Contacts of the helix formed by residues 214 - 224 (chain A) in PDB entry 2Q41
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 GLU 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A LYS* 2.6 51.2 + - + +
211A GLU* 2.8 13.7 + - - +
213A PHE* 1.3 86.2 - - - +
215A LYS* 1.3 69.0 + - - +
216A PRO* 3.3 15.9 - - + +
217A PHE* 3.3 10.9 + - - +
218A PHE* 3.1 16.8 + - - -
251A ASN* 3.5 10.5 + - - +
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A GLU* 1.3 72.1 + - - +
216A PRO* 1.4 72.6 - - + +
218A PHE* 4.0 6.6 - - - +
219A GLN* 3.2 22.8 + - + +
251A ASN* 2.9 28.0 - - - +
254A GLU* 3.0 39.8 + - + +
255A ILE* 3.5 27.8 - - + -
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Residues in contact with PRO 216 (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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188A LYS* 6.1 2.9 - - - -
211A GLU* 6.4 2.0 - - + -
214A GLU* 3.3 19.3 - - + +
215A LYS* 1.4 93.2 - - + +
217A PHE* 1.3 58.5 + - - +
219A GLN* 3.7 5.8 + - + +
220A SER* 3.3 20.3 + - - -
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Residues in contact with PHE 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 ILE* 4.3 11.2 - - + -
184A VAL* 4.6 15.5 - - + -
187A LEU* 3.4 27.4 - - + -
200A VAL* 3.6 27.8 - - + -
211A GLU* 3.0 24.8 + - + +
212A LEU* 3.3 54.1 - - + -
214A GLU 3.3 3.2 + - - +
215A LYS 3.2 0.2 - - - -
216A PRO* 1.3 77.2 - - - +
218A PHE* 1.3 61.2 + + - +
219A GLN 3.0 2.0 - - - -
220A SER* 2.8 11.5 + - - -
221A VAL* 2.7 56.7 + - + +
233A THR* 5.3 0.4 - - + -
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Residues in contact with PHE 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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212A LEU 3.6 14.8 - - - -
213A PHE* 3.1 37.7 - + - -
214A GLU 3.1 16.9 + - - +
215A LYS* 3.5 4.7 + - - +
217A PHE* 1.3 83.0 - + - +
219A GLN* 1.3 56.7 + - - +
221A VAL* 3.3 9.8 + - + +
222A ALA 3.0 21.5 + - - -
231A VAL* 6.0 1.8 - - + -
233A THR* 4.7 19.5 - - + -
248A ILE* 4.0 19.3 - - + -
251A ASN* 3.7 27.4 - - + -
252A CYS* 4.0 23.3 - - - -
255A ILE* 3.5 18.2 - - + +
256A PHE* 3.6 19.8 - + + -
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Residues in contact with GLN 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* 3.2 16.6 + - + +
216A PRO* 3.9 6.5 - - + +
217A PHE 3.0 0.8 - - - -
218A PHE* 1.3 75.3 - - - +
220A SER* 1.3 60.0 + - - +
221A VAL 3.1 0.4 - - - -
222A ALA* 3.6 6.7 + - - +
223A ARG* 3.1 30.1 + - - +
255A ILE* 3.0 41.4 + - + +
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Residues in contact with SER 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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184A VAL 4.3 1.5 + - - -
187A LEU* 3.2 43.2 + - - +
188A LYS* 3.6 15.6 + - - +
216A PRO 3.3 12.8 + - - -
217A PHE* 2.8 16.1 + - - -
219A GLN* 1.3 79.2 - - - +
221A VAL* 1.3 59.1 + - - +
223A ARG* 2.9 30.4 - - - +
224A ALA 3.6 0.7 + - - -
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Residues in contact with VAL 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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187A LEU* 3.3 23.1 - - + -
198A VAL* 3.8 16.2 - - + +
217A PHE* 2.7 40.2 + - + +
218A PHE* 3.5 13.5 - - + +
219A GLN 3.1 0.2 - - - -
220A SER* 1.3 76.1 - - - +
222A ALA* 1.3 66.7 + - - +
224A ALA* 3.0 14.9 + - - +
225A LEU* 3.1 19.3 + - + +
231A VAL* 3.6 38.8 - - + -
256A PHE* 4.4 1.6 - - + -
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Residues in contact with ALA 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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218A PHE 3.0 17.6 + - - +
219A GLN* 4.0 10.1 - - - +
221A VAL* 1.3 76.1 - - - +
223A ARG* 1.3 65.0 + - - +
225A LEU* 3.0 23.3 + - - +
255A ILE* 4.2 13.7 - - + +
256A PHE* 3.7 24.0 - - + -
282A THR* 4.1 14.9 - - + +
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Residues in contact with ARG 223 (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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187A LEU 3.6 17.0 - - - +
188A LYS* 4.2 12.2 + - - +
190A ALA 2.7 29.1 + - - -
191A ALA 3.9 0.8 - - - -
192A GLU* 3.2 48.3 + - + +
193A GLY 3.1 19.9 + - - -
219A GLN* 3.1 17.1 + - - +
220A SER* 2.9 27.4 - - - +
221A VAL 3.2 0.4 - - - -
222A ALA* 1.3 76.6 - - - +
224A ALA* 1.3 63.3 + - - +
225A LEU 3.4 2.3 + - - +
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Residues in contact with ALA 224 (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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187A LEU* 3.4 32.3 - - + -
190A ALA* 4.3 5.2 - - + -
191A ALA 3.7 15.0 - - - +
193A GLY 3.8 0.9 - - - -
194A SER 3.1 9.5 + - - -
195A TYR* 3.0 44.3 + - + -
198A VAL* 5.0 2.0 - - + -
220A SER 4.0 0.9 - - - +
221A VAL 3.0 6.1 + - - +
223A ARG* 1.3 81.8 - - + +
225A LEU* 1.3 58.3 + - - +
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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