Contacts of the helix formed by residues 224 - 238 (chain B) in PDB entry 5LDH
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 ASN 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B LYS* 5.1 0.4 - - - -
219B ASP* 5.2 12.9 - - - +
221B ASP* 4.7 1.8 - - - +
222B SER* 2.1 47.5 + - - +
223B GLU* 1.3 77.0 - - - +
225B TRP* 1.3 75.1 + - - +
226B LYS* 3.0 5.3 - - - +
227B GLU* 2.9 40.4 + - + +
228B VAL* 2.8 16.8 + - - +
230B LYS* 5.6 0.7 - - - -
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Residues in contact with TRP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 3.3 34.3 - - - -
203B TRP* 4.9 4.0 - - + -
214B PRO* 4.2 28.2 + - + +
216B MET 4.1 6.1 - - - -
217B GLY 3.4 24.5 + - - -
218B THR* 3.1 18.6 - - + +
219B ASP 5.3 1.8 - - - +
221B ASP* 4.3 7.9 + - + -
223B GLU* 2.3 68.5 + - + -
224B ASN* 1.3 70.2 - - - +
226B LYS* 1.3 56.5 + - - +
228B VAL* 2.6 46.8 + - + +
229B HIS* 3.4 0.9 + - - +
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Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TRP* 2.4 51.0 - - + -
218B THR* 3.0 36.4 + - - +
219B ASP* 3.6 22.8 + - + +
224B ASN* 4.7 2.0 - - - +
225B TRP* 1.3 80.5 - - - +
227B GLU* 1.3 65.6 + - - +
228B VAL 2.9 1.0 + - - -
229B HIS* 3.1 14.8 + - - +
230B LYS* 3.2 17.8 + - - +
314B GLN* 5.8 4.6 - - - +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU 4.0 3.1 - - - +
224B ASN* 2.9 44.8 + - + +
226B LYS* 1.3 76.6 - - - +
228B VAL* 1.3 54.1 + - - +
230B LYS* 2.9 30.0 - - + +
231B MET* 2.7 70.1 + - + +
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PHE* 4.3 16.6 - - + -
175B LEU* 4.2 21.9 - - + +
176B MET* 5.4 8.1 - - + -
179B LYS* 4.0 32.1 - - + +
224B ASN 2.8 5.8 + - - +
225B TRP* 2.6 28.8 + - + +
227B GLU* 1.3 72.1 - - - +
229B HIS* 1.3 88.4 + - + +
231B MET* 3.5 15.2 - - + +
232B VAL* 3.2 24.2 + - + +
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Residues in contact with HIS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PHE* 4.4 13.9 - + + -
191B ILE* 5.2 2.8 - - + +
198B SER 4.2 1.8 + - - -
199B SER* 2.5 45.0 + - - -
200B VAL* 4.1 1.1 - - - -
201B ALA* 3.8 28.1 + - + +
203B TRP* 5.8 8.5 - + + -
225B TRP 4.7 0.7 - - - +
226B LYS* 3.1 8.1 + - - +
228B VAL* 1.3 84.4 - - + +
230B LYS* 1.3 67.5 - - + +
232B VAL* 1.8 41.0 - - + +
233B VAL* 3.1 9.6 + - + +
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ASP* 4.9 5.5 + - - -
224B ASN* 5.4 0.8 + - - -
226B LYS* 3.2 10.9 + - - +
227B GLU* 2.9 47.7 + - + +
229B HIS* 1.3 83.9 - - + +
231B MET* 1.3 86.6 + - + +
233B VAL* 2.6 22.0 + - - +
234B GLU* 2.9 15.0 + - + +
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Residues in contact with MET 231 (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 LEU* 5.3 9.0 - - + -
227B GLU* 2.7 54.6 + - + +
228B VAL* 3.5 16.4 - - + +
230B LYS* 1.3 83.0 - - + +
232B VAL* 1.3 51.3 + - + +
234B GLU* 2.8 15.0 + - + +
235B SER* 2.4 35.3 + - - -
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ASP* 6.1 0.4 - - - +
171B ARG* 4.1 23.1 + - + +
172B PHE* 4.2 9.9 - - + +
175B LEU* 3.3 36.1 - - + -
228B VAL* 3.2 9.4 + - + +
229B HIS* 1.8 57.4 - - + +
231B MET* 1.3 71.9 - - - +
233B VAL* 1.3 56.7 + - + +
235B SER* 2.6 28.8 + - - -
236B ALA* 2.7 18.7 + - - +
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Residues in contact with VAL 233 (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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109B ARG* 4.2 1.1 + - - +
168B ASP* 5.2 7.0 - - - +
196B GLY* 4.4 8.7 - - - -
197B ASP* 4.2 19.5 - - - +
198B SER 5.7 0.9 - - - +
199B SER* 3.0 32.3 - - - +
229B HIS* 3.7 17.9 - - + +
230B LYS* 2.6 14.0 + - - +
232B VAL* 1.3 77.3 - - + +
234B GLU* 1.3 52.6 + - + +
236B ALA* 3.0 10.7 + - - +
237B TYR* 2.7 52.6 + - + +
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Residues in contact with GLU 234 (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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230B LYS* 2.9 10.1 + - + +
231B MET* 2.8 20.1 + - + +
233B VAL* 1.3 79.9 - - + +
235B SER* 1.3 53.3 + - - +
237B TYR* 2.5 46.7 + - + +
238B GLU* 3.0 43.1 + - - +
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Residues in contact with SER 235 (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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64A MET* 5.4 4.0 - - - +
68A HIS* 4.7 15.7 + - - -
171B ARG* 5.2 10.3 - - - -
231B MET 2.4 23.0 + - - -
232B VAL* 2.6 27.5 + - - -
234B GLU* 1.3 67.1 - - - +
236B ALA* 1.3 61.3 + - - +
238B GLU* 4.8 5.4 + - - -
239B VAL* 3.3 24.0 - - - +
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Residues in contact with ALA 236 (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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68A HIS* 6.2 0.4 - - - -
109B ARG* 3.5 22.0 - - - +
168B ASP* 5.9 2.2 - - - +
171B ARG* 3.5 32.5 - - - +
195B HIS* 5.0 1.1 - - + +
232B VAL 2.7 12.2 + - - +
233B VAL* 3.3 10.5 - - - +
235B SER* 1.3 75.2 - - - +
237B TYR* 1.3 67.5 + - - +
239B VAL* 4.9 3.6 - - - +
246B THR* 4.8 9.2 + - - -
332B LNC 3.5 15.8 - - - +
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Residues in contact with TYR 237 (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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106B GLY 5.1 4.5 - - - +
107B GLU* 3.4 50.4 - - + +
108B SER* 3.4 8.6 + - - -
109B ARG* 3.6 26.5 - - - -
197B ASP* 1.7 43.1 + - - -
233B VAL* 2.7 25.3 + - + +
234B GLU* 2.5 32.2 + - + +
236B ALA* 1.3 76.5 - - - +
238B GLU* 1.3 73.4 + - - +
239B VAL 3.4 2.1 + - - +
240B ILE* 3.3 12.5 - - - +
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Residues in contact with GLU 238 (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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64A MET* 5.9 0.7 - - - +
106B GLY 5.6 1.3 + - - -
234B GLU* 3.0 43.1 - - - +
235B SER* 4.7 3.1 - - - +
237B TYR* 1.3 76.6 - - - +
239B VAL* 1.3 70.1 + - + +
240B ILE* 1.8 50.0 + - - +
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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