Contacts of the helix formed by residues 234 - 253 (chain A) in PDB entry 1YRT
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 ASP 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A LEU* 4.4 8.0 - - - +
233A LEU* 1.3 72.3 + - - +
235A ARG* 1.4 60.7 + - - +
236A GLU* 3.2 17.4 + - - +
237A ARG* 3.2 37.0 + - + +
238A ILE* 3.1 27.0 + - - +
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Residues in contact with ARG 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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233A LEU* 3.7 29.3 - - + +
234A ASP* 1.4 70.4 + - - +
236A GLU* 1.3 67.0 + - + +
238A ILE* 3.5 8.6 + - + +
239A ASP* 3.1 22.3 + - - +
127B GLU* 3.6 31.5 + - - +
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Residues in contact with GLU 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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219A LEU* 4.6 13.1 - - + +
223A ARG* 3.5 39.0 + - - +
234A ASP* 3.2 10.2 + - - +
235A ARG* 1.3 77.6 - - + +
237A ARG* 1.3 58.1 + - - +
239A ASP* 3.3 7.1 + - - +
240A LEU* 2.9 30.5 + - + +
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Residues in contact with ARG 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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215A VAL* 4.3 11.0 - - + +
216A THR* 4.1 17.8 + - - +
219A LEU* 3.6 28.1 - - + +
234A ASP* 3.2 34.6 + - + +
235A ARG 3.2 0.4 - - - -
236A GLU* 1.3 76.5 - - - +
238A ILE* 1.3 63.1 + - + +
239A ASP 3.0 1.8 - - - -
240A LEU* 3.0 5.9 + - - +
241A LEU* 2.8 60.4 + - - +
114B GLU* 5.0 3.2 + - - -
116B LEU* 4.0 12.7 - - - +
120B GLU* 2.6 32.3 + - - +
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Residues in contact with ILE 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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233A LEU* 4.7 3.6 - - - +
234A ASP* 3.1 26.4 + - + +
235A ARG* 3.5 8.3 + - + +
237A ARG* 1.3 81.8 - - + +
239A ASP* 1.3 59.5 + - - +
241A LEU* 3.3 13.7 + - + +
242A TRP* 3.0 30.9 + - + -
120B GLU* 4.9 1.8 - - + +
123B GLU* 3.3 43.1 - - + +
124B MET* 3.8 26.9 - - + -
127B GLU* 3.6 29.8 - - + -
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG 3.1 16.1 + - - +
236A GLU* 3.4 7.9 - - - +
237A ARG 3.0 0.6 - - - -
238A ILE* 1.3 83.7 - - - +
240A LEU* 1.3 57.7 + - - +
242A TRP* 3.3 6.3 + - - +
243A LYS* 2.6 61.1 + - - +
127B GLU* 4.8 9.3 - - - +
144B MET* 4.3 17.8 - - - +
147B ALA* 5.5 4.0 - - - +
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Residues in contact with LEU 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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209A VAL* 4.0 24.0 - - + +
210A THR* 5.7 1.8 - - - +
215A VAL* 4.5 15.7 - - + +
218A TYR* 3.4 40.2 - - + -
219A LEU* 3.7 26.9 - - + -
236A GLU* 2.9 13.3 + - + +
237A ARG* 3.0 8.0 + - - +
239A ASP* 1.3 73.4 - - - +
241A LEU* 1.3 61.6 + - - +
243A LYS* 3.0 17.2 + - + +
244A ILE* 2.8 35.0 + - + +
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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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215A VAL* 3.9 16.2 - - + -
237A ARG* 2.8 48.1 + - - +
238A ILE* 3.6 15.5 - - + +
239A ASP 3.3 0.2 - - - -
240A LEU* 1.3 77.2 - - - +
242A TRP* 1.3 62.3 + - - +
244A ILE* 3.1 8.1 + - - +
245A ALA* 3.0 22.0 + - - +
109B MET* 3.8 9.1 - - + +
114B GLU* 3.7 37.7 - - + +
116B LEU* 4.0 20.6 - - + -
120B GLU* 4.7 2.0 - - + +
124B MET* 3.8 20.2 - - + -
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Residues in contact with TRP 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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238A ILE* 3.0 33.7 + - + +
239A ASP* 3.7 8.5 - - - +
240A LEU 3.3 0.2 - - - -
241A LEU* 1.3 77.3 - - - +
243A LYS* 1.3 59.4 + - + +
245A ALA* 3.3 9.2 + - + +
246A ARG* 3.0 29.8 + - - +
92B PHE* 3.8 26.0 - + - -
100B ILE* 5.6 2.5 - - + -
105B LEU* 4.0 28.7 - - + -
124B MET* 2.9 41.4 + - + +
125B ILE 4.7 0.2 - - - -
127B GLU* 4.1 6.8 - - - +
128B ALA* 3.9 15.7 - - + -
136B VAL* 4.7 16.6 - - + -
141B PHE* 4.9 7.0 - + - -
144B MET* 3.7 47.0 - - + -
145B MET* 4.5 9.0 - - + +
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Residues in contact with LYS 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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209A VAL* 3.3 29.3 - - + +
239A ASP* 2.6 45.0 + - - +
240A LEU* 3.0 29.6 + - + +
242A TRP* 1.3 78.3 - - + +
244A ILE* 1.3 60.9 + - - +
246A ARG* 3.8 10.8 - - - +
247A ALA* 3.1 17.5 + - - +
147B ALA* 4.5 18.3 + - - +
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Residues in contact with ILE 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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205A ALA* 3.7 17.8 - - + +
206A ARG* 5.7 8.5 - - + +
209A VAL* 4.2 21.1 - - + -
210A THR* 5.4 4.7 - - - +
215A VAL* 3.7 20.0 - - + -
