Contacts of the helix formed by residues 213 - 225 (chain A) in PDB entry 2AFW
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 LEU 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A GLY 3.4 4.4 + - - -
201A GLU* 2.9 32.9 + - + +
207A TRP* 5.9 0.2 - - + -
212A SER* 1.3 85.1 - - - +
214A TYR* 1.3 65.2 + - - +
215A GLY 3.4 2.5 - - - -
216A SER* 3.5 10.8 - - - +
217A ARG* 3.0 35.1 + - + +
304A GLN* 4.2 22.9 - - + +
305A ASP* 3.4 44.0 - - - +
306A ASP* 3.7 10.8 - - - +
308A ILE* 4.3 10.1 - - + -
309A PRO* 4.3 7.9 - - + -
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Residues in contact with TYR 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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109A PHE* 3.3 14.4 - - + -
111A SER* 3.3 18.4 - - - -
112A GLN 3.3 21.1 - - - -
113A THR* 3.5 8.6 - - + -
114A PRO* 3.3 19.4 - - - +
120A PHE* 3.6 35.2 - + + -
200A GLY 2.8 27.8 + - - +
202A GLU 3.9 7.2 - - - -
204A PHE* 3.6 16.8 - + - -
210A GLN 3.8 10.6 + - - -
211A ASP* 2.7 37.2 + - - -
212A SER 3.6 11.9 - - - -
213A LEU* 1.3 74.9 - - - +
215A GLY* 1.3 61.2 + - - +
217A ARG* 3.8 11.4 - - - +
218A HIS* 3.2 18.9 + - - +
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Residues in contact with GLY 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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109A PHE* 3.6 12.8 - - - -
122A ASN* 3.0 28.2 + - - -
198A PHE* 3.9 1.8 - - - -
199A ASP 3.1 23.5 + - - -
214A TYR* 1.3 79.0 - - - +
216A SER* 1.3 57.9 + - - +
218A HIS* 3.4 0.9 + - - +
219A LEU* 2.9 25.3 + - - +
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Residues in contact with SER 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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198A PHE* 3.6 25.0 - - - -
213A LEU* 3.5 14.2 - - - +
215A GLY* 1.3 73.9 - - - +
217A ARG* 1.3 66.8 + - - +
220A ALA* 2.9 28.6 + - - +
306A ASP* 2.7 54.9 + - - -
309A PRO* 3.8 5.2 - - - +
310A PHE* 3.9 1.8 - - - -
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Residues in contact with ARG 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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111A SER* 4.9 4.0 + - - -
209A PRO 4.2 13.4 + - - -
210A GLN* 3.3 24.3 + - - +
212A SER 2.9 28.5 + - - -
213A LEU* 3.0 24.9 + - + +
214A TYR* 3.8 22.0 - - - +
216A SER* 1.3 75.6 + - - +
218A HIS* 1.3 63.2 + - - +
220A ALA* 4.2 1.0 - - - +
221A ALA* 3.3 23.2 + - - +
309A PRO* 3.7 24.4 - - + +
313A ARG* 4.8 3.4 + - - +
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Residues in contact with HIS 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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107A ASP* 2.7 44.7 + - - -
108A THR 5.1 0.6 + - - -
109A PHE* 3.4 47.6 - + + +
214A TYR 3.2 16.2 + - - +
215A GLY 3.7 2.9 - - - +
216A SER 3.2 0.2 - - - -
217A ARG* 1.3 80.6 - - - +
219A LEU* 1.3 58.4 + - - +
221A ALA* 3.3 6.1 + - - +
222A LYS* 2.9 40.3 + - + +
225B SER* 5.0 11.5 + - - -
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Residues in contact with LEU 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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107A ASP* 3.6 18.2 - - - +
122A ASN* 3.7 9.6 - - + +
124A ILE* 3.9 24.2 - - + -
196A ILE* 3.7 39.5 - - + -
198A PHE* 3.9 10.8 - - + -
215A GLY 2.9 18.9 + - - +
216A SER 4.3 0.9 - - - +
218A HIS* 1.3 78.6 + - - +
220A ALA* 1.3 62.0 + - - +
222A LYS* 4.2 11.9 - - + -
223A MET* 2.8 50.0 + - + +
310A PHE* 4.4 1.6 - - + -
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Residues in contact with ALA 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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216A SER 2.9 19.6 + - - +
217A ARG 4.2 0.4 - - - +
219A LEU* 1.3 77.4 - - - +
221A ALA* 1.3 57.4 + - - +
223A MET* 3.5 0.8 + - - -
224A ALA* 2.9 31.5 + - - +
238A LEU* 3.6 4.4 - - + +
309A PRO* 3.5 37.7 - - + +
310A PHE* 3.7 25.0 - - + -
313A ARG* 3.8 6.7 - - - +
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Residues in contact with ALA 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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217A ARG 3.3 16.9 + - - +
218A HIS* 3.7 4.7 - - - +
219A LEU 3.2 0.4 - - - -
220A ALA* 1.3 76.0 - - - +
222A LYS* 1.3 66.6 + - - +
224A ALA* 3.4 3.4 + - - +
225A SER* 3.0 24.5 + - - -
313A ARG* 3.7 24.3 - - - +
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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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107A ASP* 3.0 36.8 + - - +
108A THR 5.8 0.6 + - - -
218A HIS* 2.9 28.9 + - + +
219A LEU* 3.2 13.9 + - + +
221A ALA* 1.3 76.5 - - - +
223A MET* 1.3 58.8 + - + +
225A SER* 3.1 15.9 + - - +
226A THR* 2.7 32.2 + - - +
237A GLN* 5.6 1.1 - - - +
222B LYS* 6.5 0.4 - - - +
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Residues in contact with MET 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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194A GLN* 4.0 20.6 - - - +
196A ILE* 4.7 4.5 - - - -
219A LEU* 2.8 50.9 + - + +
220A ALA 4.0 0.2 - - - +
222A LYS* 1.3 72.1 - - + +
224A ALA* 1.3 61.8 + - - +
225A SER 3.2 0.5 + - - -
226A THR 3.2 9.0 + - - -
237A GLN* 3.3 60.5 + - + +
238A LEU* 3.6 15.5 - - + -
241A MET* 3.9 26.9 - - + +
310A PHE* 4.0 16.8 - - - -
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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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220A ALA 2.9 19.7 + - - +
221A ALA* 3.7 5.6 - - - +
222A LYS 3.3 0.2 - - - -
223A MET* 1.3 77.4 - - - +
225A SER* 1.3 57.5 + - - +
226A THR 3.4 0.2 - - - -
236A SER* 3.4 17.4 - - - -
238A LEU* 3.6 21.9 - - + +
313A ARG* 3.8 17.0 - - + +
110B LEU* 4.2 8.7 - - - +
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Residues in contact with SER 225 (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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221A ALA 3.0 16.3 + - - -
222A LYS* 3.2 10.0 + - - +
223A MET 3.1 0.6 - - - -
224A ALA* 1.3 80.2 - - - +
226A THR* 1.3 55.9 + - - +
108B THR 4.4 0.5 - - - +
109B PHE* 3.1 15.5 - - - +
110B LEU* 2.8 42.8 + - - -
218B HIS* 4.8 13.5 + - - -
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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