Contacts of the helix formed by residues 243 - 256 (chain B) in PDB entry 2Q5E
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 THR 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B PRO 5.5 0.2 - - - -
145B TYR* 3.9 25.6 - - + +
241B ALA* 3.2 19.4 + - - +
242B ASP* 1.3 76.9 - - - +
244B GLU* 1.3 61.0 + - - +
245B LEU 3.3 2.9 - - - -
246B LEU* 3.1 9.8 + - - +
247B ASN* 2.8 44.8 + - - -
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Residues in contact with GLU 244 (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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143B ARG* 3.7 14.1 - - - +
232B PRO 5.1 0.5 - - - +
233B VAL* 4.1 11.9 - - + -
234B GLN* 3.4 44.5 + - - +
242B ASP* 3.2 22.5 + - - +
243B THR* 1.3 75.8 - - - +
245B LEU* 1.3 67.1 + - - +
247B ASN* 3.3 15.2 + - - +
248B LEU* 3.0 36.2 + - - +
119H PRO* 4.4 7.7 - - - +
120H ILE* 5.6 6.2 - - - -
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Residues in contact with LEU 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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111B THR* 4.1 8.1 - - + +
112B LEU* 4.3 6.3 - - + -
143B ARG* 3.6 37.2 - - + +
144B PRO 3.9 14.6 + - - +
145B TYR 4.4 2.0 - - - +
146B VAL* 3.7 42.0 - - + -
149B PHE* 3.5 51.8 - - + -
216B LEU* 5.0 4.5 - - + -
233B VAL* 4.6 4.3 - - + -
242B ASP* 4.3 1.0 + - - -
243B THR 3.3 0.4 - - - -
244B GLU* 1.3 79.3 - - - +
246B LEU* 1.3 63.5 + - - +
248B LEU* 3.3 19.9 + - + +
249B ILE* 3.5 5.0 + - - +
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Residues in contact with LEU 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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145B TYR* 3.8 55.9 - - + +
148B GLU* 4.6 11.0 - - + -
243B THR* 3.1 12.7 + - - +
245B LEU* 1.3 77.1 - - - +
247B ASN* 1.3 67.1 + - - +
248B LEU 3.0 1.0 + - - -
249B ILE* 3.2 35.7 + - + +
250B PRO* 3.5 9.4 - - - +
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Residues in contact with ASN 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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243B THR* 2.8 42.4 + - - +
244B GLU* 3.3 18.0 + - - +
246B LEU* 1.3 72.9 - - - +
248B LEU* 1.3 62.1 + - - +
250B PRO* 3.5 17.9 - - - +
251B ILE* 4.1 11.1 - - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE* 4.5 3.4 - - + -
216B LEU* 3.6 30.1 - - + -
231B VAL* 3.9 24.0 - - + -
232B PRO 4.7 6.5 - - - +
233B VAL* 4.1 16.8 - - + -
244B GLU* 3.0 30.9 + - - +
245B LEU* 3.3 14.1 + - + +
246B LEU 3.0 1.0 + - - -
247B ASN* 1.3 78.3 - - - +
249B ILE* 1.3 59.7 + - - +
250B PRO 3.5 0.2 - - - -
251B ILE* 2.8 33.8 + - + +
252B PHE* 2.8 29.0 + - + -
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Residues in contact with ILE 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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148B GLU* 4.6 3.6 - - + +
149B PHE* 4.2 26.0 - - + -
152B ARG* 4.2 25.4 - - + -
153B MET* 5.5 2.2 - - - -
245B LEU 3.5 10.1 + - - +
246B LEU* 3.2 34.1 + - + +
248B LEU* 1.3 71.7 - - - +
250B PRO* 1.3 76.4 - - + +
251B ILE 2.9 1.5 + - - -
252B PHE* 3.1 6.9 + - - +
253B GLU* 2.7 47.3 + - + +
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Residues in contact with PRO 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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246B LEU 3.5 9.9 - - - +
247B ASN* 3.5 17.0 - - - +
249B ILE* 1.3 90.9 - - + +
251B ILE* 1.3 65.5 + - + +
253B GLU* 3.3 15.8 + - + +
254B GLU* 3.2 21.7 + - - +
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Residues in contact with ILE 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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231B VAL* 4.9 9.4 - - + -
247B ASN 4.1 12.8 - - - +
248B LEU* 2.8 29.4 + - + +
250B PRO* 1.3 82.1 - - + +
252B PHE* 1.3 61.9 + - + +
254B GLU* 3.3 15.0 + - - +
255B LEU* 3.5 23.4 + - + +
265B LEU* 6.2 0.4 - - + -
268B LEU* 4.2 28.3 - - + +
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Residues in contact with PHE 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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104B VAL* 4.3 9.0 - - + -
149B PHE* 4.3 9.6 - + - -
153B MET* 3.4 41.3 - - + -
156B LEU* 4.8 2.0 - - + -
157B PHE* 3.4 30.1 - + + -
214B LEU* 3.8 26.9 - - + -
216B LEU* 4.4 17.3 - - + -
231B VAL* 4.1 33.0 - - + -
248B LEU* 2.8 36.9 + - + +
249B ILE* 4.0 3.8 - - - +
251B ILE* 1.3 74.8 - - + +
253B GLU* 1.3 62.7 - - - +
255B LEU* 3.8 5.8 - - + +
256B SER* 3.0 22.0 + - - -
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Residues in contact with GLU 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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152B ARG* 2.5 38.9 + - - +
156B LEU* 3.5 22.9 - - + -
249B ILE* 2.7 34.9 + - + +
250B PRO* 3.5 13.0 - - + +
251B ILE 3.2 0.4 - - - -
252B PHE* 1.3 78.5 - - + +
254B GLU* 1.3 58.1 + - - +
256B SER* 2.9 19.2 + - - -
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Residues in contact with GLU 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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250B PRO 3.2 11.7 + - - +
251B ILE* 3.6 10.8 - - - +
252B PHE 3.2 0.2 - - - -
253B GLU* 1.3 80.4 - - - +
255B LEU* 1.3 60.2 + - + +
257B GLY 4.6 4.2 + - - -
258B ALA* 4.9 4.2 + - - +
264B SER* 5.3 4.4 - - - -
268B LEU* 4.3 25.5 - - + +
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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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102B ILE* 3.0 15.0 - - + +
157B PHE* 4.5 1.3 - - + -
214B LEU* 3.8 31.2 - - + -
231B VAL* 4.4 6.1 - - + -
251B ILE* 3.5 22.7 - - + +
252B PHE* 3.3 15.6 + - + +
254B GLU* 1.3 76.4 - - + +
256B SER* 1.3 60.4 + - - +
257B GLY 3.1 3.1 - - - -
258B ALA* 2.8 27.8 + - + +
261B VAL* 5.2 4.0 - - + +
264B SER* 3.6 29.4 - - - +
265B LEU* 3.8 34.5 - - + +
268B LEU* 4.5 13.2 - - + -
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Residues in contact with SER 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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100B GLY 5.4 2.3 - - - +
101B ARG* 5.4 1.4 - - - -
102B ILE* 3.5 17.2 + - - +
156B LEU* 4.0 39.2 - - - +
157B PHE* 3.6 20.4 - - - -
252B PHE 3.0 15.4 + - - -
253B GLU 2.9 15.5 + - - -
255B LEU* 1.3 76.7 - - - +
257B GLY* 1.3 58.7 + - - +
258B ALA 4.6 0.2 - - - +
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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