Contacts of the helix formed by residues 218 - 228 (chain C) in PDB entry 1C7G
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 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C PHE* 4.0 19.1 - - - -
182C VAL* 3.2 17.8 + - + -
215C ALA* 3.0 22.7 + - + +
216C THR 3.7 0.2 - - - -
217C ARG* 1.3 75.5 - - - +
219C VAL* 1.3 72.3 + - - +
221C ASN* 3.4 5.2 - - - +
222C ALA* 2.9 25.8 + - - +
241C VAL* 4.6 3.7 - - + +
244C MET* 3.8 23.4 - - + +
245C PHE* 3.8 21.5 - - + -
253C MET* 4.2 5.8 - - - -
258C ASP* 3.4 0.4 + - - -
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Residues in contact with VAL 219 (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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218C CYS* 1.3 83.2 - - - +
220C GLU* 1.3 66.3 + - - +
221C ASN 3.1 1.1 - - - -
222C ALA* 3.1 6.2 + - - +
223C TYR 3.1 17.3 + - - -
237C ILE* 4.2 15.7 - - + +
241C VAL* 4.8 2.5 - - + -
258C ASP* 2.9 26.1 + - + +
306C LEU* 5.0 3.4 - - + -
309C ALA* 3.3 35.0 - - + +
310C MET* 3.7 24.2 - - + -
314C TYR* 5.9 0.2 - - + -
315C ILE* 3.7 21.2 - - + +
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Residues in contact with GLU 220 (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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183C THR* 4.4 6.9 + - + -
217C ARG* 3.5 27.1 - - - +
219C VAL* 1.3 75.3 - - - +
221C ASN* 1.3 64.1 + - - +
223C TYR* 3.2 10.7 + - - +
224C PHE* 3.0 22.5 + - + -
258C ASP* 3.1 18.7 + - - +
315C ILE* 4.0 15.9 - - + -
318C ARG* 2.9 28.6 + - - +
319C VAL* 4.6 7.2 - - + -
342C GLY* 3.3 33.7 + - - +
343C HIS* 3.6 3.0 + - - +
409C ARG* 3.0 24.1 + - - -
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Residues in contact with ASN 221 (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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182C VAL* 3.7 21.0 - - + +
183C THR* 3.4 19.5 - - + +
191C PRO* 3.1 10.5 - - - +
192C VAL 2.9 45.1 + - - -
197C MET* 3.8 8.5 - - - +
217C ARG 3.3 6.9 + - - +
218C CYS 3.4 10.8 - - - +
220C GLU* 1.3 79.7 - - - +
222C ALA* 1.3 62.3 + - - +
224C PHE* 3.1 18.3 + - - +
225C ILE* 3.2 20.8 + - - +
244C MET* 4.3 3.2 - - + +
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Residues in contact with ALA 222 (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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218C CYS 2.9 14.7 + - - +
219C VAL* 3.1 10.0 + - - +
221C ASN* 1.3 77.6 - - - +
223C TYR* 1.3 62.5 + - - +
225C ILE* 3.3 4.7 + - - +
226C LYS* 3.1 21.7 + - - +
237C ILE* 4.1 12.8 - - + -
240C ILE* 3.7 26.0 - - + +
241C VAL* 3.8 24.9 - - + -
244C MET* 4.3 4.7 - - - -
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Residues in contact with TYR 223 (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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219C VAL 3.1 5.9 + - - -
220C GLU 3.4 9.0 - - - +
221C ASN 3.1 0.4 - - - -
222C ALA* 1.3 76.8 - - - +
224C PHE* 1.3 56.0 + + - +
226C LYS* 3.0 4.4 + - + +
227C GLU* 2.5 78.9 + - + +
237C ILE* 3.9 7.6 - - - +
312C TYR* 3.6 28.8 + + - -
315C ILE* 3.9 25.4 - - + -
316C GLU* 3.6 35.7 - - + +
319C VAL* 3.8 35.9 - - + -
320C LYS* 3.5 19.4 + - + -
323C ARG* 4.3 1.6 - - - -
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Residues in contact with PHE 224 (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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154C PHE* 3.7 4.8 - - + -
183C THR* 5.0 1.3 - - + -
189C GLY 4.7 5.4 - - - -
191C PRO* 3.6 38.6 - - + -
220C GLU* 3.0 29.6 + - + -
221C ASN* 3.1 7.7 + - - +
223C TYR* 1.3 81.2 - + - +
225C ILE* 1.3 54.3 + - - +
227C GLU* 4.3 2.9 - - - -
228C GLN* 2.7 57.8 + - - +
319C VAL* 3.7 21.3 - - + -
323C ARG* 3.8 19.3 - - - -
340C THR 4.1 10.5 - - - -
341C GLY* 3.9 20.2 - - - -
342C GLY* 3.8 19.3 - - - -
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Residues in contact with ILE 225 (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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154C PHE* 4.1 11.0 - - + -
192C VAL 3.7 15.5 - - - +
194C MET* 3.9 22.0 - - + +
197C MET* 3.8 14.4 - - + -
221C ASN* 3.2 27.2 + - - +
222C ALA 3.5 7.2 - - - +
223C TYR 3.2 0.4 - - - -
224C PHE* 1.3 76.5 - - - +
226C LYS* 1.3 61.4 + - - +
229C GLU* 2.8 50.7 + - - +
232C TYR* 3.7 25.3 - - + +
240C ILE* 3.9 18.4 - - + -
244C MET* 4.3 3.8 - - + -
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Residues in contact with LYS 226 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C ALA 3.1 8.1 + - - +
223C TYR* 3.0 10.2 + - - +
225C ILE* 1.3 77.4 - - - +
227C GLU* 1.3 60.0 + - - +
229C GLU 5.0 1.0 + - - +
232C TYR 3.8 15.7 - - - +
233C GLU* 3.0 39.6 + - - +
234C ASN* 3.9 2.8 - - - +
235C VAL 2.6 31.5 + - - +
236C SER* 4.6 3.5 - - - +
237C ILE* 3.9 14.4 - - + +
240C ILE* 3.5 16.8 - - + -
312C TYR* 3.5 45.8 - - + +
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Residues in contact with GLU 227 (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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223C TYR* 2.5 54.8 + - + +
224C PHE* 3.9 3.2 - - - +
226C LYS* 1.3 78.1 - - - +
228C GLN* 1.3 80.7 + - + +
233C GLU* 6.1 0.7 - - - +
320C LYS* 4.1 3.1 - - - -
323C ARG* 2.6 45.7 + - - -
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Residues in contact with GLN 228 (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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153C PRO* 3.6 25.9 - - + +
154C PHE* 4.2 17.2 + - + -
191C PRO* 5.8 1.4 - - - +
224C PHE* 2.7 44.3 + - - +
227C GLU* 1.3 106.7 + - + +
229C GLU* 1.3 59.3 + - - +
230C ALA 3.7 1.7 + - - -
323C ARG* 4.0 3.0 - - - +
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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