Contacts of the strand formed by residues 212 - 224 (chain A) in PDB entry 1D2H
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 LYS 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLY* 4.8 11.3 + - - +
208A THR* 3.6 1.8 - - - +
209A VAL* 2.9 52.5 + - + +
210A ASN* 3.3 8.7 - - - +
211A ASN* 1.3 77.7 - - - +
213A ALA* 1.3 59.9 + - - +
214A HIS* 2.7 35.9 + - + +
243A TYR* 4.9 11.2 - - - +
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Residues in contact with ALA 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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181A LEU* 3.8 27.4 - - + -
206A VAL* 4.9 4.5 - - + -
207A LEU 3.4 11.7 - - - +
208A THR* 4.1 5.7 - - + +
211A ASN 3.8 4.0 + - - -
212A LYS* 1.3 71.8 - - - +
214A HIS* 1.3 61.3 + - - +
243A TYR* 4.1 8.0 + - - -
244A PRO* 3.2 29.3 - - + +
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Residues in contact with HIS 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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145A ASP* 3.3 35.0 + - + +
146A SER 5.1 1.2 + - - -
148A GLY* 4.0 23.5 - - - -
207A LEU* 3.0 18.5 + - + +
209A VAL* 3.3 39.4 - - + +
212A LYS* 2.7 19.9 + - + +
213A ALA* 1.3 71.9 - - - +
215A MET* 1.3 66.1 + - + +
243A TYR* 2.8 34.6 - + - -
244A PRO* 3.3 3.2 - - - +
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Residues in contact with MET 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO* 5.6 12.3 - - + -
206A VAL* 3.6 0.5 - - - +
207A LEU* 3.1 56.9 + - + +
214A HIS* 1.3 84.7 - - + +
216A VAL* 1.3 79.5 + - - +
217A THR* 4.2 13.0 - - - +
241A SER* 4.0 23.8 - - - -
242A TYR 3.5 12.8 - - - +
244A PRO* 4.0 1.0 - - - +
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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
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177A TYR* 4.6 15.7 - - + -
180A ILE* 5.5 3.8 - - + -
181A LEU* 4.4 4.9 - - + -
186A ALA* 5.9 0.4 - - + -
204A THR* 4.0 11.4 - - + -
205A SER 3.8 5.6 - - - +
206A VAL* 3.9 20.4 - - + -
215A MET* 1.3 88.8 - - - +
217A THR* 1.3 59.3 + - - +
218A LEU* 3.5 27.3 + - + -
241A SER* 3.5 2.2 - - - -
242A TYR* 3.0 38.3 + - + +
244A PRO* 3.8 27.1 - - + -
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Residues in contact with THR 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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203A THR 3.4 1.0 - - - +
205A SER* 2.9 48.5 + - - -
207A LEU* 6.0 0.9 - - - +
215A MET* 4.2 17.3 - - - +
216A VAL* 1.3 69.3 + - - +
218A LEU* 1.3 62.4 + - - +
219A ASP* 3.9 1.4 + - - +
239A ARG* 2.6 49.3 + - + +
240A LEU 4.2 0.2 - - - +
241A SER* 2.8 26.8 + - - +
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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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175A LYS* 4.9 11.4 - - + +
177A TYR* 5.6 2.5 - - + +
180A ILE* 6.2 0.2 - - + -
186A ALA* 3.5 24.7 - - + -
202A ILE* 4.0 12.8 - - + -
203A THR 3.8 1.6 - - - -
204A THR* 3.1 37.7 - - + -
216A VAL* 3.5 18.1 + - + -
217A THR* 1.3 73.6 - - - +
219A ASP* 1.3 61.5 + - - +
220A TYR* 3.6 30.9 - - + +
239A ARG* 3.6 2.8 - - - +
240A LEU 2.9 36.9 + - - +
242A TYR* 4.0 15.3 - - + -
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Residues in contact with ASP 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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201A ASP 3.4 1.6 - - - +
202A ILE* 3.1 7.5 - - - -
203A THR* 3.0 45.4 + - - +
205A SER* 3.9 15.9 + - - -
217A THR 4.4 0.9 - - - +
218A LEU* 1.3 74.1 - - - +
220A TYR* 1.3 61.3 + - - +
221A THR* 5.1 0.7 + - - -
237A LYS* 4.1 22.6 - - + +
238A PHE 3.7 4.3 - - - +
239A ARG* 2.9 51.4 + - - +
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Residues in contact with TYR 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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175A LYS* 5.1 2.4 + - - -
200A LYS* 4.6 14.4 - - + -
201A ASP 3.4 5.4 - - - +
202A ILE* 3.6 32.1 - - + -
218A LEU* 3.6 31.1 - - + +
219A ASP* 1.3 72.6 - - - +
221A THR* 1.3 57.5 + - - +
222A VAL* 4.8 3.4 - - + -
237A LYS* 2.6 38.2 - - - +
238A PHE* 3.0 49.7 + + + -
240A LEU* 2.8 27.4 - - + -
242A TYR* 2.6 32.7 + - - -
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Residues in contact with THR 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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199A THR 3.9 0.5 - - - +
200A LYS* 3.5 2.3 - - - -
201A ASP* 3.0 45.3 + - + +
219A ASP 5.1 0.3 + - - -
220A TYR* 1.3 72.0 + - - +
222A VAL* 1.3 60.6 + - - +
223A GLN 3.8 1.2 + - - -
235A PHE* 4.2 36.9 - - + +
237A LYS* 3.2 32.8 + - + +
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Residues in contact with VAL 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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198A LEU* 3.7 30.1 - - + -
199A THR 3.7 4.0 - - - +
200A LYS* 3.6 23.8 - - + +
220A TYR* 4.1 1.5 - - + -
221A THR* 1.3 71.6 - - - +
223A GLN* 1.3 75.6 - - - +
224A VAL* 3.6 2.3 + - - +
235A PHE* 3.6 1.9 - - - -
236A SER* 3.0 36.2 + - - +
238A PHE* 3.8 29.2 - - + -
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Residues in contact with GLN 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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198A LEU* 4.3 5.4 - - - +
199A THR* 3.0 36.1 + - - +
221A THR 3.8 1.2 + - - +
222A VAL* 1.3 81.8 - - - +
224A VAL* 1.3 62.4 + - - +
225A PRO* 3.3 18.3 - - - +
233A PRO* 2.6 41.0 - - - +
234A GLY 3.6 5.2 - - - +
235A PHE* 3.2 36.1 - - + -
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Residues in contact with VAL 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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222A VAL* 3.6 3.2 + - - +
223A GLN* 1.3 70.4 - - - +
225A PRO* 1.3 58.7 - - + +
226A GLY 2.5 39.9 + - - +
227A ALA* 3.1 5.8 - - + -
233A PRO* 2.9 19.5 - - - +
234A GLY* 2.6 58.7 + - - +
235A PHE* 3.4 3.1 - - - +
236A SER* 4.7 7.9 - - - +
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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