Contacts of the helix formed by residues 210 - 225 (chain A) in PDB entry 2CPN
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 LYS 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A VAL* 4.3 18.2 - - + -
192A PHE* 3.5 44.4 - - + +
194A MET* 3.9 15.5 - - + +
209A SER* 1.3 70.9 - - - +
211A LYS* 1.3 72.5 + - + +
213A ALA* 3.1 17.2 + - - +
214A LYS* 3.2 11.8 + - - +
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Residues in contact with LYS 211 (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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209A SER* 3.4 5.7 - - - -
210A LYS* 1.3 81.3 - - + +
212A LEU* 1.3 65.7 + - + +
214A LYS* 3.6 31.6 + - - +
215A ARG* 3.8 19.6 + - - +
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Residues in contact with LEU 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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207A GLY* 4.5 6.3 - - - -
208A THR* 3.0 29.8 - - + +
209A SER* 3.3 17.3 + - - +
210A LYS 3.2 0.6 - - - -
211A LYS* 1.3 77.8 - - + +
213A ALA* 1.3 70.1 + - - +
215A ARG* 2.8 44.3 + - + +
216A ASN* 3.0 18.5 + - - +
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Residues in contact with ALA 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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192A PHE* 3.7 21.3 - - + +
194A MET* 3.6 25.1 - - + +
206A SER* 4.0 5.1 + - - -
207A GLY* 3.8 13.4 - - - +
209A SER 2.9 14.4 + - - +
210A LYS* 3.1 11.9 + - - +
212A LEU* 1.3 74.3 - - - +
214A LYS* 1.3 66.2 + - - +
216A ASN* 2.7 16.1 + - - +
217A ALA* 3.0 11.8 + - - +
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Residues in contact with LYS 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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161A VAL* 3.6 27.6 - - + -
178A TYR* 2.9 58.3 - - + +
194A MET* 3.3 25.8 - - - +
210A LYS 3.2 5.3 + - - +
211A LYS* 3.6 31.7 + - - +
213A ALA* 1.3 77.6 - - - +
215A ARG* 1.3 56.3 + - + +
217A ALA* 3.3 1.8 + - - +
218A ALA* 2.9 27.2 + - - +
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Residues in contact with ARG 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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159A ASN* 5.5 9.4 - - - +
160A PRO* 3.8 17.5 - - + +
161A VAL* 3.3 28.7 - - + +
211A LYS* 3.9 20.3 + - - +
212A LEU* 2.8 39.3 + - + +
214A LYS* 1.3 70.0 - - + +
216A ASN* 1.3 67.7 + - - +
217A ALA 3.0 0.2 + - - -
218A ALA* 3.1 0.6 + - - -
219A ALA* 2.8 28.5 + - - +
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Residues in contact with ASN 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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205A GLY* 4.5 2.2 - - - -
206A SER 2.8 35.8 + - - +
207A GLY* 4.2 4.1 - - - -
212A LEU* 3.0 22.4 + - - +
213A ALA 2.7 13.8 + - - +
215A ARG* 1.3 73.6 - - - +
217A ALA* 1.3 60.2 + - - +
219A ALA* 4.1 4.2 - - - +
220A LYS* 3.6 30.9 + - - +
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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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178A TYR* 5.1 1.1 - - + -
194A MET* 3.8 23.6 - - + +
195A THR 4.6 0.9 - - - -
196A CYS* 3.9 15.3 - - + +
203A GLU* 3.7 23.9 - - - +
204A ILE 4.8 0.2 - - - -
205A GLY* 4.0 7.6 - - - +
213A ALA 3.0 7.5 + - - +
214A LYS* 3.6 9.0 - - - +
216A ASN* 1.3 76.6 - - - +
218A ALA* 1.3 67.5 + - - +
220A LYS* 3.2 6.2 + - - +
221A MET* 3.0 19.9 + - - +
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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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160A PRO* 4.0 14.4 - - + -
