Contacts of the helix formed by residues 225 - 239 (chain D) in PDB entry 1T9D
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 GLU 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D VAL* 5.0 0.2 - - - +
219D MET 4.2 3.1 - - - +
220D VAL* 3.8 11.2 - - + -
221D LYS* 3.5 26.3 + - - +
222D SER* 3.4 23.0 + - - +
224D GLU* 1.3 76.9 - - + +
226D LEU* 1.3 64.7 + - - +
227D PRO 3.3 2.5 - - - -
228D LEU* 3.3 18.8 + - + +
229D ARG* 3.0 58.6 + - + +
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Residues in contact with LEU 226 (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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94D GLY* 3.3 39.5 - - - +
97D ILE* 4.4 6.1 - - + -
98D PHE* 4.4 13.0 - - + +
220D VAL* 3.9 20.9 - - + -
222D SER 3.6 2.6 + - - -
223D VAL* 3.2 14.0 + - + +
225D GLU* 1.3 77.7 - - - +
227D PRO* 1.3 71.4 - - + +
229D ARG* 3.4 1.0 + - - -
230D ILE* 3.0 47.1 + - + +
247D VAL* 5.3 0.2 - - + -
249D LEU* 3.6 31.0 - - + -
253D VAL* 5.4 3.6 - - + -
254D THR* 5.3 6.5 - - + -
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Residues in contact with PRO 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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89D PHE* 4.2 4.7 - - + -
97D ILE* 3.8 22.9 - - + -
101D MET* 4.0 22.7 - - + -
223D VAL 3.7 9.2 - - - +
224D GLU 3.8 7.4 - - - +
225D GLU 3.5 2.9 - - - -
226D LEU* 1.3 95.3 - - + +
228D LEU* 1.3 61.6 + - - +
230D ILE* 3.3 4.1 + - + +
231D ASN* 3.0 29.6 + - - -
262D ILE* 3.9 18.4 - - + -
266D THR* 3.3 15.5 - - - +
267D THR* 4.1 9.6 - - + -
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Residues in contact with LEU 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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225D GLU* 3.3 21.0 + - + +
227D PRO* 1.3 80.4 - - - +
229D ARG* 1.3 78.4 + - - +
231D ASN* 3.3 5.7 + - + +
232D GLU* 3.0 55.9 + - + +
265D LYS 5.5 1.1 - - - +
266D THR* 3.3 41.5 + - + -
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Residues in contact with ARG 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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216D TRP* 4.1 12.7 - - - -
218D VAL* 3.9 33.0 - - + +
220D VAL* 4.0 23.6 - - + -
225D GLU* 3.0 50.7 + - - +
226D LEU 3.9 2.9 - - - +
228D LEU* 1.3 89.1 - - - +
230D ILE* 1.3 58.8 + - - +
232D GLU* 2.7 37.9 + - - +
233D ALA* 2.9 31.2 + - - +
247D VAL* 4.6 5.1 - - + +
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Residues in contact with ILE 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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98D PHE* 4.0 24.0 - - + -
101D MET* 3.8 36.3 - - + -
102D MET* 4.3 4.7 - - + -
105D GLN* 4.4 6.7 - - + -
187D PHE* 4.0 18.4 - - + -
226D LEU* 3.0 41.8 + - + +
227D PRO* 3.7 6.1 - - + +
229D ARG* 1.3 76.3 - - - +
231D ASN* 1.3 66.0 + - - +
233D ALA* 3.3 6.1 + - - +
234D PHE* 3.1 49.7 + - + -
247D VAL* 5.5 1.1 - - + -
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Residues in contact with ASN 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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101D MET* 4.8 6.6 - - - +
105D GLN* 2.8 34.6 + - - +
227D PRO 3.0 14.7 + - - +
228D LEU* 3.8 5.2 - - + +
230D ILE* 1.3 76.5 - - - +
232D GLU* 1.3 65.1 + - + +
234D PHE* 3.6 1.7 + - - +
235D GLU* 3.1 24.0 + - - +
265D LYS 5.3 0.2 + - - -
266D THR 3.0 28.9 + - - +
267D THR* 3.6 19.9 + - - +
268D LEU 3.8 5.4 + - - +
269D PRO* 3.6 19.9 - - + +
