Contacts of the helix formed by residues 240 - 250 (chain C) in PDB entry 2ATW
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 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236C ILE* 3.2 28.7 - - - -
237C GLY 2.9 5.7 + - - -
238C PRO 2.9 3.0 + - - -
239C MET* 1.3 77.8 - - - +
241C GLN* 1.3 57.3 + - - +
243C VAL* 3.4 7.5 - - - +
244C ARG* 2.8 34.6 + - - +
1D G 4.0 3.6 - - - -
2D A 4.1 9.2 - - - -
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Residues in contact with GLN 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C ILE 3.6 0.6 + - - -
237C GLY 4.3 0.2 - - - -
238C PRO* 3.0 21.5 + - + +
239C MET* 3.2 7.1 - - + +
240C GLY* 1.3 76.1 - - - +
242C ARG* 1.3 64.0 + - + +
244C ARG* 4.3 10.8 - - - +
245C ASN* 2.9 63.3 + - - +
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Residues in contact with ARG 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C PHE* 5.2 0.4 - - - -
196C GLU* 3.7 30.1 + - + +
197C VAL* 3.7 10.1 - - + +
198C PRO* 3.7 22.4 - - - +
199C GLU* 2.9 27.9 + - - -
234C ALA 2.9 25.9 + - - -
235C CYS 3.5 8.5 - - - +
236C ILE 3.2 8.5 + - - +
237C GLY* 3.8 14.6 - - - -
238C PRO* 4.8 4.8 - - + +
241C GLN* 1.3 76.9 - - + +
243C VAL* 1.3 63.5 + - - +
245C ASN* 3.1 15.9 + - - +
246C VAL* 3.3 15.7 + - - +
0D A 3.3 29.2 + - - -
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Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C PHE* 3.9 17.7 - - + -
235C CYS 3.7 12.8 - - - +
236C ILE* 3.4 16.1 + - - +
240C GLY* 3.4 15.9 - - - +
242C ARG* 1.3 78.4 - - - +
244C ARG* 1.3 60.5 + - - +
246C VAL* 3.0 4.7 + - - +
247C MET* 2.9 32.8 + - + +
255C ILE* 4.0 19.1 - - + +
257C ILE* 3.7 19.7 - - + -
2D A 3.8 32.3 - - - +
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Residues in contact with ARG 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C MET 4.5 10.5 - - - -
240C GLY 2.8 21.0 + - - +
241C GLN* 3.9 13.5 - - - +
243C VAL* 1.3 77.8 - - - +
245C ASN* 1.3 57.8 + - - +
247C MET* 3.3 27.8 + - + +
248C SER* 2.9 29.8 + - - -
2D A 4.0 16.2 + - - +
3D A 4.7 12.7 + - - -
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Residues in contact with ASN 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ARG* 5.7 0.7 + - - -
196C GLU* 3.0 39.0 + - - +
241C GLN* 2.9 50.9 + - - +
242C ARG* 3.1 4.2 + - - +
244C ARG* 1.3 75.7 - - - +
246C VAL* 1.3 62.7 + - - +
248C SER* 3.5 7.7 + - - -
249C GLU* 3.2 21.1 + - - +
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C VAL* 5.0 1.6 - - + +
192C LEU* 4.1 22.7 - - + +
193C PHE* 4.0 39.7 - - + -
196C GLU* 3.9 17.9 - - + -
242C ARG 3.5 13.0 - - - +
243C VAL 3.0 6.7 + - - +
245C ASN* 1.3 75.6 - - - +
247C MET* 1.3 66.7 + - - +
249C GLU* 3.1 7.1 + - - +
250C LEU* 3.0 42.2 + - + +
255C ILE* 4.0 10.8 - - + -
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Residues in contact with MET 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C VAL* 2.9 15.5 + - + +
244C ARG* 3.3 42.4 + - + +
246C VAL* 1.3 77.7 - - - +
248C SER* 1.3 61.6 + - - +
250C LEU* 2.9 13.4 + - - +
251C SER 3.2 0.2 + - - -
252C GLY* 3.0 25.7 + - - +
253C GLU 3.2 25.1 - - - +
254C LYS* 4.0 9.9 - - + -
255C ILE* 3.3 32.5 - - + +
2D A 4.3 10.5 - - - +
3D A 4.8 16.6 - - - +
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Residues in contact with SER 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ARG 2.9 17.6 + - - -
245C ASN* 3.6 8.5 - - - -
246C VAL 3.2 0.2 - - - -
247C MET* 1.3 76.8 - - - +
249C GLU* 1.3 63.8 + - - +
251C SER* 3.1 13.0 + - - +
252C GLY* 4.5 3.1 - - - +
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Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ARG* 4.7 3.6 + - - +
163C LEU* 3.3 9.6 - - - +
164C ARG* 2.6 59.5 + - + +
183C ARG* 2.7 45.4 + - - +
192C LEU* 3.6 35.7 - - + -
245C ASN 3.2 9.8 + - - +
246C VAL* 3.1 9.6 + - - +
248C SER* 1.3 80.1 - - - +
250C LEU* 1.3 51.2 + - - +
251C SER* 3.2 2.1 + - - -
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Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLU* 4.1 4.2 - - - +
183C ARG* 3.7 7.6 - - - +
188C LEU* 3.8 22.4 - - + -
189C VAL* 3.9 22.2 - - + -
192C LEU* 3.5 24.0 - - + -
212C ARG* 4.0 11.0 - - - +
215C GLY* 5.3 3.3 - - - -
246C VAL* 3.2 32.8 - - + +
247C MET* 2.9 6.5 + - - +
249C GLU* 1.3 80.9 - - - +
251C SER* 1.3 70.1 + - - +
252C GLY 3.3 2.0 - - - -
253C GLU* 3.2 37.2 + - + +
255C ILE* 4.3 11.4 - - + -
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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