Contacts of the helix formed by residues 207 - 222 (chain A) in PDB entry 1IC8
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ASN* 3.7 10.5 - - - +
205A LYS 3.4 5.7 + - - -
206A TRP* 1.3 75.6 - - - +
208A PRO* 1.3 76.2 - - - +
209A ALA 3.0 3.8 + - - -
210A SER* 3.0 12.1 + - - -
211A GLN* 3.1 12.7 + - - +
240A GLU* 3.7 24.5 + - - -
243A GLN* 5.6 0.7 - - - -
244A ARG* 5.2 0.4 - - - -
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Residues in contact with PRO 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN 5.6 4.0 - - - +
127A ASN* 5.6 2.5 - - - +
206A TRP 3.6 3.0 - - - +
207A GLY* 1.3 81.6 - - - +
209A ALA* 1.3 57.4 + - - +
211A GLN* 3.2 10.5 + - + +
212A GLN* 2.9 41.9 + - + +
243A GLN* 3.6 19.7 - - - +
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLY 3.0 0.2 + - - -
208A PRO* 1.3 83.2 - - - +
210A SER* 1.3 64.2 + - - +
211A GLN 3.2 0.7 + - - -
212A GLN* 3.3 18.8 + - - +
213A ILE* 3.6 9.7 + - - +
239A ALA* 4.0 25.4 - - + +
240A GLU* 3.3 9.9 - - - +
243A GLN* 3.3 22.7 - - + +
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A TRP* 3.5 29.8 - - - -
207A GLY 3.0 2.9 + - - -
209A ALA* 1.3 73.6 - - - +
211A GLN* 1.3 57.0 + - - +
213A ILE* 2.8 9.9 - - - +
214A LEU* 2.8 30.9 + - - +
236A CYS* 3.2 24.6 + - - +
239A ALA* 4.7 0.9 - - - +
240A GLU* 2.3 47.2 + - - +
259A VAL* 3.6 0.9 - - - +
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Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LYS* 5.3 1.4 - - - -
206A TRP* 2.9 39.4 - - + +
207A GLY 3.1 18.0 + - - +
208A PRO* 3.6 9.6 - - + +
209A ALA 3.1 0.2 - - - -
210A SER* 1.3 73.6 - - - +
212A GLN* 1.3 65.1 + - - +
213A ILE 2.7 6.8 + - - -
214A LEU* 2.7 22.5 + - + -
215A PHE* 2.9 35.1 + - + -
267A TRP* 3.5 20.2 - - - +
271A ARG* 3.8 10.9 - - - +
415F A 4.2 6.8 + - - -
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Residues in contact with GLN 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PRO* 2.9 31.1 + - + +
209A ALA* 3.6 10.8 - - - +
211A GLN* 1.3 76.1 - - + +
213A ILE* 1.3 50.5 + - - +
215A PHE* 3.9 14.5 - - - +
216A GLN* 2.4 27.1 + - - +
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Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA 3.6 4.3 + - - +
210A SER* 2.8 24.7 - - - +
211A GLN 2.7 3.6 + - - -
212A GLN* 1.3 75.6 - - - +
214A LEU* 1.3 54.2 + - - +
215A PHE 2.8 5.2 - - - -
216A GLN* 2.5 63.7 + - + +
217A ALA 3.7 2.1 + - - -
220A ARG* 5.3 0.9 - - - +
232A LEU* 4.0 22.1 - - + +
235A GLU* 4.1 24.5 - - + +
236A CYS* 3.4 25.8 - - - -
239A ALA* 6.1 0.7 - - + -
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A TRP* 3.2 51.1 - - + -
210A SER 2.8 19.3 + - - +
211A GLN* 2.7 21.4 + - + +
213A ILE* 1.3 73.6 - - - +
215A PHE* 1.3 58.6 + - - +
217A ALA 3.9 0.6 + - - -
218A TYR 3.7 9.5 + - - -
232A LEU* 5.1 6.1 - - + -
236A CYS* 4.0 9.9 - - - -
264A VAL* 4.1 19.7 - - + -
267A TRP* 2.7 64.2 - - + +
268A PHE* 3.8 10.8 - - + -
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Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLN* 2.9 47.3 + - + +
212A GLN* 3.9 12.6 - - - +
213A ILE 2.8 0.4 - - - -
214A LEU* 1.3 77.0 - - - +
216A GLN* 1.3 54.1 + - - +
218A TYR* 3.0 11.3 + + + +
219A GLU* 2.7 48.3 + - + +
267A TRP* 3.4 30.5 - + - -
271A ARG* 4.1 17.0 - - - -
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLN 2.4 29.7 + - - +
213A ILE* 2.5 44.1 + - + +
215A PHE* 1.3 64.9 - - - +
217A ALA* 1.3 55.5 + - - +
218A TYR 2.5 5.1 + - - -
219A GLU* 2.5 58.3 + - - -
220A ARG* 2.6 43.0 + - - +
232A LEU* 5.5 0.9 - - + -
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE 3.7 1.8 + - - -
214A LEU 4.2 0.4 - - - +
215A PHE 3.6 0.2 - - - -
216A GLN* 1.3 77.5 - - - +
218A TYR* 1.3 50.0 + - - +
220A ARG* 3.0 15.2 - - - +
221A GLN* 2.3 53.1 + - + +
223A ASN 5.5 2.2 - - - +
228A GLU 5.5 2.5 - - - +
232A LEU* 3.4 21.5 - - + +
268A PHE* 3.3 29.8 - - + -
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Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU 3.7 6.6 + - - +
215A PHE* 3.0 20.5 + + + +
216A GLN 2.5 4.8 + - - -
217A ALA* 1.3 75.7 - - - +
219A GLU* 1.3 66.5 + - + +
220A ARG 3.3 0.3 + - - -
221A GLN* 3.5 4.9 + - - -
222A LYS* 3.7 36.3 + - + +
267A TRP* 4.2 7.4 - + + -
268A PHE* 3.7 29.1 - + - -
271A ARG* 3.0 49.2 + - + -
272A ARG* 3.4 9.3 + - + +
275A GLU* 3.0 33.8 + - + -
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 2.7 22.0 + - + +
216A GLN* 2.5 41.3 + - - +
218A TYR* 1.3 74.0 - - + +
220A ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 5.3 1.0 - - - +
216A GLN* 2.6 37.7 + - - +
217A ALA* 3.0 36.5 - - - +
218A TYR 4.0 0.4 - - - -
219A GLU* 1.3 76.4 - - - +
221A GLN* 1.3 75.5 + - + +
232A LEU* 5.4 4.8 - - - +
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Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ALA* 2.3 38.4 + - - +
218A TYR 3.5 2.6 + - - -
220A ARG* 1.3 89.1 - - + +
222A LYS* 1.3 63.7 + - - +
223A ASN* 2.4 64.6 + - + +
225A SER* 4.9 0.3 + - - -
228A GLU* 4.9 13.9 - - - +
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ALA 3.3 4.1 + - - -
218A TYR* 3.7 41.0 + - + +
221A GLN* 1.3 77.7 - - - +
223A ASN* 1.3 64.7 + - - +
268A PHE* 4.2 8.2 - - - -
272A ARG* 2.6 53.5 + - - +
275A GLU* 5.9 4.0 - - - +
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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