Contacts of the helix formed by residues 212 - 224 (chain A) in PDB entry 4A8X
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 ASN 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A THR* 3.6 6.6 - - - +
210A PHE* 3.3 4.4 - - - +
211A GLU* 1.3 87.9 + - + +
213A PRO* 1.3 75.6 - - + +
214A ASP* 2.9 28.7 + - - +
215A GLU* 3.0 44.2 + - - +
216A ALA* 3.4 8.3 + - - +
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Residues in contact with PRO 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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158A MET* 6.6 0.4 - - + -
159A LYS* 3.8 42.6 - - + +
160A PRO 3.6 19.8 - - - +
161A THR* 3.5 8.9 - - + -
211A GLU 4.8 0.2 - - - +
212A ASN* 1.3 91.7 - - + +
214A ASP* 1.3 61.0 + - - +
216A ALA* 3.8 2.1 - - + +
217A GLU* 2.9 32.2 + - - +
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Residues in contact with ASP 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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159A LYS* 5.7 4.0 + - - +
212A ASN* 2.9 15.3 + - - +
213A PRO* 1.3 80.9 - - - +
215A GLU* 1.3 63.1 + - + +
217A GLU* 3.4 15.1 - - - +
218A LYS* 3.0 22.7 + - - +
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Residues in contact with GLU 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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184A TYR* 3.5 24.9 - - - +
185A GLY* 3.3 3.5 - - - -
186A LYS* 2.9 30.5 + - - +
210A PHE* 3.9 11.4 - - + -
211A GLU* 3.2 17.1 + - - +
212A ASN* 3.0 49.1 + - - +
214A ASP* 1.3 77.0 - - + +
216A ALA* 1.3 58.1 + - - +
218A LYS* 3.0 6.8 + - - +
219A ALA* 2.9 28.8 + - - +
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Residues in contact with ALA 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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160A PRO* 3.8 21.1 - - + +
161A THR* 3.6 29.2 - - - +
162A LYS 5.4 0.2 - - - +
163A VAL* 3.9 10.4 - - + +
210A PHE* 3.7 15.3 - - + -
212A ASN 3.4 3.3 + - - +
213A PRO 3.3 3.4 + - - +
215A GLU* 1.3 77.7 - - - +
217A GLU* 1.3 58.0 + - - +
219A ALA* 3.2 2.9 + - - +
220A LEU* 2.9 37.5 + - + +
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Residues in contact with GLU 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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159A LYS* 4.0 29.4 + - - +
213A PRO 2.9 17.6 + - - +
214A ASP* 3.4 14.3 - - - +
216A ALA* 1.3 75.1 - - - +
218A LYS* 1.3 57.6 + - - +
220A LEU* 3.3 12.0 + - + +
221A LYS* 2.8 35.0 + - + +
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Residues in contact with LYS 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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183A THR 4.6 8.1 + - - -
184A TYR* 4.1 32.4 - - + +
214A ASP 3.0 14.0 + - - +
215A GLU* 3.0 11.6 + - - +
217A GLU* 1.3 73.1 - - - +
219A ALA* 1.3 67.8 + - - +
221A LYS* 3.3 9.7 - - + +
222A HIS* 2.9 53.9 + - + +
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Residues in contact with ALA 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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163A VAL* 5.1 4.7 - - + -
181A PHE* 4.2 14.6 - - + -
184A TYR* 3.9 19.2 - - + +
210A PHE* 3.8 28.5 - - + -
215A GLU 2.9 12.2 + - - +
216A ALA 3.6 7.4 - - - +
218A LYS* 1.3 78.8 - - - +
220A LEU* 1.3 57.1 + - + +
222A HIS 3.4 0.3 + - - -
223A MET* 2.9 36.3 + - - +
235A ALA* 5.3 1.1 - - - -
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Residues in contact with LEU 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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160A PRO* 5.8 2.0 - - + -
163A VAL* 3.8 17.0 - - + -
216A ALA* 2.9 25.8 + - + +
217A GLU* 3.6 9.2 - - + +
219A ALA* 1.3 79.5 - - + +
221A LYS* 1.3 62.7 + - - +
224A ASP* 3.2 27.4 + - + +
235A ALA* 3.4 42.0 - - + +
236A THR* 3.4 13.0 - - - +
237A ALA* 4.0 24.7 - - + +
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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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217A GLU* 2.8 22.8 + - + +
218A LYS* 3.3 11.0 - - + +
220A LEU* 1.3 77.6 - - - +
222A HIS* 1.3 78.7 + - + +
675B LEU* 3.6 17.7 - - - +
680B ILE* 3.4 40.2 - - + +
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Residues in contact with HIS 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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184A TYR* 3.5 35.4 - + + +
218A LYS* 2.9 48.8 + - + +
219A ALA 4.3 0.2 - - - +
221A LYS* 1.3 100.6 - - - +
223A MET* 1.3 60.0 + - - +
674B PRO* 3.4 14.1 - - + +
675B LEU* 2.9 33.0 + - - +
680B ILE* 3.6 22.7 - - + +
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Residues in contact with MET 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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180A ILE* 4.1 6.3 - - + -
181A PHE* 3.9 19.7 - - + -
184A TYR* 3.7 24.5 - - + -
219A ALA 2.9 13.6 + - - +
222A HIS* 1.3 79.3 - - - +
224A ASP* 1.3 61.5 + - - +
225A GLY 3.1 1.4 + - - -
226A GLY* 2.9 17.4 + - - +
227A GLN 4.0 7.9 - - - +
228A ILE* 3.6 37.7 - - + -
233A ILE* 3.3 25.4 - - + +
235A ALA* 4.0 4.8 - - + +
672B TRP* 3.8 21.8 - - + -
673B LEU 4.2 1.8 - - - +
674B PRO* 3.6 31.0 - - - -
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Residues in contact with ASP 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 LEU* 3.2 19.6 + - + +
223A MET* 1.3 73.2 - - - +
225A GLY* 1.3 57.2 + - - +
234A THR* 3.5 10.7 - - - +
235A ALA* 2.8 48.7 + - + +
236A THR* 4.8 2.2 - - - +
675B LEU* 3.4 20.1 - - - +
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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