Contacts of the helix formed by residues 220 - 235 (chain A) in PDB entry 4HNI
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 THR 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ALA 4.6 0.9 - - - -
219A ALA* 1.3 81.1 - - + +
221A LYS* 1.3 73.4 + - - +
222A ARG* 3.5 10.5 + - + +
223A GLN* 2.7 48.8 + - + +
224A LYS* 2.7 12.7 + - - -
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Residues in contact with LYS 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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220A THR* 1.3 73.4 + - - +
222A ARG* 1.3 55.6 + - - +
224A LYS* 2.7 40.9 + - + +
225A TYR* 2.9 45.7 + - + -
303A SO4 4.0 8.3 + - - -
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Residues in contact with ARG 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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220A THR* 3.0 8.7 + - + +
221A LYS* 1.3 77.6 - - - +
223A GLN* 1.3 69.6 + - + +
224A LYS 3.0 0.2 + - - -
225A TYR* 3.1 10.9 + - + +
226A GLU* 2.8 35.6 + - + +
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Residues in contact with GLN 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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218A ALA* 4.1 1.8 - - + -
219A ALA* 2.8 39.9 - - - +
220A THR* 2.7 29.5 + - + +
222A ARG* 1.3 80.6 - - + +
224A LYS* 1.3 53.1 + - - +
226A GLU* 3.2 9.1 + - - +
227A ARG* 2.7 45.5 + - + +
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Residues in contact with LYS 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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216A LEU* 5.0 7.1 - - + +
218A ALA* 3.3 26.9 - - + +
220A THR 2.7 8.5 + - - +
221A LYS* 2.7 28.3 + - + +
223A GLN* 1.3 66.6 - - - +
225A TYR* 1.3 74.7 + - + +
226A GLU 2.9 4.9 + - - -
227A ARG* 3.2 2.5 + - - +
228A ILE* 3.0 45.5 + - + +
303A SO4 4.0 25.1 + - - -
305A SO4 3.1 35.5 + - - +
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Residues in contact with TYR 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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173A LEU* 3.8 31.6 - - + -
177A ALA* 3.6 16.8 - - + -
185A HIS* 4.4 4.2 + - - +
221A LYS* 2.9 41.5 + - + -
222A ARG* 3.1 8.2 + - + +
224A LYS* 1.3 90.5 - - + +
226A GLU* 1.3 62.0 + - - +
228A ILE* 4.1 6.0 - - - +
229A SER* 3.1 24.4 + - - -
303A SO4 2.6 50.0 + - - -
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Residues in contact with GLU 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 ARG* 2.8 25.8 + - + +
223A GLN* 3.2 14.8 - - - +
225A TYR* 1.3 78.0 - - - +
227A ARG* 1.3 65.9 + - + +
229A SER* 3.3 9.3 + - - -
230A GLU* 3.0 50.4 + - - +
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Residues in contact with ARG 227 (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 LEU* 3.5 27.2 - - + +
217A LYS* 2.4 82.2 + - - +
218A ALA* 4.3 5.2 - - + +
223A GLN* 2.7 29.8 + - + +
224A LYS* 3.8 3.6 - - - +
226A GLU* 1.3 72.7 - - + +
228A ILE* 1.3 58.5 + - - +
230A GLU* 3.1 14.7 + - - +
231A LYS* 2.8 30.5 + - - +
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Residues in contact with ILE 228 (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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177A ALA* 4.2 20.6 - - + +
178A ARG 4.9 0.2 - - - +
185A HIS* 4.2 16.4 - - + +
213A TRP* 3.5 38.2 - - + +
216A LEU* 3.4 15.7 - - + -
224A LYS* 3.0 41.5 + - + +
225A TYR* 4.1 4.0 - - - +
227A ARG* 1.3 73.6 - - - +
229A SER* 1.3 58.6 + - - +
231A LYS* 3.2 1.4 + - - +
232A LYS* 2.8 34.3 + - - +
305A SO4 3.3 26.9 - - - +
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Residues in contact with SER 229 (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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185A HIS* 3.5 41.8 + - - +
186A LEU* 5.9 0.3 - - - +
225A TYR 3.1 17.6 + - - -
226A GLU* 3.5 13.5 + - - -
227A ARG 3.3 0.2 - - - -
228A ILE* 1.3 78.7 - - - +
230A GLU* 1.3 62.6 + - - +
232A LYS* 3.4 2.2 + - - +
233A MET* 3.1 41.7 + - - +
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Residues in contact with GLU 230 (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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226A GLU* 3.0 48.5 + - - +
227A ARG* 3.4 13.7 + - - +
229A SER* 1.3 77.1 - - - +
231A LYS* 1.3 56.2 + - - +
233A MET* 3.3 6.0 + - - +
234A SER* 2.6 34.7 + - - +
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Residues in contact with LYS 231 (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 PRO* 3.7 33.4 - - - +
213A TRP* 3.8 14.1 - - + -
216A LEU* 4.0 11.4 - - + -
227A ARG 2.8 19.1 + - - +
228A ILE 3.7 3.1 - - - +
230A GLU* 1.3 70.9 - - - +
232A LYS* 1.3 61.3 + - - +
234A SER* 3.5 9.7 + - - -
235A THR* 2.7 50.3 + - - +
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Residues in contact with LYS 232 (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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177A ALA 2.7 20.1 + - - -
178A ARG 3.7 2.2 + - - -
180A ALA 2.6 30.2 + - - +
182A ILE* 4.3 22.6 - - + +
185A HIS* 2.6 36.5 + - + +
201A TYR* 4.3 8.7 - - + +
213A TRP* 3.6 55.5 - - + +
228A ILE* 2.8 18.3 + - - +
229A SER* 3.7 5.6 - - - +
231A LYS* 1.3 79.1 - - - +
233A MET* 1.3 61.2 + - + +
234A SER 3.5 0.5 + - - -
235A THR* 3.5 17.5 + - - +
256A ARG* 5.2 1.6 + - - +
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Residues in contact with MET 233 (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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182A ILE* 3.5 40.8 - - + +
185A HIS* 5.4 1.8 - - + -
186A LEU* 3.2 37.0 - - + -
229A SER* 3.1 31.8 + - - +
230A GLU* 3.3 6.3 + - - +
231A LYS 3.3 0.2 - - - -
232A LYS* 1.3 77.4 - - + +
234A SER* 1.3 59.5 + - - +
235A THR 3.4 1.5 - - - +
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Residues in contact with SER 234 (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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230A GLU* 2.6 24.0 + - - +
231A LYS* 3.5 13.5 + - - -
232A LYS 3.3 0.2 - - - -
233A MET* 1.3 78.0 - - - +
235A THR* 1.3 61.3 + - - +
236A PRO* 2.9 15.0 - - - +
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Residues in contact with THR 235 (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 PRO* 4.2 19.3 - - + +
213A TRP* 4.2 8.3 - - + -
231A LYS* 2.7 40.8 + - - +
232A LYS 3.5 13.2 + - - +
233A MET 3.4 2.0 - - - -
234A SER* 1.3 79.0 - - - +
236A PRO* 1.3 74.6 - - + +
237A ILE 3.6 1.2 + - - -
239A VAL* 4.4 8.1 - - + -
240A LEU* 3.9 25.4 - - + +
256A ARG* 4.5 9.4 + - - -
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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