240A LEU* 2.8 20.4 + - + +
241A LEU* 3.1 10.0 + - - +
243A LYS* 1.3 76.2 - - - +
245A ALA* 1.3 63.0 + - - +
247A ALA* 3.3 1.6 + - - -
248A GLY* 2.8 27.0 + - - -
109B MET* 3.5 15.5 - - + -
112B LEU* 3.4 43.2 - - + +
114B GLU* 4.3 7.2 - - + +
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Residues in contact with ALA 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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241A LEU 3.0 11.3 + - - +
242A TRP* 3.6 13.5 - - + +
244A ILE* 1.3 77.3 - - - +
246A ARG* 1.3 64.1 + - - +
248A GLY* 3.3 0.9 + - - -
249A ALA* 3.0 25.3 + - - +
92B PHE* 3.6 30.3 - - + -
108B VAL* 4.4 1.5 - - + +
109B MET* 3.6 22.0 - - - -
112B LEU* 3.8 14.3 - - - +
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Residues in contact with ARG 246 (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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242A TRP 3.0 14.1 + - - +
243A LYS* 3.8 9.9 - - - +
245A ALA* 1.3 79.0 - - - +
247A ALA* 1.3 68.1 + - - +
249A ALA* 3.3 2.1 + - - +
250A ARG* 3.0 69.4 + - - +
80B ASP* 4.5 7.1 + - - -
92B PHE* 4.2 2.9 - - - -
144B MET 5.4 1.6 - - - -
145B MET* 3.3 64.5 + - + +
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Residues in contact with ALA 247 (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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205A ALA* 3.9 16.4 - - - +
208A SER* 4.1 11.7 - - - +
209A VAL* 3.6 20.2 - - + -
243A LYS 3.1 15.8 + - - +
244A ILE 3.3 3.1 + - - +
246A ARG* 1.3 88.8 - - + +
248A GLY* 1.3 64.5 + - - +
250A ARG* 3.4 6.3 + - - +
251A SER* 2.9 25.3 + - - -
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Residues in contact with GLY 248 (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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198A LEU* 4.3 2.2 - - - +
201A PHE* 3.8 5.8 - - - +
205A ALA* 3.6 14.7 - - - +
244A ILE 2.8 20.0 + - - -
245A ALA 3.8 0.9 - - - -
247A ALA* 1.3 73.4 - - - +
249A ALA* 1.3 55.8 + - - +
251A SER* 3.1 8.0 + - - -
252A ALA* 2.8 30.5 + - - +
112B LEU* 3.9 18.8 - - - -
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Residues in contact with ALA 249 (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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198A LEU* 5.0 0.2 - - - -
245A ALA 3.0 10.0 + - - +
246A ARG* 3.8 4.0 - - - +
248A GLY* 1.3 75.3 - - - +
250A ARG* 1.3 58.8 + - - +
252A ALA* 3.2 4.2 + - - +
253A VAL* 3.1 32.1 + - - +
88B ALA* 3.9 23.1 - - + +
91B VAL* 4.0 20.2 - - + +
92B PHE* 3.5 32.1 - - + -
108B VAL* 6.4 0.2 - - + -
112B LEU* 4.8 1.0 - - - +
145B MET* 6.1 0.2 - - - -
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Residues in contact with ARG 250 (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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246A ARG* 3.0 66.5 + - + +
247A ALA* 3.8 5.2 - - - +
249A ALA* 1.3 74.1 - - - +
251A SER* 1.3 60.0 + - - +
254A GLY* 3.0 5.4 + - - -
255A THR* 3.0 50.1 + - - +
256A GLU* 2.7 44.7 + - + +
259A ARG* 4.3 3.2 - - - +
80B ASP* 2.7 40.2 + - - +
88B ALA* 4.6 13.9 - - + -
145B MET* 5.3 3.4 - - - -
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Residues in contact with SER 251 (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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201A PHE* 3.2 30.3 - - - +
204A SER* 3.5 24.9 - - - -
247A ALA 2.9 14.9 + - - -
248A GLY* 3.1 9.5 + - - -
250A ARG* 1.3 74.8 - - - +
252A ALA* 1.3 69.1 + - - +
254A GLY* 3.0 13.5 + - - +
273A THR* 5.1 3.6 - - - -
275A PHE* 5.6 1.0 + - - +
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Residues in contact with ALA 252 (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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196A PRO* 4.2 10.2 - - - +
198A LEU* 4.1 5.2 - - + -
201A PHE* 3.6 35.7 - - + -
248A GLY 2.8 18.8 + - - +
249A ALA* 3.3 8.5 - - - +
251A SER* 1.3 78.9 + - - +
253A VAL* 1.3 59.8 + - - +
254A GLY 3.3 0.6 + - - -
273A THR* 5.0 4.5 + - - +
275A PHE* 5.7 0.9 - - - +
343A VAL* 4.0 26.0 - - + +
345A TYR* 4.9 5.0 - - - -
91B VAL* 4.6 1.3 - - + -
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Residues in contact with VAL 253 (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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249A ALA 3.1 10.0 + - - +
252A ALA* 1.3 76.3 - - - +
254A GLY* 1.3 64.2 + - - +
255A THR* 3.3 9.0 - - - +
258A ARG* 2.9 38.5 + - - +
273A THR* 3.6 7.1 - - - +
343A VAL* 3.7 25.6 - - + -
344A PHE 5.0 0.9 - - - +
345A TYR* 3.5 31.2 - - + -
87B GLU* 3.8 22.7 - - + +
88B ALA* 5.3 1.3 - - - +
91B VAL* 3.9 17.0 - - + -
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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
------------------------------------------------------------
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