161A VAL* 4.2 8.7 - - - +
164A LEU* 4.4 14.3 - - + +
178A TYR* 3.6 20.4 - - - +
196A CYS* 4.6 4.2 - - - +
214A LYS 2.9 17.6 + - - +
215A ARG* 3.6 4.5 - - - +
217A ALA* 1.3 74.1 - - - +
219A ALA* 1.3 67.5 + - - +
221A MET* 2.7 26.2 + - - +
222A LEU* 3.0 8.9 + - - +
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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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160A PRO* 3.3 23.8 - - + +
215A ARG 2.8 20.6 + - - +
216A ASN* 4.1 5.2 - - - +
218A ALA* 1.3 71.5 - - - +
220A LYS* 1.3 66.2 + - + +
222A LEU* 2.9 30.0 + - + +
223A LEU* 3.8 4.6 + - - +
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Residues in contact with LYS 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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203A GLU* 3.2 34.8 + - + +
204A ILE 4.1 13.2 + - - +
205A GLY* 5.7 1.8 - - - -
216A ASN* 3.6 18.1 + - - +
217A ALA 3.2 4.1 + - - +
219A ALA* 1.3 79.4 - - + +
221A MET* 1.3 63.6 + - - +
222A LEU 3.2 0.5 + - - -
223A LEU* 3.2 15.3 + - + +
224A ARG* 3.1 21.9 + - - +
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Residues in contact with MET 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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164A LEU* 4.1 13.9 - - + -
196A CYS* 3.4 22.4 - - - +
198A VAL* 3.2 32.8 - - + -
201A PHE* 3.5 6.5 - - - -
202A ILE* 3.4 30.3 - - - +
203A GLU* 3.5 9.1 - - + +
217A ALA 3.0 10.6 + - - +
218A ALA* 2.7 23.0 + - - +
220A LYS* 1.3 72.1 - - - +
222A LEU* 1.3 62.8 + - - +
224A ARG* 2.9 14.8 + - - -
225A VAL* 2.8 52.6 + - + +
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Residues in contact with LEU 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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160A PRO* 3.9 17.0 - - + +
163A ALA* 4.1 9.2 - - + -
164A LEU* 3.8 40.6 - - + +
167A LEU* 3.9 18.2 - - + +
218A ALA 3.0 10.1 + - - +
219A ALA* 2.9 29.4 + - + +
221A MET* 1.3 75.6 - - - +
223A LEU* 1.3 61.4 + - + +
225A VAL* 3.0 9.1 - - - +
226A SER* 2.8 30.2 + - - -
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Residues in contact with LEU 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 ALA 4.7 6.3 - - - +
220A LYS* 3.2 12.9 + - - +
221A MET 3.2 0.6 - - - -
222A LEU* 1.3 75.1 - - + +
224A ARG* 1.3 68.9 + - + +
226A SER* 2.9 9.0 + - - +
227A GLY 2.9 23.4 + - - -
228A PRO* 3.6 26.9 - - + +
229A SER* 5.1 3.4 - - - +
230A SER* 5.3 15.0 - - - +
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Residues in contact with ARG 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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201A PHE* 3.3 18.5 - - + -
202A ILE 4.8 8.8 + - - +
203A GLU* 3.2 36.8 + - + +
220A LYS 3.1 14.5 + - - +
221A MET* 2.9 21.2 + - - +
223A LEU* 1.3 80.8 - - - +
225A VAL* 1.3 59.9 + - - +
227A GLY* 3.9 9.7 + - - +
229A SER* 3.8 31.9 + - - +
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Residues in contact with VAL 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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164A LEU* 4.7 10.5 - - + -
167A LEU* 5.0 9.9 - - + -
171A LYS* 4.2 23.5 + - - -
173A TRP* 4.2 19.5 - - + -
198A VAL* 4.9 2.0 - - + -
201A PHE* 3.4 43.5 - - + -
221A MET* 2.8 33.3 + - + +
222A LEU* 3.0 17.7 - - - +
224A ARG* 1.3 71.5 - - - +
226A SER* 1.3 73.5 + - - +
227A GLY* 4.4 0.5 - - - -
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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