Contacts of the helix formed by residues 226 - 245 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B VAL* 4.0 34.8 - - + +
4B LYS* 4.9 1.1 - - - -
173D ILE* 4.3 24.7 - - + -
176D LYS* 3.4 51.4 - - + +
177D LEU* 4.3 16.4 - - + -
200D TRP* 3.0 33.2 - + + -
213D LEU* 4.9 8.1 - - + -
218D GLY* 4.5 6.0 - - - -
220D ASP* 3.2 44.4 + - - +
223D LYS 4.9 0.2 + - - -
224D GLN 3.6 10.0 + - - -
225D HIS* 1.3 81.1 + - - +
227D LYS* 1.3 58.9 - - - +
228D ASN* 2.8 10.2 - - - +
229D VAL* 2.7 31.3 + - + +
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Residues in contact with LYS 227 (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 TRP* 4.1 10.5 - - - +
221D LYS* 4.4 26.9 - - - +
223D LYS* 5.3 8.7 + - - +
225D HIS* 4.0 25.4 - - + +
226D TRP* 1.3 86.2 - - - +
228D ASN* 1.3 88.3 + - - +
230D HIS* 2.7 15.2 + - - +
231D LYS* 2.7 71.9 + - - +
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Residues in contact with ASN 228 (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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176D LYS* 5.8 1.8 - - - +
225D HIS* 5.4 2.7 - - + -
226D TRP 4.7 3.6 - - - +
227D LYS* 1.3 106.7 + - + +
229D VAL* 1.3 56.9 - - - +
230D HIS 2.9 1.3 - - - -
231D LYS* 3.1 24.0 - - - +
232D GLN* 2.4 54.5 + - - +
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Residues in contact with VAL 229 (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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169D PHE* 3.4 20.9 - - + +
172D LEU* 3.2 29.4 - - + +
173D ILE* 3.6 21.1 - - + +
176D LYS* 3.5 26.9 - - - +
200D TRP* 3.2 21.8 - - + -
226D TRP* 2.7 25.3 + - + +
228D ASN* 1.3 71.5 - - - +
230D HIS* 1.3 56.1 + - - +
232D GLN* 3.2 9.2 + - - +
233D VAL* 2.6 39.3 + - - +
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Residues in contact with HIS 230 (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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169D PHE* 5.0 0.6 - - - -
188D VAL* 3.7 10.1 - - + +
194D ASP 6.2 0.2 - - - -
196D SER* 2.3 51.9 + - - -
198D PRO* 3.5 34.5 - - + +
200D TRP* 4.6 4.7 - - + +
226D TRP 4.5 2.0 - - - +
227D LYS* 2.7 16.2 + - - +
229D VAL* 1.3 82.8 - - + +
231D LYS* 1.3 64.4 + - + -
233D VAL* 3.2 13.8 + - + +
234D VAL* 3.1 34.5 + - + +
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Residues in contact with LYS 231 (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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227D LYS* 2.7 76.2 + - - +
228D ASN* 2.8 17.6 + - - +
230D HIS* 1.3 77.6 - - + +
232D GLN* 1.3 57.1 + - - +
234D VAL* 3.3 10.4 - - + +
235D GLU* 3.1 35.8 + - + +
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Residues in contact with GLN 232 (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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66B HIS* 5.6 0.2 + - - -
172D LEU* 2.9 38.9 - - + +
175D GLU* 3.7 17.4 + - - -
176D LYS* 5.8 3.1 + - - +
228D ASN* 2.4 37.9 + - - +
229D VAL* 3.2 8.6 - - - +
231D LYS* 1.3 71.8 - - - +
233D VAL* 1.3 59.8 + - - +
235D GLU* 4.2 3.1 - - - +
236D GLY* 2.8 27.7 + - - -
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Residues in contact with VAL 233 (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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165D ASP* 4.2 31.8 - - + +
168D ARG* 3.9 16.0 - - + +
169D PHE* 3.7 37.2 - - + +
172D LEU* 3.4 17.5 - - + -
188D VAL* 5.0 4.5 - - + -
196D SER* 5.7 1.3 - - - -
229D VAL 2.6 26.5 + - - +
230D HIS* 3.2 22.4 + - + +
232D GLN* 1.3 70.6 - - - +
234D VAL* 1.3 72.4 + - + +
236D GLY* 2.9 16.6 + - - -
237D GLY 3.4 2.9 + - - -
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Residues in contact with VAL 234 (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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165D ASP* 5.9 2.0 - - - -
193D GLY 3.1 27.6 - - - +
194D ASP* 3.4 31.6 - - + +
196D SER* 5.3 1.8 - - - -
230D HIS* 3.1 29.4 - - + +
231D LYS* 3.3 16.4 - - + +
233D VAL* 1.3 75.6 - - + +
235D GLU* 1.3 75.8 + - + +
237D GLY* 2.7 17.3 + - - -
238D TYR* 3.9 7.8 + - + -
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Residues in contact with GLU 235 (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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231D LYS* 3.1 17.9 + - + +
232D GLN* 4.2 3.4 - - - +
234D VAL* 1.3 83.4 - - + +
236D GLY* 1.3 52.7 + - - +
237D GLY 2.8 0.5 + - - -
238D TYR* 2.6 46.0 + - + +
239D GLU* 3.1 30.9 + - + +
