Contacts of the helix formed by residues 219 - 230 (chain B) in PDB entry 2W8D
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 ASP 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B ALA 5.0 4.9 + - - -
216B ASP* 3.2 45.6 + - - +
217B SER 3.2 0.8 - - - -
218B SER* 1.3 79.2 + - - +
220B VAL* 1.3 60.5 + - - +
221B THR 3.3 0.8 + - - -
222B GLU* 4.2 10.7 - - - +
223B VAL* 3.6 17.0 - - - +
607B LYS* 5.2 5.0 - - + +
613B LEU* 4.1 16.5 - - + +
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASP 4.3 1.2 + - - +
217B SER 3.5 17.8 + - - +
218B SER 3.1 1.0 - - - -
219B ASP* 1.3 79.7 - - - +
221B THR* 1.3 63.7 + - - +
222B GLU 3.6 0.2 - - - -
223B VAL* 3.4 4.8 + - + +
224B GLU* 2.9 38.4 + - + +
542B LEU* 4.1 24.5 - - + -
613B LEU* 4.0 37.4 - - + +
616B PHE* 4.1 14.6 - - + +
617B TYR* 4.2 13.2 - - + -
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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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218B SER* 3.1 23.4 + - - -
219B ASP 3.3 1.4 - - - -
220B VAL* 1.3 81.6 - - - +
222B GLU* 1.3 51.5 + - - +
224B GLU* 3.1 11.2 + - - +
225B ASN* 2.7 55.4 + - - +
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B SER 4.9 0.6 + - - +
219B ASP* 4.2 12.3 - - - +
221B THR* 1.3 79.9 - - - +
223B VAL* 1.3 56.2 + - + +
225B ASN* 3.6 12.4 - - - +
226B TYR* 2.8 35.7 + - - +
604B MSE 3.5 30.5 - - - +
607B LYS* 3.9 21.2 + - - -
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Residues in contact with VAL 223 (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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219B ASP 3.6 18.4 - - - +
220B VAL* 3.4 9.0 - - - +
221B THR 3.2 0.2 - - - -
222B GLU* 1.3 77.1 - - + +
224B GLU* 1.3 57.6 + - - +
226B TYR* 3.9 0.9 - - - +
227B MSE 2.9 37.4 + - - +
542B LEU* 4.5 9.6 - - + -
604B MSE 4.2 19.9 - - + +
607B LYS* 3.9 27.8 - - + -
608B ILE* 3.5 33.0 - - + -
613B LEU* 4.2 11.9 - - + -
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Residues in contact with GLU 224 (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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220B VAL* 2.9 22.0 + - + +
221B THR* 3.4 12.5 - - - +
223B VAL* 1.3 74.5 - - - +
225B ASN* 1.3 68.2 + - - +
227B MSE 3.8 0.3 - - - +
228B LYS* 3.0 65.8 + - + +
540B ASP* 5.2 0.3 - - - +
542B LEU* 4.3 14.8 - - + +
617B TYR* 3.7 29.4 + - + -
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Residues in contact with ASN 225 (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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221B THR* 2.7 39.1 + - - +
222B GLU* 3.3 13.9 + - - +
224B GLU* 1.3 74.1 - - - +
226B TYR* 1.3 58.9 + - - +
228B LYS* 3.4 3.4 + - - +
229B ALA* 2.9 32.2 + - - +
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Residues in contact with TYR 226 (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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222B GLU 2.8 21.0 + - - +
223B VAL 3.9 3.4 - - - +
225B ASN* 1.3 70.0 - - - +
227B MSE 1.3 69.3 + - - +
229B ALA* 3.3 4.0 + - + -
230B ASN* 2.9 59.3 + - + +
596B SER 5.3 0.2 + - - -
597B LEU* 4.2 20.6 + - - +
600B LYS* 3.6 52.8 - - + +
601B GLU* 4.9 4.0 - - + -
604B MSE 3.7 30.3 - - + -
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Residues in contact with MSE 227 (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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223B VAL* 2.9 29.5 + - + +
224B GLU 3.8 3.8 - - - +
226B TYR* 1.3 76.0 - - - +
228B LYS* 1.3 60.3 + - + +
230B ASN* 3.3 3.7 + - - -
231B TYR* 3.2 26.3 + - - +
308B LEU* 4.5 0.9 - - + -
541B TYR 4.4 4.0 - - - +
542B LEU* 3.2 28.0 - - + +
543B MSE 3.2 51.6 - - - +
544B SER* 4.0 11.7 - - - +
604B MSE 5.0 13.7 - - - +
608B ILE* 3.5 26.7 - - + -
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Residues in contact with LYS 228 (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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224B GLU* 3.0 43.4 + - + +
225B ASN* 3.9 3.4 - - - +
227B MSE 1.3 74.3 - - + +
229B ALA* 1.3 63.8 + - - +
230B ASN 3.2 2.5 + - - -
231B TYR* 3.6 18.0 + - - +
539B LYS* 3.9 33.6 + - + +
540B ASP* 3.5 17.9 + - - +
541B TYR 5.4 0.2 + - - -
542B LEU* 4.8 4.4 - - - +
617B TYR* 3.3 24.0 + - - -
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Residues in contact with ALA 229 (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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225B ASN 2.9 18.6 + - - +
226B TYR* 3.9 6.1 - - + +
228B LYS* 1.3 76.3 - - - +
230B ASN* 1.3 68.0 + - - +
231B TYR 3.6 1.1 + - - +
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Residues in contact with ASN 230 (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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226B TYR* 2.9 67.2 + - + +
227B MSE 3.5 5.4 - - - +
228B LYS 3.2 0.4 - - - -
229B ALA* 1.3 86.0 - - - +
231B TYR* 1.3 61.7 + - - +
232B ASP* 3.4 15.8 + - - +
546B SER* 5.9 0.2 - - - -
597B LEU* 5.7 4.8 - - - +
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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