Contacts of the helix formed by residues 226 - 245 (chain A) in PDB entry 2LDX
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 TRP 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ILE* 4.3 24.7 - - + -
176A LYS* 3.4 52.0 - - + +
177A LEU* 4.3 15.9 - - + -
200A TRP* 3.0 34.4 - + + -
213A LEU* 4.9 9.2 - - + -
218A GLY* 4.5 5.8 - - - -
220A ASP* 3.2 44.7 + - - +
223A LYS 4.9 0.2 + - - -
224A GLN 3.6 10.0 + - - -
225A HIS* 1.3 80.4 + - - +
227A LYS* 1.3 59.7 - - - +
228A ASN* 2.8 9.8 - - - +
229A VAL* 2.7 30.0 + - + +
3C VAL* 4.0 36.3 - - + +
4C LYS* 4.9 1.6 - - - -
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Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TRP* 4.1 10.7 - - - +
221A LYS* 4.5 26.9 - - - +
223A LYS* 5.3 8.5 + - - +
225A HIS* 4.0 25.5 - - + +
226A TRP* 1.3 86.8 - - - +
228A ASN* 1.3 89.8 + - - +
230A HIS* 2.7 15.1 + - - +
231A LYS* 2.7 70.5 + - - +
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Residues in contact with ASN 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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176A LYS* 5.8 1.8 - - - +
225A HIS* 5.4 2.5 - - + -
226A TRP 4.7 4.0 - - - +
227A LYS* 1.3 107.3 + - + +
229A VAL* 1.3 58.1 - - - +
230A HIS 2.9 1.8 - - - -
231A LYS* 3.1 24.5 - - - +
232A GLN* 2.4 52.2 + - - +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 3.4 20.9 - - + +
172A LEU* 3.2 29.5 - - + +
173A ILE* 3.6 20.0 - - + +
176A LYS* 3.5 27.9 - - - +
200A TRP* 3.2 21.8 - - + -
226A TRP* 2.7 26.1 + - + +
228A ASN* 1.3 71.8 - - - +
230A HIS* 1.3 55.7 + - - +
232A GLN* 3.2 8.8 + - - +
233A VAL* 2.6 39.7 + - - +
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Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 5.0 0.9 - - + -
188A VAL* 3.7 9.6 - - + +
194A ASP 5.9 0.2 + - - -
196A SER* 2.3 53.0 + - - -
198A PRO* 3.5 35.4 - - + +
200A TRP* 4.6 4.9 - - + +
226A TRP 4.5 1.3 - - - +
227A LYS* 2.7 16.4 + - + +
229A VAL* 1.3 81.9 - - + +
231A LYS* 1.3 64.1 + - + -
233A VAL* 3.2 13.4 + - + +
234A VAL* 3.1 33.4 + - + +
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Residues in contact with LYS 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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227A LYS* 2.7 77.5 + - - +
228A ASN* 2.8 17.7 + - - +
230A HIS* 1.3 77.6 - - + +
232A GLN* 1.3 56.7 + - - +
234A VAL* 3.3 10.4 - - + +
235A GLU* 3.1 35.9 + - + +
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Residues in contact with GLN 232 (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 LEU* 2.9 39.0 - - + +
175A GLU* 3.7 17.8 + - - -
176A LYS* 5.8 2.7 + - - +
228A ASN* 2.4 37.8 + - - +
229A VAL* 3.2 8.6 - - - +
231A LYS* 1.3 72.0 - - - +
233A VAL* 1.3 57.2 - - - +
235A GLU* 4.2 3.1 - - - +
236A GLY* 2.8 30.5 + - - -
66C HIS* 5.6 0.3 + - - -
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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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165A ASP* 4.2 31.4 - - + +
168A ARG* 3.9 15.4 + - + +
169A PHE* 3.7 36.3 - - + +
172A LEU* 3.4 16.6 - - + -
188A VAL* 5.0 3.1 - - + -
196A SER* 5.7 1.6 - - - -
229A VAL 2.6 26.3 + - - +
230A HIS* 3.3 22.9 - - + +
232A GLN* 1.3 71.3 - - - +
234A VAL* 1.3 71.7 + - + +
236A GLY* 2.9 16.3 + - - -
237A GLY 3.4 2.9 + - - -
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Residues in contact with VAL 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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165A ASP* 5.9 1.8 - - - -
193A GLY 3.1 27.6 - - - +
194A ASP* 3.4 30.3 - - + +
196A SER* 5.3 2.7 - - - -
230A HIS* 3.1 30.7 - - + +
231A LYS* 3.3 16.4 - - + +
233A VAL* 1.3 74.7 - - + +
235A GLU* 1.3 74.8 + - + +
237A GLY* 2.7 18.2 + - - -
238A TYR* 3.9 7.1 + - + -
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Residues in contact with GLU 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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231A LYS* 3.1 17.6 + - + +
232A GLN* 4.2 4.0 - - - +
234A VAL* 1.3 82.3 - - + +
236A GLY* 1.3 51.8 + - - +
237A GLY 2.8 0.3 + - - -
238A TYR* 2.6 44.8 + - + +
239A GLU* 3.1 30.8 + - + +
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Residues in contact with GLY 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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168A ARG* 4.5 1.1 - - - -
232A GLN 2.8 17.7 + - - -
