Contacts of the helix formed by residues 205 - 217 (chain I) in PDB entry 2ZHX
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 ARG 205 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100I GLU* 3.0 24.0 + - - -
103I ALA* 3.8 29.7 + - - +
104I ASP* 3.1 40.4 - - - +
203I GLY* 3.7 28.5 - - - +
204I SER* 1.3 76.2 - - - +
206I PRO* 1.4 69.1 - - - +
208I SER* 4.0 4.7 - - - +
209I ARG* 3.0 28.5 + - + +
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Residues in contact with PRO 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I GLU* 3.8 12.3 - - + -
104I ASP* 4.2 1.1 - - - +
166I ILE* 4.1 21.4 - - + +
168I TRP* 4.2 19.1 - - + +
187I ILE* 3.7 20.3 - - + +
201I PHE* 4.4 5.6 - - + -
204I SER* 3.3 20.2 - - - +
205I ARG* 1.4 88.5 - - - +
207I PHE* 1.3 77.4 + - + +
210I ALA* 2.8 33.1 + - - +
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Residues in contact with PHE 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I ILE* 5.3 0.2 - - + -
97I ILE* 3.7 28.0 - - + -
100I GLU* 4.3 2.7 - - + -
101I TYR* 3.4 43.7 - + + -
104I ASP* 2.9 15.6 + - + +
105I LEU* 3.9 15.7 - - + -
118I TRP* 3.6 25.1 - + - -
166I ILE* 5.2 2.9 - - + -
168I TRP* 4.6 10.5 - + - -
201I PHE* 5.5 0.4 - + - -
206I PRO* 1.3 94.3 - - + +
208I SER* 1.3 64.5 + - - +
210I ALA* 3.5 1.6 + - - +
211I ASN* 3.2 14.9 + - - -
224I TRP* 3.1 56.5 + + + +
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Residues in contact with SER 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ASP* 2.5 39.4 + - - -
105I LEU* 3.9 13.1 - - - +
205I ARG* 3.7 5.7 + - - +
207I PHE* 1.3 70.2 - - - +
209I ARG* 1.3 56.6 + - - +
211I ASN* 3.0 8.7 + - - +
212I GLU* 2.7 54.8 + - - +
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Residues in contact with ARG 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ILE* 3.7 39.6 - - + +
188I GLU 4.2 13.3 + - - -
204I SER* 2.8 34.4 + - - +
205I ARG* 3.0 27.2 + - + +
206I PRO* 4.0 3.5 - - + +
208I SER* 1.3 77.9 + - - +
210I ALA* 1.3 62.8 + - - +
212I GLU* 3.2 15.3 + - - +
213I LEU* 2.9 31.9 + - + +
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Residues in contact with ALA 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I VAL* 4.6 6.7 - - + -
164I VAL* 3.6 28.9 - - + +
166I ILE* 4.5 8.3 - - + -
187I ILE* 4.3 1.7 - - + +
206I PRO 2.8 23.7 + - - +
207I PHE 3.7 5.6 - - - +
208I SER 3.2 0.2 - - - -
209I ARG* 1.3 72.2 - - - +
211I ASN* 1.3 58.1 + - - +
213I LEU* 3.2 7.4 - - - +
214I LEU* 2.9 31.3 + - - +
224I TRP* 4.4 14.1 - - + -
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Residues in contact with ASN 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I LEU* 5.4 2.0 - - - +
207I PHE 3.2 4.7 + - - +
208I SER* 3.0 12.4 + - - +
210I ALA* 1.3 78.6 - - - +
212I GLU* 1.3 61.7 + - + +
214I LEU* 2.8 9.7 + - - +
215I VAL* 2.8 33.8 + - + +
221I PRO* 3.5 14.0 - - + +
222I ILE* 2.7 54.9 + - - +
224I TRP* 3.4 20.8 + - - +
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Residues in contact with GLU 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I SER* 2.7 38.4 + - - +
209I ARG* 3.7 16.8 + - - +
211I ASN* 1.3 72.9 - - + +
213I LEU* 1.3 53.3 + - - +
215I VAL* 3.7 6.9 - - + +
216I GLY* 2.7 34.5 + - - -
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Residues in contact with LEU 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I VAL* 3.5 22.7 - - + -
185I VAL* 3.8 35.2 - - + -
187I ILE* 3.6 31.9 - - + -
209I ARG* 2.9 18.6 + - + +
210I ALA* 3.2 8.5 - - - +
212I GLU* 1.3 77.1 - - - +
214I LEU* 1.3 57.0 + - - +
216I GLY* 3.2 2.9 + - - -
217I MET* 2.9 37.0 + - + +
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Residues in contact with LEU 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I ARG* 3.2 40.4 - - + +
62I VAL* 3.7 22.4 - - + -
162I PRO* 4.4 10.3 - - + +
164I VAL* 3.8 14.8 - - + +
210I ALA 2.9 16.2 + - - +
211I ASN* 2.8 27.9 + - - +
213I LEU* 1.3 68.4 - - - +
215I VAL* 1.3 66.4 + - - +
217I MET* 2.8 17.7 + - + +
218I GLY 3.1 0.2 + - - -
219I ALA* 2.9 26.0 + - + +
220I GLU 3.6 24.5 - - - +
221I PRO* 4.3 0.2 - - + -
222I ILE* 4.2 4.7 - - + -
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Residues in contact with VAL 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I ASN* 2.8 25.1 + - + +
212I GLU* 3.7 6.7 - - + +
214I LEU* 1.3 69.4 - - - +
216I GLY* 1.3 57.9 + - - +
218I GLY* 2.6 27.5 + - - -
219I ALA 3.4 13.6 + - - +
221I PRO* 4.2 24.2 - - + -
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Residues in contact with GLY 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I GLU 2.7 22.8 + - - -
213I LEU* 3.5 4.5 - - - -
214I LEU 3.1 0.2 - - - -
215I VAL* 1.3 73.5 - - - +
217I MET* 1.3 58.8 + - - +
218I GLY 3.7 0.7 + - - -
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Residues in contact with MET 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I PRO* 3.8 29.7 - - + +
163I LEU 4.4 7.6 - - - +
164I VAL* 3.7 28.0 - - + -
183I ASN* 3.6 25.4 - - - +
185I VAL* 4.3 23.6 - - + -
213I LEU* 2.9 25.5 + - + +
214I LEU* 2.8 11.7 + - + +
216I GLY* 1.3 76.7 - - - +
218I GLY* 1.3 60.6 + - - +
219I ALA 3.4 1.5 + - - -
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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