Contacts of the strand formed by residues 212 - 224 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D ASP* 5.2 4.9 + - - -
148D GLY 5.2 6.4 + - - +
150D GLN* 3.4 17.1 - - - +
208D THR* 3.6 4.1 - - - -
209D VAL* 3.0 31.9 + - + +
210D ASN 4.6 2.5 - - - +
211D ASN* 1.3 80.6 - - - +
213D ALA* 1.3 68.0 + - - +
214D HIS* 2.9 21.5 + - + +
243D TYR* 2.6 35.2 + - - -
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Residues in contact with ALA 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D LEU* 3.7 36.3 - - + -
206D VAL* 4.9 5.4 - - + -
207D LEU 3.7 9.2 - - - +
208D THR* 4.4 4.7 + - - +
211D ASN 4.3 0.8 + - - -
212D LYS* 1.3 83.7 + - - +
214D HIS* 1.3 61.5 + - - +
215D MET 3.6 1.6 - - - +
243D TYR* 4.4 4.7 + - - -
244D PRO* 3.6 18.8 - - + +
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Residues in contact with HIS 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D ASP* 3.8 39.6 + - + -
146D SER* 5.2 2.8 + - - -
148D GLY* 5.0 7.4 - - - -
207D LEU* 3.0 18.0 + - + +
209D VAL* 4.2 32.7 - - + +
212D LYS* 2.9 22.8 + - + +
213D ALA* 1.3 73.2 - - - +
215D MET* 1.3 68.6 + - + +
243D TYR* 3.7 19.6 - - - -
244D PRO* 4.2 2.2 - - - -
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Residues in contact with MET 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D SER 3.6 1.1 - - - +
206D VAL* 3.5 3.5 - - - +
207D LEU* 2.8 60.5 + - + +
213D ALA 3.6 2.0 - - - -
214D HIS* 1.3 87.6 - - + +
216D VAL* 1.3 66.5 + - - +
217D THR* 3.6 18.2 - - - +
241D SER* 3.5 26.5 - - - +
242D TYR 4.0 6.5 - - - +
244D PRO* 3.6 10.9 - - - +
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D TYR* 3.9 27.1 - - + -
180D ILE* 4.9 7.9 - - + -
181D LEU* 3.9 15.0 - - + -
204D THR* 5.1 0.4 - - + -
205D SER 3.5 3.4 - - - +
206D VAL* 3.4 29.6 - - + -
215D MET* 1.3 75.7 - - - +
217D THR* 1.3 61.9 + - - +
218D LEU* 3.7 27.6 - - + -
240D LEU 3.7 1.6 - - - +
241D SER* 3.6 0.5 - - - -
242D TYR* 3.0 37.4 + - + +
244D PRO* 3.6 13.8 - - + +
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Residues in contact with THR 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D THR 3.3 3.5 - - - +
205D SER* 2.9 39.9 + - - -
215D MET* 3.6 17.6 - - - +
216D VAL* 1.3 70.0 - - - +
218D LEU* 1.3 61.8 + - - +
219D ASP* 3.9 1.6 + - - +
239D ARG* 3.3 52.4 + - + +
240D LEU 3.2 8.7 - - - +
241D SER* 2.9 26.2 + - - +
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LYS* 6.6 0.2 - - + -
177D TYR* 5.6 0.9 - - + -
180D ILE* 5.0 4.0 - - + -
186D ALA* 3.4 20.4 - - + -
202D ILE* 3.6 15.7 - - + -
203D THR 3.5 1.3 - - - -
204D THR* 3.0 38.4 - - + +
216D VAL* 3.7 24.3 + - + -
217D THR* 1.3 74.6 - - - +
219D ASP* 1.3 61.7 + - - +
220D TYR* 3.6 36.3 - - + +
239D ARG* 3.0 2.1 - - - -
240D LEU 3.0 30.3 + - - +
242D TYR* 4.6 7.6 - - + -
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Residues in contact with ASP 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ASP 3.2 6.2 - - - +
202D ILE* 3.3 0.8 - - - -
203D THR* 3.0 47.1 + - - +
205D SER* 4.9 3.6 + - - -
217D THR 3.9 4.3 - - - +
218D LEU* 1.3 70.6 - - - +
220D TYR* 1.3 62.2 + - - +
237D LYS* 3.0 36.9 - - + +
239D ARG* 2.6 59.0 + - - +
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Residues in contact with TYR 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D LYS* 3.8 19.5 - - + -
201D ASP 3.1 7.2 - - - -
202D ILE* 2.6 38.4 - - + -
218D LEU* 3.6 28.8 - - + +
219D ASP* 1.3 69.2 - - - +
221D THR* 1.3 61.1 + - - +
222D VAL 2.9 6.1 + - - -
237D LYS* 3.3 2.6 - - - -
238D PHE* 2.6 89.6 + + + -
240D LEU* 4.1 7.2 - - + -
242D TYR* 2.6 40.3 + - - -
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Residues in contact with THR 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D THR 4.3 0.2 - - - +
200D LYS* 3.1 4.6 - - - -
201D ASP* 3.0 37.9 + - - +
220D TYR* 1.3 68.5 - - - +
222D VAL* 1.3 63.7 + - - +
223D GLN 3.7 0.7 + - - -
235D PHE* 4.6 21.4 - - + -
236D SER* 4.1 8.3 - - - +
237D LYS* 2.6 59.1 + - + +
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Residues in contact with VAL 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 3.5 36.6 - - + -
199D THR 4.6 0.2 - - - +
200D LYS* 2.8 36.6 - - + -
220D TYR 2.9 12.3 + - - +
221D THR* 1.3 73.2 - - - +
223D GLN* 1.3 67.5 + - - +
224D VAL* 4.0 1.3 + - - +
235D PHE* 3.9 2.1 - - - -
236D SER* 3.0 35.6 + - - +
238D PHE* 3.7 13.0 - - + -
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Residues in contact with GLN 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 4.7 3.8 - - - +
199D THR* 2.9 49.1 + - + +
221D THR 4.9 0.2 - - - +
222D VAL* 1.3 81.2 - - - +
224D VAL* 1.3 59.0 + - - +
225D PRO* 2.9 20.8 - - - +
233D PRO* 3.2 30.8 - - + +
234D GLY 3.3 15.7 - - - +
235D PHE* 3.6 33.7 - - + -
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Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D VAL* 4.0 1.8 + - - +
223D GLN* 1.3 69.4 - - - +
225D PRO* 1.3 59.6 - - + -
226D GLY 2.5 45.7 + - - +
227D ALA* 3.2 11.0 - - + -
233D PRO* 2.7 18.0 - - - +
234D GLY 2.9 29.6 + - - +
235D PHE* 3.8 6.1 - - - +
236D SER* 5.1 6.5 - - - +
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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