LEU 4.7 0.7 - - - +
127B LEU* 2.8 43.7 + - + +
128B GLU 5.1 1.4 + - - -
130B THR* 3.5 19.3 - - - +
247B PRO 3.1 16.4 + - - +
248B GLU* 3.8 5.2 - - - +
250B ARG* 1.3 74.3 - - - +
252B ALA* 1.3 59.3 + - - +
254B LYS* 3.0 20.9 + - - +
255B SER* 2.8 28.1 + - - -
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Residues in contact with ALA 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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123B TRP* 3.6 29.8 - - + -
126B LEU* 5.1 6.5 - - + +
127B LEU* 4.0 10.3 - - + +
174B ALA* 3.8 9.4 - - + -
248B GLU 2.9 18.8 + - - +
249B ALA 3.7 3.8 - - - +
251B GLN* 1.3 76.6 - - - +
253B ILE* 1.3 57.5 + - - +
255B SER* 3.6 7.3 - - - -
256B LEU* 2.9 38.3 + - + +
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Residues in contact with ILE 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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174B ALA* 4.0 15.7 - - + +
175B LEU* 3.7 35.9 - - + -
178B VAL* 4.6 4.9 - - + -
237B GLU* 4.1 12.8 - - + -
240B TYR* 4.2 24.5 - - + -
241B GLN* 3.9 12.8 - - - +
245B LEU* 3.7 28.0 - - + -
249B ALA* 2.9 22.0 + - + +
250B ARG 3.8 4.5 - - - +
252B ALA* 1.3 74.6 - - - +
254B LYS* 1.3 64.4 + - - +
256B LEU* 4.0 6.0 - - - +
257B THR* 2.9 31.8 + - - +
261B TYR* 5.3 0.6 - - + -
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Residues in contact with LYS 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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130B THR* 4.2 22.9 + - + +
237B GLU* 3.1 21.9 + - - +
241B GLN* 4.1 2.9 - - - +
250B ARG 3.2 13.1 + - - +
251B GLN* 3.0 23.6 + - - +
253B ILE* 1.3 77.1 - - - +
255B SER* 1.3 63.3 + - - +
257B THR* 3.3 3.8 + - - -
258B GLU* 3.1 32.7 + - + +
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Residues in contact with SER 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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126B LEU* 2.8 40.7 + - - +
129B ASP 2.9 14.7 + - - -
130B THR* 3.9 16.6 - - - -
251B GLN 2.8 14.1 + - - -
252B ALA* 3.6 5.6 - - - -
254B LYS* 1.3 78.2 - - - +
256B LEU* 1.3 57.5 + - - +
258B GLU* 3.9 0.2 - - - -
259B ARG* 2.9 44.0 + - - +
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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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126B LEU* 4.0 31.2 - - + -
134B ILE* 4.7 2.2 - - + -
167B VAL* 4.6 7.0 - - + +
170B CYS 4.6 1.3 - - - +
171B GLU* 4.1 27.8 - - + -
174B ALA* 4.3 11.7 - - + -
175B LEU* 4.1 11.7 - - + -
252B ALA* 2.9 23.5 + - + +
253B ILE* 4.1 3.1 - - - +
255B SER* 1.3 73.6 - - - +
257B THR* 1.3 58.3 + - - +
259B ARG* 5.1 0.9 - - - -
260B LEU* 3.0 35.4 + - + +
261B TYR* 2.9 51.4 + - + +
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Residues in contact with THR 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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233B ILE* 3.9 25.1 - - + +
234B ARG* 4.8 2.5 - - + -
237B GLU* 3.3 40.3 - - + +
240B TYR* 5.3 2.3 - - - -
253B ILE* 2.9 23.9 + - - +
254B LYS 3.6 4.3 - - - -
255B SER 3.2 0.2 - - - -
256B LEU* 1.3 77.3 - - - +
258B GLU* 1.3 71.7 + - - +
261B TYR* 3.6 16.1 + - - -
262B ILE* 2.9 34.3 + - + +
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Residues in contact with GLU 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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130B THR 3.5 21.5 - - - +
131B VAL* 4.5 6.6 - - - +
133B PRO* 5.6 0.5 - - - +
234B ARG* 3.2 44.3 + - - +
237B GLU* 4.6 4.9 - - - +
254B LYS* 3.1 23.9 + - + +
255B SER 4.2 0.2 - - - +
257B THR* 1.3 90.6 - - + +
259B ARG* 1.3 61.2 + - - +
262B ILE* 3.5 23.0 - - - +
263B GLY 4.9 1.0 - - - +
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Residues in contact with ARG 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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125B ASP* 2.7 40.2 + - - -
126B LEU* 3.6 11.9 - - - +
129B ASP* 2.7 44.6 + - - +
130B THR 3.6 15.3 - - - -
131B VAL 3.6 10.8 - - - +
132B THR* 2.6 40.0 + - - +
133B PRO* 3.6 6.0 + - - +
134B ILE* 2.8 55.2 + - + +
255B SER* 2.9 25.0 + - - +
258B GLU* 1.3 76.8 - - - +
260B LEU* 1.3 60.1 + - - +
263B GLY 3.5 11.4 - - - +
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Residues in contact with LEU 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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134B ILE* 4.4 16.6 - - + +
136B THR* 3.6 30.3 - - + -
163B PRO* 3.9 31.4 - - + -
167B VAL* 4.0 15.5 - - + -
171B GLU* 4.2 3.1 - - - -
256B LEU* 3.0 21.6 + - + +
258B GLU 3.6 1.0 - - - -
259B ARG* 1.3 82.1 - - - +
261B TYR* 1.3 87.3 + - + +
262B ILE 3.3 1.3 - - - -
263B GLY 3.2 5.5 + - - -
277B ARG* 2.6 31.5 + - - +
281B ALA* 5.2 0.2 - - - +
284B VAL* 4.1 10.3 - - + -
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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