Contacts of the helix formed by residues 214 - 223 (chain R) in PDB entry 2D2I
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 214 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213R THR* 1.3 72.3 + - - +
215R ALA* 1.3 56.0 + - - +
216R ALA 3.0 4.1 + - - -
217R LYS* 3.1 15.0 + - - +
218R ALA* 2.7 37.6 + - - +
6339R SO4 3.6 8.9 + - - -
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Residues in contact with ALA 215 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156R THR* 3.5 31.6 - - + -
157R THR* 3.2 28.9 + - - +
160R LEU* 3.9 4.9 - - + +
178R MET* 5.2 0.9 - - + -
213R THR* 3.0 17.8 + - + +
214R GLY* 1.3 79.4 - - - +
216R ALA* 1.3 59.1 + - - +
218R ALA* 4.2 0.4 - - - -
219R VAL* 3.4 20.8 + - - +
6339R SO4 3.1 12.7 + - - +
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Residues in contact with ALA 216 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160R LEU* 4.1 10.5 - - - +
178R MET* 4.4 8.7 - - + +
213R THR* 4.7 4.9 + - - +
214R GLY* 3.0 1.4 + - - -
215R ALA* 1.3 76.0 - - - +
217R LYS* 1.3 65.7 + - + +
219R VAL* 3.3 20.8 + - - +
220R ALA 4.5 0.2 + - - -
230R LEU* 3.4 23.0 + - + +
231R ASN* 3.3 37.5 - - - +
232R GLY* 3.6 7.4 - - - +
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Residues in contact with LYS 217 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213R THR 5.8 1.3 - - - +
214R GLY* 3.1 13.8 + - - +
216R ALA* 1.3 72.0 - - + +
218R ALA* 1.3 63.9 + - - +
219R VAL 2.9 6.6 + - - -
220R ALA* 2.9 24.3 + - - +
221R LEU* 5.1 0.7 - - - +
228R GLY 6.2 1.8 - - - +
230R LEU 4.0 4.5 - - - +
231R ASN* 3.6 28.5 - - - +
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Residues in contact with ALA 218 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124R PRO* 6.0 7.2 - - + -
132R THR* 5.6 1.5 - - + +
153R ALA* 5.6 3.4 - - + -
157R THR* 3.6 26.6 - - + +
214R GLY 2.7 23.7 + - - +
217R LYS* 1.3 70.1 - - - +
219R VAL* 1.3 67.6 + - - +
220R ALA 3.0 0.4 - - - -
221R LEU* 3.0 39.0 + - + +
222R VAL* 4.0 2.3 + - - +
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Residues in contact with VAL 219 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157R THR* 4.6 6.1 - - + -
160R LEU* 3.9 28.0 - - + -
161R ALA* 4.6 8.7 - - + +
164R ALA* 4.4 3.8 - - + -
215R ALA 3.4 12.3 + - - +
216R ALA 3.3 16.6 - - - +
217R LYS 2.9 0.8 + - - -
218R ALA* 1.3 77.6 - - - +
220R ALA* 1.3 53.0 + - - +
222R VAL* 2.9 13.0 + - - +
223R ILE* 2.8 44.4 + - + -
226R LEU* 3.7 31.9 - - + +
230R LEU* 4.0 12.1 - - + -
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Residues in contact with ALA 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217R LYS 2.9 14.8 + - - +
219R VAL* 1.3 78.6 - - - +
221R LEU* 1.3 61.5 + - + +
223R ILE 3.4 11.2 - - - -
224R PRO* 3.0 30.7 - - - +
226R LEU 4.4 3.7 + - - +
227R LYS* 3.5 40.6 - - + +
228R GLY 4.8 1.6 - - - +
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Residues in contact with LEU 221 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125R GLY 5.9 4.5 - - - +
132R THR* 3.9 38.7 - - + +
138R ASN* 4.1 5.7 + - - -
217R LYS 5.1 0.7 - - - +
218R ALA* 3.0 31.2 + - + +
220R ALA* 1.3 80.7 - - + +
222R VAL* 1.3 59.1 + - - +
224R PRO* 4.8 5.1 - - - +
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Residues in contact with VAL 222 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132R THR* 3.6 19.5 - - + +
134R VAL* 3.7 29.4 - - + +
137R VAL* 3.8 21.1 - - + +
138R ASN* 3.3 47.8 - - - +
141R GLU* 5.2 2.9 - - - +
157R THR* 5.2 1.3 - - + -
161R ALA* 4.1 10.5 - - + -
218R ALA 4.6 1.3 - - - +
219R VAL* 2.9 19.7 + - - +
221R LEU* 1.3 79.1 - - + +
223R ILE* 1.3 67.0 + - + +
224R PRO* 3.4 10.2 - - - +
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Residues in contact with ILE 223 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137R VAL* 3.6 15.7 - - + -
161R ALA* 3.6 25.1 - - - +
164R ALA* 4.2 0.2 - - + -
165R LYS* 3.7 22.7 - - + +
168R HIS* 4.8 8.1 - - + -
219R VAL* 2.8 16.3 + - + +
220R ALA* 3.1 13.8 - - - +
222R VAL* 1.3 85.2 - - + +
224R PRO* 1.3 65.4 - - + +
225R GLU* 4.3 10.8 - - + +
226R LEU* 2.9 52.2 + - + +
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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