Contacts of the helix formed by residues 218 - 228 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D PHE* 4.0 15.9 - - - -
182D VAL* 3.1 17.2 + - + -
215D ALA* 3.1 29.5 + - + +
217D ARG* 1.3 74.3 - - - +
219D VAL* 1.3 73.1 + - - +
221D ASN* 3.5 5.0 + - - +
222D ALA* 3.0 25.6 + - - +
241D VAL* 4.5 5.2 - - + +
244D MET* 4.0 8.3 - - + +
245D PHE* 3.9 29.2 - - + -
253D MET* 4.3 5.8 - - - -
258D ASP* 3.4 0.8 + - - -
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Residues in contact with VAL 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D CYS* 1.3 86.6 - - - +
220D GLU* 1.3 65.7 + - - +
221D ASN 3.1 0.2 - - - -
222D ALA* 3.2 5.5 + - - +
223D TYR 3.1 17.5 + - - -
237D ILE* 4.1 16.8 - - + +
241D VAL* 4.8 1.8 - - + -
258D ASP* 2.9 27.3 + - + +
306D LEU* 5.2 3.8 - - + -
309D ALA* 3.4 35.4 - - + +
310D MET* 3.6 23.6 - - + -
315D ILE* 3.6 20.4 - - + +
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Residues in contact with GLU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D THR* 4.3 8.1 + - + -
217D ARG* 3.4 19.7 + - - +
219D VAL* 1.3 75.5 - - - +
221D ASN* 1.3 62.5 + - - +
223D TYR* 3.3 9.9 + - - +
224D PHE* 3.0 22.5 + - - -
258D ASP* 3.0 17.1 + - - +
315D ILE* 4.0 18.8 - - + -
318D ARG* 3.3 14.6 + - - +
319D VAL* 4.5 6.7 - - + +
342D GLY* 3.0 37.7 - - - +
343D HIS* 3.3 9.0 + - - +
409D ARG* 2.8 31.5 + - - -
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Residues in contact with ASN 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D VAL* 3.7 23.2 - - + +
183D THR* 3.5 18.4 - - + +
191D PRO* 3.2 9.7 - - - +
192D VAL 2.8 44.9 + - - -
197D MET* 3.6 15.4 - - - +
217D ARG 3.2 6.9 + - - +
218D CYS 3.6 9.0 - - - +
219D VAL 3.1 0.4 - - - -
220D GLU* 1.3 79.8 - - - +
222D ALA* 1.3 62.6 + - - +
224D PHE* 3.1 16.8 + - - +
225D ILE* 3.2 17.0 + - - +
244D MET* 4.0 3.8 - - + -
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Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D CYS 3.0 18.8 + - - +
219D VAL* 3.2 7.2 + - - +
221D ASN* 1.3 77.2 - - - +
223D TYR* 1.3 61.1 + - - +
225D ILE* 3.4 4.2 + - - +
226D LYS* 3.1 22.5 + - - +
237D ILE* 4.2 11.7 - - + -
240D ILE* 3.8 28.5 - - + +
241D VAL* 3.8 20.4 - - + -
244D MET* 4.2 5.6 - - - -
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Residues in contact with TYR 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D VAL 3.1 5.7 + - - -
220D GLU 3.6 8.7 - - - +
221D ASN 3.2 0.6 - - - -
222D ALA* 1.3 73.6 - - - +
224D PHE* 1.3 66.3 + + - +
226D LYS* 3.2 3.4 + - + +
227D GLU* 2.7 72.4 + - + +
237D ILE* 3.9 7.8 - - - +
312D TYR* 3.7 28.2 + + - -
315D ILE* 3.8 26.9 - - + -
316D GLU* 3.6 33.1 - - + +
319D VAL* 3.8 37.2 - - + -
320D LYS* 3.3 20.6 + - + -
323D ARG* 4.4 1.6 - - - -
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Residues in contact with PHE 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D PHE* 3.8 5.1 - - + -
183D THR* 4.7 2.0 - - + -
189D GLY 4.3 7.2 - - - -
191D PRO* 3.6 38.8 - - + -
220D GLU 3.0 25.9 + - - -
221D ASN* 3.1 6.8 + - - +
223D TYR* 1.3 82.7 - + - +
225D ILE* 1.3 55.5 + - - +
227D GLU* 4.4 3.4 - - - -
228D GLN* 2.7 57.6 + - - +
319D VAL* 3.8 17.3 - - + -
323D ARG* 3.8 21.5 - - - -
340D THR 4.3 9.2 - - - -
341D GLY* 4.0 6.7 - - - -
342D GLY* 3.7 34.3 - - - -
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Residues in contact with ILE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D PHE* 4.2 6.1 - - + -
192D VAL 3.8 15.0 - - - +
194D MET* 3.9 24.0 - - + +
197D MET* 3.9 12.8 - - + -
221D ASN* 3.2 29.1 + - - +
222D ALA 3.6 7.0 - - - +
224D PHE* 1.3 75.0 - - - +
226D LYS* 1.3 60.7 + - - +
229D GLU* 2.9 53.5 + - - +
232D TYR* 3.7 25.3 - - + +
240D ILE* 3.9 12.3 - - + -
244D MET* 4.1 9.6 - - - -
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Residues in contact with LYS 226 (chain D).
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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222D ALA 3.1 5.8 + - - +
223D TYR* 3.2 8.0 + - - +
225D ILE* 1.3 80.7 - - - +
227D GLU* 1.3 63.1 + - - +
229D GLU 4.8 1.4 - - - +
232D TYR* 3.8 9.6 - - - +
233D GLU* 2.9 46.1 + - - +
234D ASN* 3.8 3.0 - - - +
235D VAL 2.5 37.3 + - - +
236D SER* 4.5 3.2 - - - +
237D ILE* 3.9 22.7 - - + +
240D ILE* 3.4 17.5 - - + -
312D TYR* 3.7 34.5 - - + -
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D TYR* 2.7 47.0 + - + +
224D PHE* 3.9 3.5 - - - +
226D LYS* 1.3 79.8 - - - +
228D GLN* 1.3 77.9 + - + +
233D GLU* 6.0 1.6 - - - +
320D LYS* 3.9 4.7 + - - -
323D ARG* 2.7 45.2 + - - -
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Residues in contact with GLN 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D PRO* 3.6 26.5 - - + +
154D PHE* 4.0 18.9 + - + -
191D PRO* 5.7 1.6 - - - +
224D PHE* 2.7 41.2 + - - +
227D GLU* 1.3 102.2 + - + +
229D GLU* 1.3 59.9 + - - +
230D ALA 3.7 2.1 + - - -
323D ARG* 4.0 5.1 - - - +
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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