Contacts of the helix formed by residues 217 - 226 (chain A) in PDB entry 4QQI
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 SER 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A MET* 4.4 1.6 - - - -
208A PRO 5.0 6.1 - - - -
209A GLN 5.5 0.2 - - - -
210A LEU 4.0 8.3 - - - -
211A LEU* 3.8 17.3 - - - -
215A ARG 4.0 1.0 + - - -
216A GLU* 1.3 75.2 - - - +
218A ALA* 1.3 64.5 + - - +
219A LEU* 3.3 12.0 + - - +
220A SER* 2.8 33.7 + - - -
221A LEU* 2.9 30.1 + - - +
240A ASP 5.7 0.8 + - - -
243A GLU* 5.0 4.7 - - - -
251A PRO* 4.9 3.3 - - - +
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Residues in contact with ALA 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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186A LEU* 4.2 26.7 - - + +
187A MET* 3.9 19.5 - - + +
190A ALA* 3.7 23.0 - - + +
208A PRO 4.9 7.3 + - - +
210A LEU 4.8 1.2 + - - -
217A SER* 1.3 72.2 - - - +
219A LEU* 1.3 62.4 + - - +
221A LEU* 3.4 2.8 + - - +
222A ALA* 3.0 26.0 + - - +
234A LEU* 3.9 15.3 - - + -
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Residues in contact with LEU 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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208A PRO 5.6 0.8 + - - +
217A SER* 3.1 11.2 + - - +
218A ALA* 1.3 78.4 - - - +
220A SER* 1.3 57.2 + - - +
222A ALA* 3.2 2.3 + - - +
223A CYS* 2.8 51.1 + - - -
231A VAL* 4.0 20.0 - - + +
234A LEU* 3.7 17.6 - - + +
235A LEU* 4.0 18.8 - - + -
239A VAL* 3.9 14.8 - - + -
240A ASP 3.7 22.2 - - - +
241A VAL* 3.9 19.1 - - + -
251A PRO* 3.8 20.0 - - + -
267A LEU* 4.3 1.6 - - + -
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Residues in contact with SER 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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216A GLU* 3.8 11.8 - - - +
217A SER* 2.8 34.1 + - - -
219A LEU* 1.3 76.7 - - - +
221A LEU* 1.3 58.3 + - - +
223A CYS* 3.3 1.4 + - - +
224A SER* 2.9 32.8 + - - -
245A ASP* 5.4 1.3 - - - -
251A PRO* 4.2 26.5 - - - -
254A TYR* 4.2 21.3 - - - -
93X LEU* 4.4 5.0 - - - +
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Residues in contact with LEU 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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183A PHE* 4.9 2.2 - - + -
187A MET* 3.8 38.8 - - + +
191A ALA* 4.0 28.6 - - + +
216A GLU* 4.5 17.7 - - + -
217A SER 2.9 21.3 + - - +
218A ALA* 3.8 4.3 - - - +
220A SER* 1.3 79.9 + - - +
222A ALA* 1.3 62.2 + - - +
224A SER* 3.3 16.8 + - - -
225A LYS* 3.4 13.0 + - - +
90X MET* 4.4 10.5 - - + -
91X PRO* 4.4 15.7 - - + +
92X THR 5.8 0.2 - - - -
93X LEU* 4.0 25.1 - - + -
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Residues in contact with ALA 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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190A ALA* 4.2 13.9 + - + +
218A ALA 3.0 17.4 + - - +
219A LEU 3.8 1.6 - - - +
221A LEU* 1.3 75.1 - - - +
223A CYS* 1.3 63.8 + - - +
225A LYS* 3.2 2.6 + - - -
226A GLY 3.1 17.8 + - - -
227A TYR* 3.1 17.0 + - + -
230A ILE* 3.6 31.6 - - + -
231A VAL* 3.7 16.6 - - + -
234A LEU* 4.6 1.3 - - + -
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Residues in contact with CYS 223 (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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219A LEU* 2.8 38.1 + - - +
220A SER 3.8 3.8 - - - +
222A ALA* 1.3 71.7 - - - +
224A SER* 1.3 63.4 + - - +
226A GLY* 3.1 10.8 + - - +
231A VAL* 3.7 20.2 - - - -
251A PRO* 3.5 27.6 - - + +
254A TYR* 4.5 2.7 - - + -
255A ALA* 3.9 10.9 - - + +
260A HIS* 3.4 12.1 - - - +
263A CYS* 4.7 5.6 - - - -
267A LEU* 3.7 26.9 - - - -
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Residues in contact with SER 224 (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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220A SER 2.9 10.0 + - - -
221A LEU* 3.4 11.7 - - - -
223A CYS* 1.3 76.3 - - - +
225A LYS* 1.3 62.6 - - - +
254A TYR* 3.4 25.4 - - - +
258A GLY* 5.0 3.1 - - - -
260A HIS* 3.3 14.4 + - - -
92X THR 5.9 0.2 - - - -
93X LEU* 3.0 29.7 - - - +
94X PRO* 3.4 19.3 - - - +
100X LYS* 5.5 1.9 + - - -
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Residues in contact with LYS 225 (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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191A ALA* 4.0 8.1 - - - +
221A LEU 3.4 10.0 + - - +
222A ALA 3.2 3.9 + - - +
224A SER* 1.3 79.7 - - - +
226A GLY* 1.3 62.1 + - - +
227A TYR* 3.3 50.0 + - + +
260A HIS* 3.4 13.5 + - - -
91X PRO* 3.8 35.2 - - - +
92X THR 5.8 1.1 - - - -
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Residues in contact with GLY 226 (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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222A ALA 3.1 4.5 + - - -
223A CYS 3.1 7.8 + - - -
225A LYS* 1.3 77.7 - - - +
227A TYR* 1.3 61.0 + - - +
228A THR* 2.9 13.2 + - - -
260A HIS* 3.2 29.0 - - - -
263A CYS* 3.9 11.0 - - - -
412A UNX 3.3 16.2 - - - -
413A UNL 3.5 6.1 + - - -
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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