Contacts of the helix formed by residues 209 - 217 (chain E) in PDB entry 1S9D
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 GLY 209 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LYS 3.2 5.7 + - - -
208E MET* 1.3 76.9 - - - +
210E LEU* 1.3 68.7 + - - -
211E GLU* 3.1 5.2 - - - -
212E ARG* 3.1 17.8 + - - +
213E PHE 3.2 8.0 + - - -
235E TYR* 3.3 10.0 - - - -
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Residues in contact with LEU 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E GLY* 1.3 72.5 - - - -
211E GLU* 1.4 76.5 + - - +
213E PHE* 3.1 3.6 + - + +
214E VAL* 2.9 50.1 + - + +
228E GLU* 4.8 2.9 - - - +
231E LEU 4.7 0.2 - - - +
232E ARG* 3.3 72.5 - - + +
235E TYR* 3.3 39.5 - - + -
236E ASP* 5.6 1.6 - - - +
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Residues in contact with GLU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E GLY* 3.1 2.3 - - - -
210E LEU* 1.4 104.2 + - - +
212E ARG* 1.3 61.3 + - - +
214E VAL* 3.4 7.6 + - + +
215E ALA* 3.0 25.2 + - - +
228E GLU* 5.1 3.3 - - - +
232E ARG* 4.6 5.7 + - - -
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Residues in contact with ARG 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A HIS* 3.4 45.5 + - + +
83A GLN* 3.2 30.7 + - - +
84A ASN* 5.7 5.1 - - - +
208E MET* 3.8 22.8 - - + +
209E GLY* 3.1 20.4 + - - +
211E GLU* 1.3 75.3 - - - +
213E PHE* 1.3 57.5 + - - +
215E ALA* 3.2 7.1 + - - +
216E MET* 2.8 31.2 + - - +
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Residues in contact with PHE 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E LEU* 4.5 4.0 - - + -
191E SER* 3.5 35.7 - - - -
192E VAL* 4.4 12.8 - - + -
195E LEU* 3.9 24.9 - - + -
208E MET* 4.0 16.1 - - + -
209E GLY 3.2 3.2 + - - +
210E LEU 3.1 8.8 + - - +
212E ARG* 1.3 75.8 - - - +
214E VAL* 1.3 67.8 + - + +
216E MET* 3.4 11.3 + - - +
217E ASN* 3.3 34.2 + - - -
231E LEU* 3.5 41.3 - - + -
234E LEU* 4.4 4.0 - - + -
235E TYR* 3.7 33.4 - + + -
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Residues in contact with VAL 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E LEU* 2.9 42.1 + - + +
211E GLU* 3.8 7.9 - - + +
213E PHE* 1.3 76.1 - - + +
215E ALA* 1.3 63.5 + - - +
217E ASN* 3.3 12.0 + - - +
218E ARG* 3.5 38.7 + - - +
228E GLU* 4.4 28.7 - - + +
231E LEU* 4.1 33.0 - - + +
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Residues in contact with ALA 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 2.9 25.5 + - - +
211E GLU 3.0 17.1 + - - +
212E ARG* 3.7 8.1 - - - +
214E VAL* 1.3 75.8 - - - +
216E MET* 1.3 63.0 + - - +
218E ARG* 3.1 21.3 + - + +
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Residues in contact with MET 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PRO* 4.8 0.5 - - - +
77A LEU* 3.3 49.9 + - + +
79A ARG* 3.0 24.0 + - - +
80A HIS* 4.2 9.2 - - + +
81A TYR* 3.7 14.4 - - + -
191E SER* 4.2 20.2 - - - +
194E MET* 3.5 23.6 - - + +
208E MET* 3.8 27.8 - - + +
212E ARG 2.8 17.0 + - - +
213E PHE* 3.6 10.5 - - - +
214E VAL 3.3 0.4 - - - -
215E ALA* 1.3 75.8 - - - +
217E ASN* 1.3 61.0 + - - +
218E ARG 3.4 2.0 + - - +
220E ILE* 4.6 1.6 - - - +
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Residues in contact with ASN 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.6 10.0 - - - +
187E VAL 4.5 0.2 - - - +
188E LEU* 3.7 12.2 - - - +
191E SER* 3.1 37.5 + - - -
213E PHE* 3.3 38.6 + - - +
214E VAL 3.3 6.8 + - - +
215E ALA 3.1 1.0 - - - -
216E MET* 1.3 78.9 - - - +
218E ARG* 1.3 64.9 + - - +
219E GLY 3.2 1.4 + - - -
220E ILE* 3.2 39.5 - - + +
224E GLY 4.8 0.3 - - - +
225E ASP* 4.8 4.2 - - - +
226E LEU* 5.0 2.3 + - + +
231E LEU* 4.2 17.5 - - + +
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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