Contacts of the strand formed by residues 235 - 246 (chain A) in PDB entry 3URF
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 TYR 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A THR* 4.0 13.1 + - - +
234A GLU* 1.3 78.4 - - + +
236A LEU* 1.3 65.3 - - - +
262A LYS 3.4 3.4 - - - +
263A TYR* 3.4 59.2 + + + -
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Residues in contact with LEU 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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231A LEU* 4.1 7.9 - - + -
233A THR* 3.7 32.5 - - + +
234A GLU 4.0 7.0 - - - +
235A TYR* 1.3 74.3 - - - +
237A GLN* 1.3 61.3 + - - +
238A LEU* 3.9 19.2 + - + -
261A THR* 3.2 6.2 - - - -
262A LYS* 2.8 41.0 + - + +
264A TRP* 3.4 43.1 - - + -
295A ASN* 4.0 20.4 - - - +
298A LEU* 3.9 17.7 - - + -
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Residues in contact with GLN 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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236A LEU* 1.3 73.9 - - - +
238A LEU* 1.3 55.7 + - - +
239A MET* 4.4 5.8 - - + +
260A SER 4.0 2.7 - - - -
261A THR* 4.1 18.4 - - + +
294A SER* 2.7 21.1 + - - -
295A ASN* 2.9 21.7 + - - +
93Z GLU* 3.0 27.3 - - - +
94Z ILE* 3.2 25.2 - - + +
95Z GLU* 2.8 41.8 - - - +
96Z PHE* 3.7 15.6 + - + -
98Z LEU* 4.5 7.1 - - - +
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Residues in contact with LEU 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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222A PHE* 3.9 30.7 - - + -
236A LEU* 4.0 19.1 - - + +
237A GLN* 1.3 80.4 - - - +
239A MET* 1.3 61.2 + - - +
259A GLY* 3.0 5.7 - - - -
260A SER 2.9 42.7 + - - +
262A LYS* 4.2 12.3 - - + -
264A TRP* 3.7 33.7 - - + -
273A TYR* 3.8 26.9 - - + -
275A ILE* 3.5 4.5 - - - +
294A SER* 3.5 0.7 - - - -
295A ASN* 3.9 20.0 - - + +
298A LEU* 4.3 2.9 - - + -
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Residues in contact with MET 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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222A PHE* 4.1 3.6 - - - -
237A GLN* 4.3 5.8 - - + -
238A LEU* 1.3 88.3 - - - +
240A VAL* 1.3 59.7 + - - +
241A TYR* 3.6 21.3 - - + +
257A LYS* 3.9 18.4 - - + -
258A GLY 3.1 24.2 - - - +
259A GLY* 3.9 8.5 - - - +
260A SER* 3.9 8.5 - - - +
261A THR* 6.4 0.9 - - - -
275A ILE* 3.8 4.9 - - - +
293A VAL* 3.2 27.6 - - - +
294A SER* 2.8 15.3 + - - +
94Z ILE* 3.7 22.2 - - + -
95Z GLU* 3.6 26.0 - - + -
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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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218A ALA* 4.8 3.6 - - + +
220A ILE* 3.7 28.5 - - + -
239A MET* 1.3 74.1 - - - +
241A TYR* 1.3 75.8 + - - +
242A VAL* 4.6 9.9 - - + -
257A LYS* 3.4 4.9 - - - +
258A GLY 2.7 40.2 + - - +
275A ILE* 3.6 35.0 - - + -
277A VAL* 4.4 13.2 - - + -
291A ILE* 4.1 11.4 - - + -
292A GLU 3.4 10.1 - - - +
293A VAL* 4.1 4.3 - - + -
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Residues in contact with TYR 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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181A LYS* 3.4 45.4 - - + -
239A MET* 3.6 25.1 - - + +
240A VAL* 1.3 77.5 - - - +
242A VAL* 1.3 64.1 + - - +
243A THR* 3.9 8.4 + - + +
254A THR* 4.2 23.6 - - + -
256A MET 3.4 3.8 - - - -
257A LYS* 3.8 16.6 - - + -
290A SER 3.6 0.7 - - - +
291A ILE* 3.5 4.9 - - - -
292A GLU* 2.8 53.5 + - + +
293A VAL* 5.2 1.3 - - - -
294A SER 5.2 0.9 - - - -
94Z ILE* 3.5 9.3 - - + +
95Z GLU* 2.5 43.5 + - - +
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Residues in contact with VAL 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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216A LEU* 4.8 3.6 - - + -
217A TYR 5.6 0.9 - - - +
218A ALA* 4.1 8.1 - - + -
240A VAL* 4.6 2.5 - - + -
241A TYR* 1.3 73.4 - - - +
243A THR* 1.3 56.7 + - - +
254A THR* 3.5 2.9 - - - +
255A LEU* 2.7 40.0 + - + -
256A MET* 2.8 47.4 + - + +
277A VAL* 4.0 20.2 - - + -
289A ILE* 3.5 27.1 - - + -
290A SER 3.5 4.7 - - - +
291A ILE* 3.7 20.4 - - + -
308A PHE* 5.6 1.3 - - + -
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Residues in contact with THR 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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241A TYR* 4.4 9.2 - - + +
242A VAL* 1.3 78.8 - - - +
244A LYS* 1.3 60.3 + - - +
245A THR* 4.6 1.6 + - - -
252A SER* 4.4 16.9 - - - +
253A HIS 3.3 8.7 - - - +
254A THR* 4.1 22.2 - - + +
255A LEU* 4.3 3.8 - - - -
288A GLU 3.3 0.9 - - - +
289A ILE* 3.2 9.5 - - - +
290A SER* 2.7 63.0 + - - -
292A GLU* 3.9 25.0 + - - +
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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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243A THR* 1.3 72.0 - - - +
245A THR* 1.3 68.6 + - - +
249A ILE* 6.5 0.7 - - + -
251A SER 4.2 0.9 - - - +
252A SER* 3.6 0.9 - - - -
253A HIS* 2.8 38.5 + - + +
255A LEU* 3.8 36.6 - - + +
281A PHE* 5.4 2.4 - - - +
282A LYS 3.6 17.9 + - - +
283A LEU* 3.7 15.4 - - + +
287A GLU* 3.1 42.2 - - + +
288A GLU 3.3 6.3 - - - +
289A ILE* 4.6 3.8 - - + -
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Residues in contact with THR 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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205A LYS* 4.4 17.2 + - - -
244A LYS* 1.3 79.4 + - - +
246A SER* 1.3 79.5 + - - +
249A ILE* 3.9 4.0 - - - +
250A PRO* 3.3 27.6 - - + +
251A SER 4.5 2.7 - - - +
252A SER* 3.8 14.3 - - - -
287A GLU* 3.5 4.9 - - - +
288A GLU* 2.9 43.6 + - - +
290A SER* 4.1 12.5 + - - -
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Residues in contact with SER 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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245A THR* 1.3 83.5 - - - +
247A ILE* 1.3 58.3 + - - +
248A LYS* 2.9 15.9 + - - +
249A ILE* 2.8 58.2 + - - +
250A PRO* 3.5 5.9 - - - +
286A GLY 4.1 12.6 - - - -
287A GLU* 4.5 15.9 - - - -
288A GLU* 4.1 6.1 - - - -
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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