Contacts of the helix formed by residues 210 - 224 (chain A) in PDB entry 7NG0
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A HIS* 2.9 13.5 + - - -
208A GLN 3.9 0.8 + - - -
209A LEU* 1.3 69.6 - - - +
211A VAL* 1.3 52.8 + - - +
212A LYS* 3.2 27.3 - - - +
213A GLN* 3.0 36.0 + - - +
214A THR* 2.4 32.1 + - - -
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Residues in contact with VAL 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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181A THR* 3.6 26.2 - - + +
183A ARG* 3.6 29.6 - - + +
184A HIS* 4.0 13.2 - - + +
210A ASN* 1.3 75.8 - - - +
212A LYS* 1.3 65.7 + - - +
214A THR* 3.4 2.5 + - - -
215A GLU* 3.0 48.6 + - - +
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Residues in contact with LYS 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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210A ASN* 3.2 19.3 - - - +
211A VAL* 1.3 80.3 - - - +
213A GLN* 1.3 52.8 + - + +
215A GLU* 3.2 11.1 + - - +
216A ASP* 2.8 43.8 + - - +
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Residues in contact with GLN 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 LEU* 3.9 33.4 - - + +
210A ASN* 3.0 26.1 + - - +
212A LYS* 1.3 72.3 - - + +
214A THR* 1.3 58.7 + - - +
216A ASP* 3.4 15.7 - - + +
217A ARG* 3.0 28.9 + - - +
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Residues in contact with THR 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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184A HIS* 3.1 36.9 - - - +
187A ALA* 4.4 2.5 - - + -
188A LEU* 4.4 2.9 - - + -
200A LEU* 4.5 2.9 - - + +
204A ILE* 3.7 28.4 - - + +
209A LEU* 4.0 7.8 - - - +
210A ASN 2.4 26.0 + - - -
211A VAL* 3.5 5.6 - - - -
213A GLN* 1.3 74.4 - - - +
215A GLU* 1.3 55.5 + - - +
217A ARG* 3.0 7.7 + - - +
218A VAL* 2.7 48.1 + - + +
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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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183A ARG* 4.4 5.7 - - - +
184A HIS* 6.5 0.2 - - - -
186A ARG* 6.1 0.2 - - - +
187A ALA* 3.8 20.4 - - + +
211A VAL* 3.0 38.4 + - + +
212A LYS* 3.4 12.6 - - - +
214A THR* 1.3 73.1 - - - +
216A ASP* 1.3 64.2 + - - +
218A VAL* 3.1 9.8 + - - +
219A LEU* 3.0 34.6 + - + +
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Residues in contact with ASP 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 LYS* 2.8 37.1 + - - +
213A GLN* 3.4 17.7 + - + +
215A GLU* 1.3 75.6 - - - +
217A ARG* 1.3 61.2 + - - +
219A LEU* 3.2 12.4 + - - +
220A LYS* 3.1 20.8 + - - +
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Residues in contact with ARG 217 (chain A).
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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200A LEU* 4.4 20.6 - - + -
203A GLU* 5.9 0.7 - - - +
209A LEU* 5.5 3.6 - - + -
213A GLN 3.0 19.8 + - - +
214A THR* 3.5 4.0 - - - +
216A ASP* 1.3 72.5 - - - +
218A VAL* 1.3 64.0 + - - +
220A LYS* 3.4 9.3 + - - +
221A LEU* 3.2 31.1 + - + +
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Residues in contact with VAL 218 (chain A).
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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187A ALA* 3.5 41.3 - - + +
188A LEU* 4.1 10.8 - - + -
190A ALA* 4.4 4.5 - - + -
191A LEU* 3.6 16.4 - - + +
200A LEU* 3.8 19.5 - - + -
214A THR 2.7 21.2 + - - +
215A GLU* 3.1 10.7 + - - +
217A ARG* 1.3 72.0 - - - +
219A LEU* 1.3 63.9 + - + +
221A LEU* 3.5 4.9 + - - +
222A LEU* 3.3 37.3 + - + +
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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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215A GLU* 3.0 26.4 + - + +
216A ASP* 3.5 12.1 - - - +
218A VAL* 1.3 75.2 - - + +
220A LYS* 1.3 56.1 + - - +
221A LEU 3.1 1.8 - - - -
222A LEU* 2.9 18.2 + - + +
223A GLU* 2.8 53.1 + - + +
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Residues in contact with LYS 220 (chain A).
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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216A ASP 3.1 9.7 + - - +
217A ARG* 3.4 14.3 + - - +
219A LEU* 1.3 77.2 - - - +
221A LEU* 1.3 56.3 + - + +
223A GLU* 3.6 14.7 + - - +
224A ALA* 3.0 30.3 + - - +
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Residues in contact with LEU 221 (chain A).
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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191A LEU* 4.0 20.0 - - + -
196A LYS* 5.3 13.7 - - + +
200A LEU* 4.2 23.1 - - + -
217A ARG* 3.2 21.2 + - + +
218A VAL 3.6 6.1 - - - +
219A LEU 3.1 0.8 - - - -
220A LYS* 1.3 74.9 - - + +
222A LEU* 1.3 63.3 + - - +
224A ALA* 3.4 23.4 - - + +
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Residues in contact with LEU 222 (chain A).
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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190A ALA* 3.9 30.7 - - + +
191A LEU* 4.0 22.2 - - + +
218A VAL* 3.4 31.9 - - + +
219A LEU* 2.9 17.8 + - + +
221A LEU* 1.3 73.5 - - - +
223A GLU* 1.3 65.9 + - + +
224A ALA 4.4 3.1 - - - +
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Residues in contact with GLU 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 40.7 + - + +
220A LYS* 3.6 11.8 - - - +
222A LEU* 1.3 79.1 - - + +
224A ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 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 LYS 3.0 19.5 + - - +
221A LEU* 3.4 17.0 + - - +
222A LEU 4.4 2.9 - - - +
223A GLU* 1.3 79.7 - - - +
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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