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Residues in contact with GLY 236 (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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66B HIS* 3.1 22.0 - - - -
168D ARG* 4.5 0.9 - - - -
232D GLN* 2.8 19.0 + - - -
233D VAL* 3.1 9.9 - - - -
234D VAL 2.8 0.4 + - - -
235D GLU* 1.3 75.1 - - - +
237D GLY* 1.3 56.9 + - - +
239D GLU* 4.2 8.4 - - - +
240D VAL* 2.8 28.1 + - - +
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Residues in contact with GLY 237 (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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168D ARG* 4.4 20.4 - - - +
233D VAL 3.4 3.0 + - - -
234D VAL 2.7 16.3 + - - -
236D GLY* 1.3 73.4 - - - -
238D TYR* 1.3 64.8 - - - +
240D VAL* 3.1 21.6 - - - +
241D LEU* 4.0 7.6 + - - +
247D THR* 5.3 5.4 + - - -
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Residues in contact with TYR 238 (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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102D GLY 5.4 3.8 - - - -
104D THR* 3.2 53.5 + - + +
105D ARG* 3.7 12.2 - - + +
193D GLY* 5.3 6.0 - - - -
194D ASP* 3.1 39.4 + - - -
234D VAL* 4.3 10.5 - - + -
235D GLU* 2.6 30.7 + - - +
237D GLY* 1.3 70.3 - - - +
239D GLU* 1.3 62.8 + - - +
240D VAL 3.0 3.4 + - - -
241D LEU* 3.1 23.0 + - + +
242D ASP* 3.2 19.7 + - - +
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Residues in contact with GLU 239 (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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62B LEU* 5.7 4.7 - - + -
235D GLU* 3.1 28.1 + - - +
236D GLY* 4.3 9.9 - - - +
238D TYR* 1.3 75.2 - - - +
240D VAL* 1.3 62.2 + - - +
242D ASP* 3.7 14.3 + - - +
243D MET* 3.1 45.9 + - + +
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Residues in contact with VAL 240 (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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59B GLY* 4.1 17.5 - - - +
62B LEU* 5.5 4.0 - - + -
63B ASP* 4.1 29.6 - - + +
66B HIS* 3.9 16.4 - - + +
168D ARG* 4.6 4.5 - - - +
236D GLY 2.8 28.5 - - - +
237D GLY* 3.1 14.1 - - - +
239D GLU* 1.3 75.4 - - - +
241D LEU* 1.3 70.0 - - + +
243D MET* 3.0 15.0 + - - +
244D LYS* 3.0 16.8 + - + +
246D TYR 3.9 14.8 - - - +
247D THR* 4.9 7.6 - - - +
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Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D MET* 3.7 25.1 - - + -
100D VAL* 4.1 3.8 - - - +
101D SER* 3.5 28.5 - - - +
102D GLY 6.0 0.2 - - - +
104D THR* 4.1 26.0 - - + +
237D GLY 4.5 7.9 - - - +
238D TYR* 3.1 16.3 + - + +
240D VAL* 1.3 76.1 - - + +
242D ASP* 1.3 82.1 + - - +
243D MET 2.6 4.3 + - - -
245D GLY* 2.7 27.5 + - - -
246D TYR* 3.5 28.9 - - - +
247D THR* 4.6 6.1 - - + +
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Residues in contact with ASP 242 (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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101D SER* 3.6 26.9 + - - +
102D GLY 4.6 1.6 + - - -
238D TYR* 3.2 19.1 + - - +
239D GLU* 3.9 19.3 - - + +
240D VAL 3.2 0.6 - - - -
241D LEU* 1.3 90.1 - - - +
243D MET* 1.3 63.6 + - + +
245D GLY* 4.4 2.1 + - - -
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Residues in contact with MET 243 (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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55B ASP* 4.3 18.2 - - - +
56B LYS* 3.7 17.5 + - - +
58B ARG* 2.9 45.1 - - + +
59B GLY* 3.4 10.8 - - - -
62B LEU* 4.2 11.9 - - + -
239D GLU* 3.1 32.8 - - + +
240D VAL* 3.0 5.8 + - - +
241D LEU 2.6 5.7 + - - -
242D ASP* 1.3 81.8 - - + +
244D LYS* 1.3 59.6 + - - +
245D GLY 3.1 5.1 + - - -
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Residues in contact with LYS 244 (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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56B LYS* 4.2 15.5 - - + +
59B GLY* 4.4 0.2 - - - -
60B GLU* 2.3 63.5 + - + +
63B ASP* 2.8 21.5 + - - +
240D VAL* 3.0 17.5 + - + +
243D MET* 1.3 74.7 - - - +
245D GLY* 1.3 60.0 + - - +
246D TYR* 3.0 61.9 + - + +
248D SER* 2.5 30.3 + - - -
249D TRP* 4.1 6.5 - - - +
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Residues in contact with GLY 245 (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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99D MET* 4.8 3.4 - - - +
241D LEU* 2.7 21.8 + - - -
242D ASP 4.6 2.2 - - - -
243D MET 3.1 1.8 - - - -
244D LYS* 1.3 79.6 - - - +
246D TYR* 1.3 71.7 + - - +
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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