270D SER 5.7 2.1 + - - +
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Residues in contact with GLU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D TRP* 3.6 20.2 - - + -
228D LEU* 3.0 40.0 + - + +
229D ARG* 2.7 42.8 + - - +
231D ASN* 1.3 76.8 - - + +
233D ALA* 1.3 62.8 + - - +
235D GLU* 3.3 8.8 + - - +
236D ILE* 3.0 36.5 + - + +
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Residues in contact with ALA 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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185D VAL* 4.1 8.5 - - + -
216D TRP* 3.7 12.3 - - + -
229D ARG 2.9 18.4 + - - +
230D ILE* 3.4 6.5 - - - +
232D GLU* 1.3 77.1 - - - +
234D PHE* 1.3 64.1 + - - +
237D ALA* 3.0 26.5 + - - +
245D VAL* 3.5 20.4 - - + +
247D VAL* 3.7 25.6 - - + -
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Residues in contact with PHE 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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102D MET* 4.0 10.1 - - + -
105D GLN* 3.3 42.2 - - + +
107D VAL* 3.8 31.0 - - + -
156D PRO* 4.0 20.6 - - + -
158D VAL* 3.9 18.4 - - + -
185D VAL* 3.8 26.9 - - + -
187D PHE* 3.9 23.3 - + - -
230D ILE* 3.1 33.7 + - + +
231D ASN 4.2 0.4 - - - +
233D ALA* 1.3 79.5 - - - +
235D GLU* 1.3 53.7 + - - +
237D ALA* 4.1 0.6 - - - +
238D THR* 2.6 39.1 + - + +
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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 ASN 3.1 19.1 + - - +
232D GLU* 3.7 8.0 - - - +
234D PHE* 1.3 75.2 - - - +
236D ILE* 1.3 60.2 + - + +
238D THR* 3.4 5.5 + - - -
239D SER* 2.7 46.1 + - - +
270D SER* 4.3 25.1 - - - +
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Residues in contact with ILE 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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215D LYS* 2.7 53.0 + - + +
216D TRP* 3.5 42.8 - - + +
232D GLU* 3.0 25.3 + - + +
233D ALA 4.0 2.5 - - - +
235D GLU* 1.3 82.5 - - + +
237D ALA* 1.3 60.6 + - - +
238D THR 3.3 0.9 + - - -
239D SER* 3.5 8.2 + - - -
245D VAL* 3.9 16.6 - - + -
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Residues in contact with ALA 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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156D PRO* 5.2 0.7 - - + -
183D PRO* 3.5 6.8 - - + +
184D MET 3.8 20.6 - - - +
185D VAL* 4.2 8.1 - - + -
215D LYS* 4.6 0.4 - - - -
233D ALA 3.0 18.8 + - - +
234D PHE 4.1 2.9 - - - +
236D ILE* 1.3 77.3 - - - +
238D THR* 1.3 61.0 + - + +
242D PRO* 3.2 6.6 - - - +
243D GLY 3.0 43.8 + - - +
245D VAL* 3.9 9.8 - - + +
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Residues in contact with THR 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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154D GLY 6.0 0.2 - - - +
156D PRO* 4.0 38.6 - - + -
183D PRO* 4.3 7.9 - - + -
234D PHE* 2.6 23.9 + - + +
235D GLU* 3.4 7.8 + - - -
236D ILE 3.2 0.4 - - - -
237D ALA* 1.3 79.6 - - + +
239D SER* 1.3 59.7 + - - +
240D GLY 4.9 0.2 - - - +
242D PRO* 4.4 11.7 - - - +
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Residues in contact with SER 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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215D LYS* 2.9 20.1 + - - -
235D GLU* 2.7 29.2 + - - +
236D ILE* 3.5 9.9 + - - -
238D THR* 1.3 79.2 - - - +
240D GLY* 1.3 71.8 + - - +
241D ARG 3.1 5.7 + - - +
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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