Contacts of the helix formed by residues 211 - 222 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A TYR* 3.5 14.1 - - - +
157A THR* 5.5 2.1 + - - -
181A ASP* 3.4 30.4 + - - -
182A TRP 2.7 9.6 + - - -
184A GLN* 2.9 18.9 + - - +
210A GLY* 1.3 71.6 - - - -
212A PRO* 1.3 66.9 - - - +
213A ILE* 3.1 20.8 + - - +
214A ASN* 3.2 19.7 + - - -
215A LYS 3.0 10.2 + - - -
404A GOL 3.6 0.6 + - - -
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Residues in contact with PRO 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A TYR* 3.3 50.0 - - + +
184A GLN* 3.4 29.6 - - + +
210A GLY 3.5 6.7 - - - +
211A SER* 1.3 82.2 - - - +
213A ILE* 1.3 65.8 + - + +
215A LYS* 3.6 7.6 - - + +
216A VAL* 3.0 31.7 + - + +
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Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 4.7 0.2 - - + -
133A TYR* 3.6 24.7 - - + -
138A GLU* 4.5 4.7 - - - +
157A THR* 3.6 35.2 - - + +
158A ARG 3.7 2.7 - - - +
159A ASN* 3.7 22.2 - - - +
161A VAL* 3.7 16.8 - - + -
162A ILE* 3.9 23.1 - - + -
211A SER* 3.1 8.3 + - - +
212A PRO* 1.3 79.5 - - + +
214A ASN* 1.3 65.5 + - - +
216A VAL* 3.2 5.4 + - - +
217A ILE* 3.1 45.5 + - + +
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Residues in contact with ASN 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 3.5 28.4 + - - +
131A GLY 5.1 1.6 + - - -
157A THR* 5.5 3.0 + - - +
179A SER* 3.5 15.8 - - - -
180A HIS 4.8 0.2 - - - +
181A ASP* 3.0 38.6 + - - -
183A PRO* 3.7 21.9 - - + +
211A SER* 3.2 11.8 + - - +
213A ILE* 1.3 74.1 - - - +
215A LYS* 1.3 66.6 + - - +
217A ILE* 4.3 1.6 - - - +
218A LEU* 2.9 26.3 + - - +
226A TRP* 3.6 20.7 - - + -
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PRO* 3.8 10.4 - - - +
184A GLN* 3.6 51.3 + - - +
185A GLY* 5.1 3.4 - - - -
211A SER 3.0 13.6 + - - +
212A PRO* 3.6 11.0 - - + +
213A ILE 3.3 0.2 - - - -
214A ASN* 1.3 77.8 - - - +
216A VAL* 1.3 72.5 + - + +
218A LEU* 3.4 2.8 + - - +
219A ASN* 3.0 25.0 + - + +
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ILE* 3.9 35.2 - - + -
212A PRO* 3.0 17.2 + - + +
213A ILE 3.7 5.4 - - - +
215A LYS* 1.3 83.0 - - + +
217A ILE* 1.3 59.0 + - - +
219A ASN* 3.0 7.1 + - + +
220A THR* 2.8 43.4 + - - +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 5.0 0.2 - - + -
129A VAL* 3.9 15.0 - - + -
161A VAL* 3.9 8.3 - - + -
162A ILE* 4.2 20.0 - - + +
165A LEU* 3.8 33.2 - - + -
166A SER* 6.5 0.4 - - - +
177A SER* 4.9 1.1 - - - +
213A ILE* 3.1 37.3 + - + +
214A ASN* 4.0 1.3 - - - +
215A LYS 3.3 0.2 - - - -
216A VAL* 1.3 75.3 - - - +
218A LEU* 1.3 58.5 + - - +
220A THR* 3.3 4.8 + - - -
221A LEU* 2.9 51.2 + - + +
226A TRP* 3.6 22.2 - - + -
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PRO* 3.8 28.7 - - + -
186A ILE* 4.1 15.0 - - + -
214A ASN 2.9 18.7 + - - +
215A LYS 3.8 3.1 - - - +
217A ILE* 1.3 78.7 - - - +
219A ASN* 1.3 62.2 + - + +
222A LYS* 2.9 27.4 + - + +
223A PRO* 4.4 2.9 - - + -
226A TRP* 3.5 37.6 - - + -
239A GLU* 4.0 26.2 - - + +
242A THR* 4.0 26.9 - - + +
244A PHE* 5.2 1.1 - - + -
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 3.0 21.4 + - + +
216A VAL* 3.6 6.5 - - - +
218A LEU* 1.3 80.5 - - - +
220A THR* 1.3 65.3 + - - +
222A LYS* 3.1 36.9 + - - +
239A GLU* 5.5 7.0 + - - +
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Residues in contact with THR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ILE* 5.8 1.2 - - - +
166A SER* 3.6 41.2 - - - +
169A SER* 4.2 6.2 + - - -
216A VAL* 2.8 28.5 + - - +
217A ILE* 3.8 5.6 - - - -
219A ASN* 1.3 84.0 + - - +
221A LEU* 1.3 60.5 + - + +
222A LYS* 4.5 3.3 - - - +
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 4.3 27.8 - - + -
165A LEU* 3.6 28.3 - - + +
166A SER* 3.7 16.4 - - - +
168A LEU* 4.1 1.8 - - + +
169A SER* 3.5 41.0 + - - +
173A GLN* 5.9 0.5 - - - +
174A ILE* 4.4 16.2 + - + +
177A SER* 5.5 2.7 - - - +
217A ILE* 2.9 39.2 + - + +
220A THR* 1.3 73.1 - - + +
222A LYS* 1.3 73.2 + - - +
223A PRO* 3.2 10.3 - - + +
226A TRP* 5.7 0.2 - - + -
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLN* 6.0 1.7 - - - +
174A ILE 5.8 0.3 + - - -
218A LEU* 2.9 17.1 + - + +
219A ASN* 3.1 42.9 + - - +
220A THR 4.5 3.8 - - - +
221A LEU* 1.3 79.2 - - - +
223A PRO* 1.4 72.8 - - - +
224A LYS 3.8 0.3 + - - -
241A PRO* 4.0 36.0 - - + +
242A THR* 3.5 7.2 + - - +
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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