Contacts of the helix formed by residues 211 - 222 (chain D) in PDB entry 4PEI
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 SER 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D TYR* 3.6 13.0 - - - +
157D THR* 5.3 2.4 + - - -
181D ASP* 3.4 21.9 + - - -
182D TRP 2.7 10.3 + - - -
183D PRO 3.8 0.3 - - - -
184D GLN* 2.9 20.2 + - - +
210D GLY* 1.3 68.4 - - - -
212D PRO* 1.3 67.8 - - - +
213D ILE* 3.1 20.6 + - - +
214D ASN* 3.1 29.3 + - - -
215D LYS 3.0 10.0 + - - -
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Residues in contact with PRO 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D TYR* 3.3 49.1 - - + +
184D GLN* 3.7 29.4 - - + +
210D GLY 3.3 10.8 - - - +
211D SER* 1.3 83.1 - - - +
213D ILE* 1.3 60.6 + - + +
215D LYS* 3.6 5.9 - - + +
216D VAL* 3.2 29.1 + - + +
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Residues in contact with ILE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D TYR* 3.7 26.0 - - + -
138D GLU* 4.5 4.9 - - + +
157D THR* 3.5 36.6 - - + +
158D ARG 3.7 2.2 - - - +
159D ASN* 3.6 24.0 - - + +
161D VAL* 3.7 26.7 - - + -
162D ILE* 3.8 24.4 - - + +
211D SER* 3.0 8.3 + - - +
212D PRO* 1.3 79.8 - - + +
214D ASN* 1.3 64.4 + - - +
216D VAL* 3.3 4.2 + - - +
217D ILE* 3.2 27.1 + - + +
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Residues in contact with ASN 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL* 3.5 27.5 + - - +
131D GLY 5.0 1.4 + - - -
157D THR* 5.4 3.4 + - - -
179D SER* 3.3 25.0 - - - -
180D HIS 4.7 0.4 - - - +
181D ASP* 3.1 39.2 + - - -
183D PRO* 3.8 19.7 - - + +
211D SER* 3.1 14.1 + - - +
213D ILE* 1.3 75.9 - - - +
215D LYS* 1.3 58.7 + - - +
217D ILE* 3.8 1.7 - - - +
218D LEU* 2.8 30.3 + - - +
226D TRP* 3.6 17.2 - - + -
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Residues in contact with LYS 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D PRO* 3.7 10.4 - - + +
184D GLN* 3.6 41.8 + - + +
185D GLY* 5.6 1.8 - - - -
211D SER 3.0 17.2 + - - +
212D PRO* 3.6 7.9 - - + +
214D ASN* 1.3 78.1 - - - +
216D VAL* 1.3 65.8 + - + +
218D LEU* 3.2 3.1 + - - +
219D ASN* 2.9 42.1 + - - +
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ILE* 3.6 39.9 - - + -
212D PRO* 3.2 15.0 + - + +
213D ILE 3.3 8.2 + - - +
215D LYS* 1.3 83.4 - - + +
217D ILE* 1.3 58.4 + - - +
219D ASN* 3.2 6.4 + - - +
220D THR* 2.7 43.0 + - - +
135E SER* 6.2 0.4 - - - +
136E PHE* 4.5 9.8 - - + +
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Residues in contact with ILE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D VAL* 5.2 0.4 - - + -
129D VAL* 4.0 14.8 - - + -
161D VAL* 4.1 8.5 - - + -
162D ILE* 4.0 21.1 - - + +
165D LEU* 3.9 31.4 - - + -
177D SER* 4.9 1.3 - - - +
213D ILE* 3.2 35.2 + - + +
214D ASN* 4.5 1.1 - - - +
216D VAL* 1.3 76.9 - - - +
218D LEU* 1.3 63.7 + - - +
220D THR* 4.3 5.4 - - - -
221D LEU* 2.9 44.4 + - + +
226D TRP* 3.7 22.6 - - + -
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D PRO* 3.8 24.5 - - + -
186D ILE* 4.1 19.1 - - + -
214D ASN 2.8 20.3 + - - +
215D LYS* 3.7 6.5 - - - +
217D ILE* 1.3 78.5 - - - +
219D ASN* 1.3 61.7 + - - +
222D LYS* 2.9 28.9 + - + +
223D PRO* 4.6 0.9 - - + -
226D TRP* 3.5 37.9 - - + -
239D GLU* 3.9 23.6 - - + +
242D THR* 3.8 26.7 - - + +
244D PHE* 5.0 0.2 - - + -
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Residues in contact with ASN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LYS* 2.9 44.8 + - - +
216D VAL* 3.8 3.9 - - - +
218D LEU* 1.3 83.8 - - - +
220D THR* 1.3 63.3 + - - +
222D LYS* 2.8 32.2 + - - +
239D GLU* 4.4 13.9 - - - +
136E PHE* 3.2 42.4 - - + -
137E ASP* 4.2 0.2 - - - +
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Residues in contact with THR 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ILE* 5.2 0.5 - - - +
166D SER* 3.3 45.5 + - - +
169D SER* 4.0 8.0 + - - -
216D VAL* 2.7 37.2 + - - +
217D ILE* 3.9 6.2 - - - -
219D ASN* 1.3 75.8 - - - +
221D LEU* 1.3 64.9 + - + +
222D LYS* 3.8 4.2 + - - +
136E PHE* 3.3 34.8 - - + +
137E ASP* 4.6 3.8 - - - +
140E LYS* 5.7 2.8 - - - +
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D VAL* 4.0 22.9 - - + -
165D LEU* 3.4 29.4 - - + +
166D SER 3.7 14.8 - - - +
168D LEU* 4.1 2.2 - - + +
169D SER* 3.9 36.8 + - - +
173D GLN* 5.0 1.6 + - - +
174D ILE* 4.0 26.2 + - + +
177D SER* 5.4 2.2 - - - +
217D ILE* 2.9 37.9 + - + +
220D THR* 1.3 78.8 - - + +
222D LYS* 1.3 71.9 + - - +
223D PRO* 3.3 9.6 - - + +
226D TRP* 5.7 0.7 - - + -
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Residues in contact with LYS 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D GLN* 3.1 20.3 + - - -
218D LEU* 2.9 17.4 + - + +
219D ASN* 2.8 32.1 + - - +
220D THR 4.7 3.6 - - - -
221D LEU* 1.3 76.1 - - - +
223D PRO* 1.3 70.1 - - - +
239D GLU 6.1 0.4 - - - +
241D PRO* 4.0 30.3 - - + +
242D THR* 3.6 6.5 - - - +
136E PHE* 3.8 7.7 - - - -
137E ASP* 3.1 28.0 + - - -
140E LYS* 3.7 26.5 - - - +
149E ASN 5.8 0.7 - - - +
152E VAL* 4.2 16.4 - - + +
153E SER* 4.1 8.8 - - - +
156E HIS* 5.2 0.8 + - - -
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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