233A VAL 2.9 10.3 + - - -
234A VAL 2.8 0.6 + - - -
235A GLU* 1.3 74.8 - - - +
237A GLY* 1.3 57.9 - - - +
239A GLU* 4.2 8.0 - - - +
240A VAL* 2.8 27.5 + - - +
66C HIS* 3.1 23.3 - - - -
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Residues in contact with GLY 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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168A ARG* 4.4 19.9 - - - +
233A VAL 3.4 3.0 + - - -
234A VAL 2.7 17.0 + - - -
236A GLY* 1.3 73.4 - - - -
238A TYR* 1.3 64.7 + - - +
240A VAL* 3.1 21.9 - - - +
241A LEU* 4.0 8.1 + - - +
247A THR* 5.3 5.0 + - - -
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Residues in contact with TYR 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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102A GLY 5.4 3.4 - - - -
104A THR* 3.1 55.0 + - + +
105A ARG* 3.7 12.3 - - + +
193A GLY* 5.3 5.1 - - - -
194A ASP* 3.1 39.6 + - - -
234A VAL* 4.3 10.1 - - + -
235A GLU* 2.6 31.6 + - - +
237A GLY* 1.3 70.0 - - - +
239A GLU* 1.3 62.3 + - - +
240A VAL 3.0 3.5 + - - -
241A LEU* 3.1 22.4 + - + +
242A ASP* 3.2 19.9 + - - +
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Residues in contact with GLU 239 (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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235A GLU* 3.1 28.8 + - - +
236A GLY* 4.4 9.2 - - - +
237A GLY 3.6 0.2 - - - -
238A TYR* 1.3 74.3 - - - +
240A VAL* 1.3 61.7 + - - +
242A ASP* 3.7 15.1 + - - +
243A MET* 3.1 44.8 + - + +
62C LEU* 5.7 5.2 - - + -
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Residues in contact with VAL 240 (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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168A ARG* 4.6 4.3 - - - +
236A GLY 2.8 28.9 - - - +
237A GLY* 3.1 13.9 - - - +
239A GLU* 1.3 75.6 - - - +
241A LEU* 1.3 69.3 + - + +
243A MET* 3.0 15.1 + - - +
244A LYS* 3.0 17.5 + - + +
246A TYR 3.9 14.1 - - - +
247A THR* 4.9 8.5 - - - +
59C GLY* 4.1 16.6 - - - +
62C LEU* 5.5 4.0 - - + -
63C ASP* 4.1 28.7 - - + +
66C HIS* 3.9 15.9 - - + +
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Residues in contact with LEU 241 (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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99A MET* 3.7 25.6 - - + -
100A VAL* 4.1 4.0 - - - +
101A SER* 3.5 29.2 - - - +
104A THR* 4.1 26.0 - - + +
237A GLY 4.0 7.8 + - - +
238A TYR* 3.1 16.3 + - + +
240A VAL* 1.3 76.3 - - + +
242A ASP* 1.3 81.5 + - - +
243A MET 2.6 3.6 + - - -
245A GLY* 2.7 28.0 + - - -
246A TYR* 3.5 28.9 - - - +
247A THR* 4.6 6.1 - - + +
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Residues in contact with ASP 242 (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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101A SER* 3.6 26.8 + - - +
102A GLY 4.6 1.7 + - - -
238A TYR* 3.2 18.8 + - - +
239A GLU* 3.9 19.2 - - + +
240A VAL 3.2 0.8 - - - -
241A LEU* 1.3 89.5 - - - +
243A MET* 1.3 63.7 + - + +
245A GLY* 4.4 2.3 + - - -
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Residues in contact with MET 243 (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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239A GLU* 3.1 31.0 - - + +
240A VAL* 3.0 5.3 + - - +
241A LEU 2.6 5.1 + - - -
242A ASP* 1.3 80.5 - - + +
244A LYS* 1.3 61.2 + - - +
245A GLY 3.1 4.3 - - - -
55C ASP* 4.3 18.6 - - - +
56C LYS* 3.7 17.3 + - - +
58C ARG* 2.9 45.1 - - + +
59C GLY* 3.4 11.4 - - - -
62C LEU* 4.1 12.6 - - + -
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Residues in contact with LYS 244 (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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240A VAL* 3.0 17.7 + - + +
243A MET* 1.3 74.4 - - - +
245A GLY* 1.3 60.2 + - - +
246A TYR* 3.0 61.3 + - + +
248A SER* 2.5 29.8 + - - -
249A TRP* 4.1 6.3 - - - +
56C LYS* 4.2 14.8 - - + +
60C GLU* 2.3 63.8 + - + +
63C ASP* 2.8 21.3 + - - +
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Residues in contact with GLY 245 (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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99A MET* 4.8 3.8 - - - +
241A LEU* 2.7 23.1 + - - -
242A ASP 4.6 2.2 - - - -
243A MET 3.1 2.1 - - - -
244A LYS* 1.3 80.5 - - - +
246A TYR* 1.3 72.4 + - - +
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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