Contacts of the helix formed by residues 229 - 244 (chain C) in PDB entry 3ELP
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 CYS 229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C ASP* 5.5 1.3 + - + +
227C VAL* 3.6 2.4 - - - +
228C ASN* 1.3 80.3 - - - +
230C GLU* 1.3 67.3 + - - +
231C SER* 3.8 12.1 - - - -
232C LEU* 3.5 37.4 - - + +
233C HIS* 3.1 22.2 + - - +
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Residues in contact with GLU 230 (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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82C LYS* 4.2 11.1 + - - +
83C TYR* 2.6 33.1 + - - -
228C ASN 3.3 3.2 + - - -
229C CYS* 1.3 74.8 - - - +
231C SER* 1.3 63.6 + - - +
233C HIS* 3.2 9.8 + - - +
234C ASN* 3.0 39.7 + - - +
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Residues in contact with SER 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C CYS* 3.8 11.6 - - - -
230C GLU* 1.3 77.0 - - - +
232C LEU* 1.3 68.1 + - - +
234C ASN* 3.8 11.3 - - - +
235C ARG* 3.0 44.2 + - - +
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Residues in contact with LEU 232 (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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100C LEU* 3.7 31.0 - - + -
183C ILE* 4.4 17.5 - - + -
204C ASP* 4.1 17.5 - - + +
205C ILE* 3.7 18.4 - - + -
227C VAL* 3.5 28.3 - - + -
229C CYS* 3.5 30.4 + - + +
230C GLU 3.2 0.4 - - - -
231C SER* 1.3 80.6 + - - +
233C HIS* 1.3 61.6 + - - +
235C ARG* 3.6 14.8 + - - +
236C LEU* 3.2 30.1 + - + +
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Residues in contact with HIS 233 (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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83C TYR* 3.3 56.4 - + + +
84C CYS 5.2 1.8 - - - -
85C LEU* 4.0 15.8 - - + +
227C VAL* 3.7 15.2 - - + +
229C CYS 3.1 17.6 + - - +
230C GLU* 3.4 6.1 - - - +
232C LEU* 1.3 75.3 - - - +
234C ASN* 1.3 72.2 + - - +
236C LEU* 3.3 5.7 + - - +
237C ARG* 2.9 50.4 + - + +
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Residues in contact with ASN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLU* 3.0 40.8 + - - +
231C SER* 3.3 9.9 + - - +
233C HIS* 1.3 83.6 + - - +
235C ARG* 1.3 66.8 + - + +
237C ARG* 3.4 8.1 + - - +
238C PHE* 3.1 23.6 + - - +
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Residues in contact with ARG 235 (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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100C LEU* 2.8 56.2 + - + +
101C LEU* 5.3 0.6 - - - +
183C ILE* 5.2 7.7 - - - +
231C SER* 3.0 35.5 + - - +
232C LEU* 3.9 15.7 - - - +
234C ASN* 1.3 76.4 - - + +
236C LEU* 1.3 59.0 + - - +
238C PHE* 3.4 8.1 + - - +
239C LEU* 3.1 34.4 + - + +
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Residues in contact with LEU 236 (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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85C LEU* 3.3 22.4 - - + +
87C PHE* 4.3 6.6 - - + -
96C THR* 4.5 16.8 - - + -
97C ILE* 4.6 9.0 - - + -
100C LEU* 3.3 38.8 - - + -
205C ILE* 4.5 6.1 - - + -
225C VAL* 4.2 23.1 - - + -
227C VAL* 4.6 6.7 - - + -
232C LEU* 3.2 32.3 + - + +
233C HIS* 3.5 5.2 - - - +
234C ASN 3.2 0.2 - - - -
235C ARG* 1.3 80.4 - - - +
237C ARG* 1.3 55.6 + - - +
239C LEU* 3.5 3.4 + - - +
240C GLN* 2.9 28.6 + - - +
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Residues in contact with ARG 237 (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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64C GLY* 5.5 0.2 - - - -
65C ASN 5.9 0.2 - - - +
68C ARG* 3.3 19.8 - - - +
69C ASN* 4.1 20.6 + - - +
72C GLU* 2.9 30.3 + - - -
84C CYS 4.9 0.6 + - - -
85C LEU* 3.2 11.5 - - + +
233C HIS* 2.9 32.3 + - + +
234C ASN* 3.7 9.0 - - - +
236C LEU* 1.3 74.9 - - - +
238C PHE* 1.3 64.8 + - - +
240C GLN* 2.7 36.2 + - - +
241C ASN* 3.0 43.0 + - - +
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Residues in contact with PHE 238 (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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234C ASN 3.1 16.6 + - - +
235C ARG* 3.6 8.3 - - - +
236C LEU 3.4 0.2 - - - -
237C ARG* 1.3 76.6 - - - +
239C LEU* 1.3 63.3 + - + +
241C ASN* 3.5 3.6 + - + +
242C SER* 2.5 61.9 + - - -
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Residues in contact with LEU 239 (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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96C THR* 3.4 32.1 - - + +
99C HIS* 3.7 19.3 - - + +
100C LEU* 3.4 33.0 - - + -
235C ARG 3.1 16.4 + - - +
236C LEU* 3.6 5.6 - - + +
237C ARG 3.2 0.2 - - - -
238C PHE* 1.3 83.4 - - + +
240C GLN* 1.3 66.5 + - - +
242C SER* 3.5 4.9 - - - +
243C LEU* 3.0 52.8 + - + +
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Residues in contact with GLN 240 (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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68C ARG* 3.5 17.3 - - - +
72C GLU* 3.1 16.3 - - - +
85C LEU* 3.6 13.3 - - - +
86C ALA 3.0 19.6 + - - +
87C PHE* 3.9 25.7 - - + -
236C LEU 2.9 17.6 + - - +
237C ARG* 2.7 44.6 - - - +
239C LEU* 1.3 79.5 - - - +
241C ASN* 1.3 61.8 + - - +
244C GLY* 3.5 14.6 + - - -
245C ALA 4.3 1.9 + - - -
246C VAL* 3.5 25.5 - - + +
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Residues in contact with ASN 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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64C GLY 4.8 4.9 + - - -
68C ARG* 3.5 26.5 + - - -
237C ARG* 3.0 41.3 + - - +
238C PHE* 4.2 3.2 - - - +
240C GLN* 1.3 81.7 + - - +
242C SER* 1.3 63.0 + - - +
243C LEU 3.5 0.5 + - - -
244C GLY* 3.9 6.1 + - - -
246C VAL* 5.4 1.3 - - - -
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Residues in contact with SER 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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238C PHE* 2.5 59.1 + - - -
239C LEU* 3.5 8.1 - - - +
241C ASN* 1.3 74.0 - - - +
243C LEU* 1.3 71.6 + - - +
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C THR* 5.9 2.2 - - + +
99C HIS* 3.7 31.2 - - + +
239C LEU* 3.0 35.2 + - + +
242C SER* 1.3 89.5 - - - +
244C GLY* 1.3 63.7 + - - +
245C ALA* 3.4 8.5 + - + +
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Residues in contact with GLY 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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240C GLN 3.5 11.9 + - - -
241C ASN 3.9 5.5 + - - -
242C SER 3.7 1.4 - - - -
243C LEU* 1.3 75.7 - - - +
245C ALA* 1.3 56.4 + - - +
246C VAL* 2.8 19.0 + - - +
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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