Contacts of the helix formed by residues 243 - 256 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H PRO 5.6 0.2 - - - -
145H TYR* 4.1 22.9 - - + +
241H ALA 3.6 12.2 + - - +
242H ASP* 1.3 80.7 + - - +
244H GLU* 1.3 59.2 + - - +
245H LEU 3.5 2.2 - - - -
246H LEU* 3.6 14.7 + - + -
247H ASN* 3.0 45.2 + - - -
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Residues in contact with GLU 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ARG* 3.3 22.7 - - - +
232H PRO 4.4 2.9 - - - +
233H VAL* 3.6 16.1 - - + +
234H GLN* 2.7 47.2 + - + +
242H ASP* 3.2 12.3 + - - +
243H THR* 1.3 74.5 - - - +
245H LEU* 1.3 60.6 + - - +
247H ASN* 3.3 5.6 + - - +
248H LEU* 3.0 41.4 + - - +
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Residues in contact with LEU 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H THR* 4.0 15.9 - - + +
112H LEU* 4.4 6.3 - - + -
143H ARG* 3.8 30.1 - - + +
144H PRO 3.9 11.6 + - - +
145H TYR 4.2 1.3 - - - +
146H VAL* 3.6 39.3 - - + -
149H PHE* 3.4 40.0 - - + -
216H LEU* 4.8 4.0 - - + -
233H VAL* 4.7 4.3 - - + -
242H ASP* 4.4 1.2 + - - -
243H THR 3.5 0.4 - - - -
244H GLU* 1.3 74.0 - - - +
246H LEU* 1.3 65.7 - - - +
248H LEU* 3.3 21.5 + - + +
249H ILE* 3.4 16.1 + - - +
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Residues in contact with LEU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H TYR* 3.8 60.0 - - + +
148H GLU* 5.0 4.5 - - + -
243H THR* 3.6 18.2 + - + +
244H GLU 3.4 0.4 - - - -
245H LEU* 1.3 79.8 - - - +
247H ASN* 1.3 67.8 + - - +
249H ILE* 3.3 31.1 + - + +
250H PRO* 3.5 7.6 - - - +
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Residues in contact with ASN 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H THR* 3.0 38.0 + - - +
244H GLU* 3.3 5.5 + - - +
245H LEU 3.3 0.2 - - - -
246H LEU* 1.3 86.6 - - - +
248H LEU* 1.3 59.6 + - - +
250H PRO* 3.5 11.9 - - - +
251H ILE* 3.2 21.9 - - - +
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Residues in contact with LEU 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H PHE* 4.3 4.7 - - + -
216H LEU* 3.9 26.5 - - + -
231H VAL* 3.6 26.0 - - + -
232H PRO 4.5 4.5 - - - +
233H VAL* 3.9 19.5 - - + -
244H GLU* 3.0 27.5 + - - +
245H LEU* 3.7 13.7 - - + +
246H LEU 3.2 0.4 - - - -
247H ASN* 1.3 77.2 - - - +
249H ILE* 1.4 64.2 + - - +
251H ILE* 2.9 27.0 + - + -
252H PHE* 3.0 29.8 + - + -
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Residues in contact with ILE 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H GLU* 3.8 31.0 - - + +
149H PHE* 3.8 22.0 - - + +
152H ARG* 3.5 31.0 - - + -
153H MET* 6.0 1.6 - - - -
245H LEU 3.4 15.3 - - - +
246H LEU* 3.5 19.7 - - + +
248H LEU* 1.4 78.4 - - - +
250H PRO* 1.3 71.4 - - + +
252H PHE* 3.4 4.9 + - + +
253H GLU* 2.9 33.9 + - - +
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Residues in contact with PRO 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H LEU 3.5 7.6 - - - +
247H ASN* 3.5 17.9 - - - +
249H ILE* 1.3 97.4 - - + +
251H ILE* 1.3 66.1 + - + +
253H GLU* 3.9 17.3 - - - +
254H GLU* 3.3 20.3 + - - +
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Residues in contact with ILE 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H VAL* 5.1 7.0 - - + -
247H ASN 3.2 27.6 - - - +
248H LEU* 2.9 26.3 + - + +
250H PRO* 1.3 80.9 - - + +
252H PHE* 1.3 66.1 + - + +
254H GLU* 3.1 9.9 - - - +
255H LEU* 3.0 38.9 + - + +
268H LEU* 4.0 15.5 - - + -
269H ARG* 5.8 4.3 - - - +
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Residues in contact with PHE 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H VAL* 4.0 15.0 - - + -
149H PHE* 4.1 19.3 - + - -
153H MET* 3.6 37.2 - - + -
156H LEU* 5.6 1.1 - - + -
157H PHE* 3.4 25.4 - + + -
214H LEU* 3.8 25.4 - - + -
216H LEU* 4.6 11.2 - - + -
231H VAL* 4.2 34.1 - - + -
248H LEU* 3.0 34.4 + - + +
249H ILE* 3.8 3.6 - - - +
251H ILE* 1.3 71.2 - - + +
253H GLU* 1.3 67.5 + - - +
254H GLU 3.0 2.0 - - - -
255H LEU* 2.9 5.9 + - + +
256H SER* 2.7 23.9 + - - -
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Residues in contact with GLU 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H ARG* 3.3 41.4 + - - +
156H LEU* 3.9 16.3 - - + +
249H ILE* 2.9 35.9 + - + +
250H PRO* 3.9 15.8 - - - +
251H ILE 3.4 0.4 - - - -
252H PHE* 1.3 71.4 - - - +
254H GLU* 1.3 62.7 + - - +
256H SER* 2.7 21.2 + - - -
257H GLY 4.2 1.0 + - - -
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Residues in contact with GLU 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H PRO 3.3 11.1 + - - +
251H ILE* 3.1 12.5 - - - +
253H GLU* 1.3 82.0 - - - +
255H LEU* 1.3 61.8 + - - +
256H SER 3.4 0.2 + - - -
257H GLY* 4.1 5.0 + - - -
258H ALA* 4.9 2.3 + - - +
264H SER* 5.5 1.7 - - - -
267H GLN 5.4 0.7 - - - +
268H LEU* 3.6 37.1 - - + +
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Residues in contact with LEU 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H ILE* 3.2 11.7 - - + +
157H PHE* 4.3 1.1 - - + -
214H LEU* 3.9 29.8 - - + -
231H VAL* 4.2 7.6 - - + -
251H ILE* 3.0 35.7 + - + +
252H PHE* 2.9 11.5 + - + +
254H GLU* 1.3 75.9 - - - +
256H SER* 1.3 65.5 + - - +
257H GLY 3.2 0.4 - - - -
258H ALA* 3.0 20.3 + - + +
261H VAL* 4.7 4.3 - - + +
264H SER* 3.8 13.7 - - - -
265H LEU* 3.6 50.9 - - + +
268H LEU* 3.9 12.1 - - + -
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Residues in contact with SER 256 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H ARG* 5.8 1.4 - - - -
102H ILE* 3.9 11.9 + - - +
156H LEU* 3.7 33.4 - - - +
157H PHE* 3.3 35.4 - - - -
252H PHE 2.7 9.1 + - - -
253H GLU 2.7 17.7 + - - -
255H LEU* 1.3 76.9 - - - +
257H GLY* 1.3 58.4 + - - +
258H ALA 3.4 0.6 - - - +
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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
------------------------------------------------------------
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