Contacts of the strand formed by residues 212 - 224 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ASP* 4.3 9.7 + - - -
148B GLY* 4.6 7.0 + - - +
150B GLN* 6.0 2.2 - - - +
208B THR* 4.4 1.1 - - - -
209B VAL* 3.0 34.4 + - - +
210B ASN 3.3 3.1 - - - +
211B ASN* 1.3 78.8 - - - +
213B ALA* 1.3 82.7 + - + +
214B HIS* 2.9 33.6 + - - +
243B TYR* 3.6 20.4 + - - +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.2 19.5 - - + -
206B VAL* 4.9 5.8 - - + -
207B LEU 4.3 4.7 - - - -
208B THR* 4.5 7.7 + - - +
211B ASN 4.1 2.0 + - - -
212B LYS* 1.3 86.0 + - + +
214B HIS* 1.3 60.7 + - - +
215B MET 4.5 0.2 - - - +
243B TYR* 3.9 9.2 + - - -
244B PRO* 3.2 33.1 - - + +
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Residues in contact with HIS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PRO* 6.1 1.5 - - - +
145B ASP* 3.4 34.0 + - + +
146B SER 5.4 1.3 - - - -
148B GLY* 5.0 7.6 - - - -
207B LEU* 3.0 33.6 + - + +
209B VAL* 3.5 27.3 - - + +
212B LYS* 2.9 24.0 + - - +
213B ALA* 1.3 73.3 - - - +
215B MET* 1.3 73.3 + - + +
243B TYR* 3.9 15.4 - + - -
244B PRO* 3.9 4.0 - - - -
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Residues in contact with MET 215 (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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205B SER 4.2 0.2 - - - +
206B VAL* 3.5 6.4 - - - +
207B LEU* 3.0 51.8 + - + -
214B HIS* 1.3 92.3 - - + +
216B VAL* 1.3 68.3 + - - +
217B THR* 3.6 19.5 - - + +
241B SER* 3.3 26.9 - - - +
242B TYR 3.3 13.5 - - - +
244B PRO* 3.3 7.9 - - - +
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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
----------------------------------------------------------
177B TYR* 3.8 28.5 - - + -
180B ILE* 4.5 7.0 - - + -
181B LEU* 4.4 4.3 - - + -
204B THR* 4.5 14.4 - - + -
205B SER 4.0 2.7 - - - -
206B VAL* 4.1 14.8 - - + +
215B MET* 1.3 77.7 - - - +
217B THR* 1.3 61.2 + - - +
218B LEU* 3.4 25.4 - - + -
241B SER* 3.3 1.2 - - - -
242B TYR* 3.0 34.6 + - - +
244B PRO* 3.4 30.3 - - + -
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Residues in contact with THR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B THR 3.4 3.3 - - - +
205B SER* 3.0 50.8 + - - +
215B MET* 3.6 18.4 - - + +
216B VAL* 1.3 72.0 - - - +
218B LEU* 1.3 64.9 + - - +
219B ASP* 3.7 0.4 + - - -
239B ARG* 3.4 48.5 - - + +
240B LEU 3.7 1.3 - - - +
241B SER* 2.7 24.9 + - - +
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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
----------------------------------------------------------
175B LYS* 5.5 6.7 - - + +
177B TYR* 4.8 6.1 - - + +
180B ILE* 6.0 1.3 - - + -
186B ALA* 4.0 13.7 - - + -
202B ILE* 4.3 5.2 - - + -
203B THR 4.0 1.8 - - - -
204B THR* 3.8 18.6 - - - +
216B VAL* 3.4 24.0 - - + -
217B THR* 1.3 77.7 - - - +
219B ASP* 1.3 59.8 + - - +
220B TYR* 3.4 30.1 + - + +
239B ARG* 3.0 22.9 - - - +
240B LEU 2.9 18.1 + - - +
242B TYR* 2.9 44.0 - - + +
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ASP 3.2 7.8 - - - +
202B ILE* 3.4 0.2 - - - -
203B THR* 3.0 56.2 + - - +
205B SER* 4.5 5.4 + - - -
217B THR 5.3 0.2 - - - -
218B LEU* 1.3 69.6 - - - +
220B TYR* 1.3 63.4 + - - +
221B THR* 3.6 0.9 + - - -
237B LYS* 3.4 25.2 - - - +
239B ARG* 2.7 61.1 + - - +
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Residues in contact with TYR 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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175B LYS* 5.4 3.6 + - - -
200B LYS* 4.6 13.2 - - + -
201B ASP 3.9 3.1 - - - -
202B ILE* 3.7 33.4 - - + +
218B LEU* 3.4 30.2 + - + +
219B ASP* 1.3 71.6 - - - +
221B THR* 1.3 52.6 + - - +
222B VAL 3.6 0.4 - - - -
237B LYS* 2.6 35.4 - - - +
238B PHE* 2.9 69.6 + + + +
239B ARG* 4.9 0.2 - - - -
240B LEU* 5.2 6.7 - - + -
242B TYR* 2.6 28.7 + - - -
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Residues in contact with THR 221 (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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200B LYS* 3.5 3.6 - - - -
201B ASP* 3.0 47.4 + - + +
203B THR* 5.4 2.6 + - - -
219B ASP 4.9 1.0 + - - -
220B TYR* 1.3 69.4 - - - +
222B VAL* 1.3 62.2 + - - +
223B GLN* 3.6 0.9 + - - +
235B PHE* 3.6 31.6 - - + -
236B SER 4.0 0.7 - - - -
237B LYS* 3.4 26.6 + - + +
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 3.4 28.7 - - + -
200B LYS* 3.5 20.4 - - + -
220B TYR 3.6 0.6 - - - -
221B THR* 1.3 74.8 - - - +
223B GLN* 1.3 62.3 + - - +
224B VAL* 3.7 16.2 - - + +
235B PHE* 3.4 7.1 - - - -
236B SER* 2.6 47.3 + - - +
238B PHE* 3.2 34.8 - - + -
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Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 5.2 2.5 - - - +
199B THR* 3.1 39.4 + - - +
200B LYS* 5.3 0.4 - - - -
221B THR 3.6 1.3 + - - +
222B VAL* 1.3 75.9 - - - +
224B VAL* 1.3 62.9 + - - +
225B PRO* 3.3 7.3 - - - +
233B PRO* 2.9 37.7 - - + +
234B GLY 3.5 3.6 - - - +
235B PHE* 3.7 31.6 - - + -
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 5.0 2.5 - - + -
222B VAL* 3.6 12.7 - - + +
223B GLN* 1.3 71.5 - - - +
225B PRO* 1.3 71.6 - - + -
226B GLY 4.2 15.5 - - - +
227B ALA* 3.9 5.6 - - + -
233B PRO* 2.6 31.4 - - - +
234B GLY* 2.6 47.0 + - - +
236B SER* 4.5 14.4 - - - +
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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