Contacts of the helix formed by residues 211 - 222 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B TYR* 3.5 14.4 - - - +
157B THR* 5.3 2.6 + - - -
181B ASP* 3.4 22.3 + - - -
182B TRP 2.7 9.2 + - - -
184B GLN* 2.9 20.2 + - - +
210B GLY* 1.3 69.4 - - - -
212B PRO* 1.3 67.0 - - - +
213B ILE* 3.2 10.6 + - - +
214B ASN* 3.2 35.8 + - - -
215B LYS 3.0 11.6 + - - -
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Residues in contact with PRO 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B TYR* 3.4 47.8 - - + +
162B ILE* 5.7 0.2 - - - -
184B GLN* 3.7 30.3 - - + +
210B GLY 3.6 7.2 - - - +
211B SER* 1.3 84.8 - - - +
213B ILE* 1.3 60.7 + - + +
215B LYS* 3.4 13.6 + - - +
216B VAL* 3.1 28.2 + - - +
304C SER 5.3 6.7 - - - +
307C THR* 6.2 0.9 - - + -
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 5.0 0.2 - - + -
133B TYR* 3.5 30.5 - - + -
138B GLU* 3.7 11.9 - - - +
157B THR* 3.6 40.8 - - + +
158B ARG 3.7 1.8 - - - +
159B ASN* 3.6 24.0 - - - +
161B VAL* 3.8 19.3 - - + -
162B ILE* 4.0 19.2 - - + +
211B SER* 3.1 8.4 + - - +
212B PRO* 1.3 78.2 - - + +
214B ASN* 1.3 65.9 + - - +
216B VAL* 3.1 5.5 + - - +
217B ILE* 3.1 29.7 + - + +
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Residues in contact with ASN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 3.5 30.0 + - - +
131B GLY 5.1 1.4 + - - -
157B THR* 5.4 3.4 + - - -
179B SER* 3.5 19.1 - - - -
181B ASP* 3.0 38.8 + - - -
183B PRO* 3.7 20.1 - - + +
211B SER* 3.2 12.5 + - - +
213B ILE* 1.3 79.4 - - - +
215B LYS* 1.3 57.1 + - - +
217B ILE* 4.4 2.8 - - - +
218B LEU* 2.9 30.5 + - - +
226B TRP* 3.8 16.5 - - + -
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B PRO* 3.8 10.4 - - + +
184B GLN* 3.5 44.2 + - + +
185B GLY* 5.8 0.7 - - - -
211B SER 3.0 12.6 + - - +
212B PRO* 3.4 24.0 - - + +
213B ILE 3.2 0.2 - - - -
214B ASN* 1.3 77.2 - - - +
216B VAL* 1.3 72.9 + - - +
218B LEU* 3.2 4.1 + - - +
219B ASN* 2.9 40.2 + - - +
304C SER 4.9 2.0 + - - -
306C ARG 3.3 23.3 + - - -
307C THR* 3.9 14.3 - - - +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.5 35.9 - - + -
212B PRO 3.1 11.4 + - - +
213B ILE 3.1 7.0 + - - +
215B LYS* 1.3 88.6 - - - +
217B ILE* 1.3 55.5 + - - +
219B ASN* 3.1 9.4 + - - +
220B THR* 2.7 42.6 + - - +
170C GLN* 5.9 1.3 - - - +
303C LEU 5.5 0.2 - - - +
304C SER* 3.9 33.0 - - - +
306C ARG 5.6 1.3 - - - +
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 5.2 0.2 - - + -
129B VAL* 4.0 13.0 - - + -
161B VAL* 3.9 28.5 - - + -
162B ILE* 4.1 20.9 - - + +
165B LEU* 3.9 23.1 - - + -
166B SER* 6.0 0.4 - - - +
177B SER* 4.9 0.9 - - - +
213B ILE* 3.1 25.5 + - + +
214B ASN* 3.9 4.9 - - - +
216B VAL* 1.3 75.7 - - - +
218B LEU* 1.3 64.0 + - - +
220B THR* 4.4 5.2 - - - -
221B LEU* 2.9 50.9 + - + +
226B TRP* 3.6 16.8 - - + -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PRO* 3.8 28.3 - - + -
186B ILE* 4.4 19.3 - - + -
214B ASN 2.9 21.6 + - - +
215B LYS* 3.6 5.2 - - - +
217B ILE* 1.3 73.1 - - - +
219B ASN* 1.3 64.4 + - - +
222B LYS* 2.9 27.2 + - + +
223B PRO* 4.6 1.1 - - + -
226B TRP* 3.5 36.9 - - + -
239B GLU* 3.9 25.8 - - + +
242B THR* 4.0 24.5 - - + +
244B PHE* 5.3 0.7 - - + -
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LYS* 2.9 40.9 + - - +
216B VAL* 3.1 6.9 + - - +
218B LEU* 1.3 89.4 - - - +
220B THR* 1.3 59.8 + - - +
222B LYS* 3.0 34.2 + - - +
239B GLU* 4.4 14.4 - - - +
170C GLN* 3.6 24.7 + - + +
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ILE* 6.2 0.2 - - - -
166B SER* 3.4 43.5 + - - +
169B SER* 4.8 4.5 - - - -
216B VAL* 2.7 26.8 + - - +
217B ILE* 3.9 5.6 - - - -
219B ASN* 1.3 80.3 - - - +
221B LEU* 1.3 64.3 + - - +
222B LYS* 4.2 4.3 - - - +
170C GLN* 3.3 22.9 + - - +
220C THR* 6.5 0.9 - - + -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.3 28.0 - - + -
165B LEU* 3.5 33.2 - - + +
166B SER* 3.8 11.0 - - - +
168B LEU* 3.9 2.7 - - + +
169B SER* 2.8 50.9 + - - +
173B GLN* 4.6 1.7 - - - +
174B ILE* 4.5 7.6 - - + -
177B SER* 5.2 2.5 - - - +
217B ILE* 2.9 41.3 + - + +
220B THR* 1.3 75.3 - - - +
222B LYS* 1.3 74.1 + - - +
223B PRO* 3.2 9.8 - - + +
226B TRP* 5.4 0.7 - - + -
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Residues in contact with LYS 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLN* 3.0 25.6 + - + +
218B LEU* 2.9 13.0 + - + +
219B ASN* 3.0 36.5 + - - +
220B THR 4.2 3.8 - - - +
221B LEU* 1.3 78.9 - - - +
223B PRO* 1.3 71.5 - - - +
241B PRO* 3.8 30.1 - - + +
242B THR* 3.4 6.1 - - - +
169C SER 4.8 3.6 - - - -
170C GLN* 3.3 35.3 + - - +
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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