Contacts of the helix formed by residues 224 - 238 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LYS* 5.0 1.0 + - - -
219A ASP* 5.2 13.1 + - - +
221A ASP* 4.7 2.4 - - - +
222A SER* 2.1 47.1 + - - +
223A GLU* 1.3 78.2 - - - +
225A TRP* 1.3 75.4 + - - +
226A LYS* 3.0 4.4 - - - +
227A GLU* 2.9 41.8 + - + +
228A VAL* 2.8 16.1 + - - +
230A LYS* 5.4 0.6 + - - -
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Residues in contact with TRP 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 3.3 32.8 - - - -
203A TRP* 4.9 3.8 - - + -
214A PRO* 4.2 27.2 + - + +
216A MET 4.1 6.3 + - - -
217A GLY 3.4 25.5 + - - -
218A THR* 3.1 18.1 - - + +
219A ASP 5.3 1.8 - - - +
221A ASP* 4.3 6.8 + - + -
223A GLU* 2.3 68.3 + - + -
224A ASN* 1.3 69.8 - - - +
226A LYS* 1.3 56.6 + - - +
228A VAL* 2.6 47.3 + - + +
229A HIS* 4.7 0.6 - - - +
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 2.4 51.3 - - + -
218A THR* 3.0 36.7 + - - +
219A ASP* 3.6 23.2 + - + +
224A ASN* 4.7 2.2 - - - +
225A TRP* 1.3 80.7 - - - +
227A GLU* 1.3 64.9 + - - +
228A VAL 2.9 1.2 + - - -
229A HIS* 3.1 15.1 + - - +
230A LYS* 3.2 17.5 + - - +
314A GLN* 5.8 4.4 - - - +
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Residues in contact with GLU 227 (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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223A GLU 4.0 3.1 - - - +
224A ASN* 2.9 45.5 + - + +
226A LYS* 1.3 75.4 - - - +
228A VAL* 1.3 54.3 + - - +
230A LYS* 2.9 30.2 - - + +
231A MET* 2.7 69.4 + - + +
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Residues in contact with VAL 228 (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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172A PHE* 4.3 16.8 - - + -
175A LEU* 4.2 21.3 - - + +
176A MET* 5.4 7.9 - - + -
179A LYS* 4.0 32.3 - - + +
224A ASN 2.8 6.1 + - - +
225A TRP* 2.6 29.3 + - + +
227A GLU* 1.3 72.3 - - - +
229A HIS* 1.3 88.2 + - + +
231A MET* 3.5 14.8 - - + +
232A VAL* 3.2 24.1 + - - +
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Residues in contact with HIS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE* 4.4 13.0 - + + -
191A ILE* 5.2 3.5 - - + +
198A SER 4.2 2.7 + - - -
199A SER* 2.5 44.4 + - - -
200A VAL* 4.1 1.3 - - + -
201A ALA* 3.8 27.3 + - + +
203A TRP* 5.8 8.3 - - + -
225A TRP 4.7 0.9 - - - +
226A LYS* 3.1 8.1 + - - +
228A VAL* 1.3 84.4 - - + +
230A LYS* 1.3 68.6 + - + +
232A VAL* 1.8 42.5 - - + +
233A VAL* 3.1 8.9 + - + +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP* 4.9 5.9 + - - -
224A ASN* 5.4 0.6 + - - -
226A LYS* 3.2 11.9 + - - +
227A GLU* 2.9 49.2 + - + +
229A HIS* 1.3 84.3 - - + +
231A MET* 1.3 86.8 + - + +
233A VAL* 2.6 22.1 + - - +
234A GLU* 2.9 13.5 + - + +
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Residues in contact with MET 231 (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 LEU* 5.3 8.7 - - + -
227A GLU* 2.7 54.5 + - + +
228A VAL* 3.5 16.4 - - + +
230A LYS* 1.3 82.4 - - + +
232A VAL* 1.3 50.5 + - - +
234A GLU* 2.8 13.8 + - + +
235A SER* 2.4 36.2 + - - -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 6.1 0.4 - - - +
171A ARG* 4.1 23.1 - - + +
172A PHE* 4.2 11.0 - - + +
175A LEU* 3.3 36.3 - - + -
228A VAL* 3.2 8.8 + - + +
229A HIS* 1.8 57.9 - - + +
231A MET* 1.3 71.5 - - - +
233A VAL* 1.3 57.4 + - + +
235A SER* 2.6 28.8 + - - -
236A ALA* 2.7 19.2 + - - +
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Residues in contact with VAL 233 (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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109A ARG* 4.2 1.7 + - - +
168A ASP* 5.2 6.5 - - - +
196A GLY* 4.4 8.1 - - - -
197A ASP* 4.2 18.8 - - - +
198A SER 5.7 1.1 - - - +
199A SER* 3.0 32.8 - - - +
229A HIS* 3.7 17.9 - - + +
230A LYS* 2.6 15.1 + - - +
232A VAL* 1.3 77.1 - - + +
234A GLU* 1.3 52.5 + - + +
236A ALA* 3.0 10.2 + - - +
237A TYR* 2.7 53.6 + - + +
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Residues in contact with GLU 234 (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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230A LYS* 2.9 10.9 + - + +
231A MET* 2.8 19.9 + - - +
233A VAL* 1.3 79.3 - - + +
235A SER* 1.3 54.4 + - - +
237A TYR* 2.5 47.2 + - + +
238A GLU* 3.0 42.2 + - - +
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Residues in contact with SER 235 (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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171A ARG* 5.2 10.2 - - - -
231A MET 2.4 23.7 + - - -
232A VAL* 2.6 27.3 + - - -
234A GLU* 1.3 67.0 - - - +
236A ALA* 1.3 62.1 + - - +
238A GLU* 4.8 5.4 + - - -
239A VAL* 3.3 24.4 - - - +
64B MET* 5.4 4.3 - - - +
68B HIS* 4.7 15.6 + - - -
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Residues in contact with ALA 236 (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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109A ARG* 3.5 23.1 + - - +
168A ASP* 5.9 3.1 - - - +
171A ARG* 3.5 32.5 - - - +
195A HIS* 5.0 0.9 - - + +
232A VAL 2.7 12.7 + - - +
233A VAL* 3.3 10.5 - - - +
235A SER* 1.3 75.4 - - - +
237A TYR* 1.3 67.0 + - - +
239A VAL* 4.9 4.0 - - - +
246A THR* 4.8 9.6 + - - -
332A LNC 3.5 15.1 - - - +
68B HIS* 6.2 0.2 - - - -
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Residues in contact with TYR 237 (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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106A GLY 5.1 4.9 - - - +
107A GLU* 3.4 51.8 - - + +
108A SER* 3.4 8.4 + - - -
109A ARG* 3.6 26.5 - - - -
197A ASP* 1.7 43.5 + - - -
233A VAL* 2.7 25.1 + - + +
234A GLU* 2.5 32.4 + - + +
236A ALA* 1.3 77.6 - - - +
238A GLU* 1.3 74.0 + - - +
239A VAL 3.4 2.3 + - - +
240A ILE* 3.3 12.4 - - - +
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Residues in contact with GLU 238 (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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106A GLY 5.6 1.1 + - - -
234A GLU* 3.0 41.4 - - - +
235A SER* 5.2 2.7 - - - -
237A TYR* 1.3 76.4 - - - +
239A VAL* 1.3 68.3 + - + +
240A ILE* 1.8 50.5 + - - +
64B MET* 5.9 1.0 - - - +
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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