Contacts of the strand formed by residues 234 - 246 (chain A) in PDB entry 4U8T
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 ARG 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A LEU* 6.3 0.8 - - - +
228A SER* 3.0 22.5 + - - -
229A VAL 4.2 0.2 + - - -
232A SER* 3.4 37.8 + - - +
233A GLY* 1.3 80.1 - - - +
235A PHE* 1.3 69.6 + - - +
236A CYS* 5.3 4.7 - - + +
273A ASP* 3.0 41.6 + - - -
274A VAL 3.1 18.2 - - - +
275A HIS* 4.0 19.1 + - + -
276A ASN* 3.5 9.2 + - - +
321A GLN* 5.1 4.0 + - - -
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Residues in contact with PHE 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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182A VAL* 4.0 20.2 - - + -
184A LYS* 5.5 2.5 - - - -
226A LEU* 3.8 33.2 - - + -
227A PHE 3.2 17.7 - - - +
228A SER* 3.7 18.6 - - - -
234A ARG* 1.3 82.0 - - - +
236A CYS* 1.3 61.4 + - - +
237A GLY 3.8 0.4 - - - -
272A ARG 4.2 0.7 - - - -
273A ASP* 3.4 3.1 - - - -
274A VAL* 2.9 33.0 + - + +
276A ASN* 3.9 11.9 - - - -
279A LEU* 3.6 26.7 - - + -
292A VAL* 3.9 23.8 - - + -
293A THR* 4.2 14.6 - - - -
309A ILE* 6.3 1.1 - - + -
313A PHE* 3.7 20.2 - + + -
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Residues in contact with CYS 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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188A LEU* 4.8 2.7 - - + -
191A VAL* 4.1 9.4 - - - -
227A PHE* 2.8 30.0 + - - -
228A SER* 4.4 2.0 - - - -
229A VAL* 4.4 19.7 - - + +
234A ARG* 5.3 5.6 - - + +
235A PHE* 1.3 74.8 - - - +
237A GLY* 1.3 58.7 + - - +
271A VAL* 4.0 0.2 - - - -
272A ARG 3.2 26.3 + - - -
273A ASP* 3.9 14.6 - - - +
323A PHE* 3.6 38.2 - - + -
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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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226A LEU* 3.7 1.6 - - - -
227A PHE 3.0 26.4 + - - -
236A CYS* 1.3 81.6 - - - +
238A VAL* 1.3 68.5 - - - +
268A TRP* 4.0 11.7 - - - -
270A VAL 3.3 15.0 - - - -
272A ARG 3.7 2.7 + - - -
313A PHE* 3.7 14.1 - - - -
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Residues in contact with VAL 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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172A ILE* 5.6 0.7 - - + -
224A TYR* 4.2 17.5 - - + -
225A LEU 3.3 8.7 - - - +
226A LEU* 3.9 17.3 - - + -
237A GLY* 1.3 80.2 - - - +
239A ALA* 1.3 69.5 + - - +
268A TRP* 3.7 5.6 - - - -
269A ILE* 3.0 31.3 + - + -
270A VAL* 3.0 33.8 + - + +
310A LEU* 4.1 11.7 - - + -
313A PHE* 3.8 29.6 - - + -
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Residues in contact with ALA 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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224A TYR* 3.4 4.5 - - - +
225A LEU* 2.7 37.4 + - + +
227A PHE* 3.9 22.6 - - + -
238A VAL* 1.3 78.2 - - - +
240A GLU* 1.3 66.1 + - - +
266A VAL* 4.3 7.2 - - + -
267A ARG 3.5 12.8 - - - +
268A TRP* 4.0 20.9 - - + +
269A ILE* 4.4 1.1 - - - +
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Residues in contact with GLU 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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222A LYS* 3.0 47.4 + - + +
223A ILE 3.3 8.5 - - - +
224A TYR* 4.1 14.3 + - + -
225A LEU* 4.8 1.6 - - - -
239A ALA* 1.3 74.4 - - - +
241A MSE 1.3 68.0 + - - +
266A VAL* 3.1 9.2 - - - +
267A ARG* 2.9 58.3 + - + +
269A ILE* 3.5 32.3 - - + +
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Residues in contact with MSE 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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210A LEU* 4.0 31.6 - - + +
211A SER* 4.8 2.7 - - - +
214A TYR* 3.8 33.1 - - + -
222A LYS* 5.6 3.5 - - - +
223A ILE* 3.0 48.8 + - + +
225A LEU* 4.1 8.1 - - + -
240A GLU* 1.3 83.0 - - - +
242A SER* 1.3 60.0 + - - +
243A SER 3.5 22.7 - - - +
244A ASN* 4.8 3.6 - - - -
245A LEU 5.3 0.2 - - - +
264A PHE* 3.6 42.6 - - + -
265A LYS 3.7 4.3 - - - -
266A VAL* 4.5 0.7 - - - +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TYR* 3.7 9.0 + - - -
241A MSE 1.3 76.5 - - - +
243A SER* 1.3 62.7 + - - +
246A ARG* 5.4 0.9 + - - -
265A LYS* 2.8 35.7 + - - +
266A VAL* 3.5 6.8 + - - -
267A ARG* 3.7 41.9 - - - +
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Residues in contact with SER 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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214A TYR* 3.4 17.2 + - - -
241A MSE 3.5 20.1 - - - +
242A SER* 1.3 84.9 + - - +
244A ASN* 1.3 79.9 + - - +
246A ARG* 4.1 21.9 + - - +
264A PHE* 3.6 4.0 - - - +
265A LYS* 2.8 39.1 + - - +
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Residues in contact with ASN 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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211A SER* 2.8 40.7 + - - -
214A TYR* 3.3 29.6 - - + -
215A GLU* 4.1 19.2 + - - +
241A MSE 4.8 1.3 - - - -
243A SER* 1.3 92.8 + - - +
245A LEU* 1.3 83.2 + - - +
246A ARG* 3.5 5.6 + - - +
264A PHE* 3.4 5.6 - - - +
285C PRO* 3.4 18.7 - - + +
302C PRO* 5.4 3.2 - - - +
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Residues in contact with LEU 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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207A ASN* 3.8 43.7 - - + +
211A SER* 4.6 3.4 - - - +
241A MSE 5.3 0.6 - - - +
244A ASN* 1.3 89.0 + - - +
246A ARG* 1.3 59.8 + - - +
262A HIS* 3.9 8.1 - - + -
263A ALA* 3.6 21.8 - - - +
264A PHE* 3.6 29.0 - - + +
285C PRO* 3.5 29.8 - - + +
288C ASP* 5.4 3.1 - - - +
289C MSE 3.4 37.8 - - + +
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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 SER 5.4 1.0 + - - -
243A SER* 4.1 18.9 - - - +
244A ASN 3.7 8.7 - - - +
245A LEU* 1.3 79.1 - - - +
247A GLU* 1.3 62.8 + - - +
248A ASP* 3.3 30.0 + - - +
249A LEU* 4.2 16.1 - - + +
262A HIS* 3.7 10.4 - - - +
263A ALA 3.0 28.5 + - - +
265A LYS* 3.1 38.2 - - - +
289C MSE 3.8 8.0 - - - +
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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
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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