Contacts of the strand formed by residues 264 - 275 (chain E) 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 PHE 264 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199E ILE* 3.2 4.9 - - - +
200E TRP* 3.0 53.6 + + + +
201E SER* 4.4 1.1 - - - -
202E SER 4.7 0.2 - - - -
207E ASN* 3.9 18.6 - - - -
210E LEU* 3.7 20.9 - - + -
225E LEU* 4.0 3.8 - - + -
241E MSE 3.4 48.2 - - + -
243E SER* 3.4 22.9 - - - +
244E ASN 3.4 10.8 - - - +
245E LEU* 3.8 16.6 - - + -
249E LEU* 3.9 6.1 - - - -
263E ALA* 1.3 73.4 - - - +
265E LYS* 1.3 65.4 + - - +
266E VAL* 3.8 17.7 - - + -
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Residues in contact with LYS 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E GLY 3.5 10.1 - - - +
199E ILE* 4.3 2.2 - - + +
241E MSE 3.4 6.8 - - - +
242E SER* 2.7 43.9 + - - +
243E SER* 2.7 29.6 + - - +
246E ARG* 3.6 31.8 - - - +
249E LEU* 4.4 18.2 - - + -
264E PHE* 1.3 74.5 - - - +
266E VAL* 1.3 56.9 + - - +
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Residues in contact with VAL 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E SER* 3.9 2.2 - - - +
198E GLY* 2.8 39.4 + - - +
199E ILE 3.6 11.4 - - - +
200E TRP* 3.8 13.5 - - + +
225E LEU* 4.3 11.2 - - + -
227E PHE* 5.6 0.9 - - + -
239E ALA* 4.3 8.3 - - + -
240E GLU 3.2 11.9 - - - +
241E MSE 4.3 0.7 - - - -
242E SER* 3.7 5.5 + - - -
264E PHE* 3.8 25.1 - - + -
265E LYS* 1.3 78.6 - - - +
267E ARG* 1.3 60.4 + - - +
268E TRP* 3.8 24.2 + - + +
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Residues in contact with ARG 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E LYS* 4.5 13.3 - - - +
239E ALA* 3.4 0.8 - - - -
240E GLU* 2.8 75.8 + - - +
242E SER* 4.0 17.8 + - - +
266E VAL* 1.3 73.8 - - - +
268E TRP* 1.3 68.0 + - - +
269E ILE* 3.5 7.0 + - + +
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Residues in contact with TRP 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E ILE* 6.6 0.4 - - - -
191E VAL* 3.6 37.9 - - + -
194E SER* 3.4 20.7 + - - -
195E PHE* 3.6 45.9 - + + +
198E GLY* 5.3 1.6 - - - -
227E PHE* 3.7 33.4 - + + -
237E GLY* 4.0 26.7 - - - -
238E VAL 3.6 15.7 - - - -
239E ALA* 4.0 8.1 - - + +
266E VAL* 3.8 18.4 + - + +
267E ARG* 1.3 75.1 + - - +
269E ILE* 1.3 58.5 + - - +
270E VAL 3.7 0.9 - - - -
271E VAL* 3.6 23.1 - - + -
323E PHE* 4.2 7.4 - + - -
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Residues in contact with ILE 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ILE* 3.9 13.9 - - - +
169E PRO* 3.5 29.5 - - + +
171E TRP 5.7 0.4 - - - +
172E ILE* 4.2 19.3 - - + -
224E TYR* 3.7 18.8 - - + -
238E VAL* 2.9 14.9 + - + +
240E GLU* 3.1 46.0 - - + +
267E ARG* 4.1 7.6 - - + +
268E TRP* 1.3 76.4 - - - +
270E VAL* 1.3 75.7 + - + +
271E VAL* 5.6 0.2 - - - -
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Residues in contact with VAL 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ILE 3.7 10.8 - - - +
168E ILE* 5.1 0.4 - - - -
169E PRO* 3.9 12.3 - - + -
172E ILE* 4.0 16.2 - - + -
237E GLY* 3.1 2.6 - - - -
238E VAL* 2.8 48.5 + - + +
268E TRP* 3.7 0.5 - - - -
269E ILE* 1.3 97.8 - - + +
271E VAL* 1.3 69.5 + - - +
272E ARG* 4.2 9.0 - - + -
313E PHE* 3.8 43.1 - - + +
314E LYS* 5.7 0.2 - - + -
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Residues in contact with VAL 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E ALA* 3.4 6.2 - - - +
167E ILE* 3.1 40.4 + - + +
195E PHE* 3.9 25.4 - - + -
236E CYS 3.8 2.5 - - - -
268E TRP* 3.6 24.0 - - + -
269E ILE 5.6 0.2 - - - -
270E VAL* 1.3 78.6 - - - +
272E ARG* 1.3 65.1 + - - +
322E SER* 3.5 7.2 - - - -
323E PHE* 3.4 38.1 - - + -
324E LEU* 4.0 16.8 - - + -
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Residues in contact with ARG 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E ALA* 4.6 2.9 - - + -
168E ILE* 3.8 23.4 - - + +
235E PHE 3.7 0.9 - - - +
236E CYS* 3.0 27.5 + - - +
237E GLY* 4.2 0.6 - - - -
270E VAL* 4.1 10.6 - - + -
271E VAL* 1.3 77.1 - - - +
273E ASP* 1.3 79.4 + - - +
274E VAL* 3.7 5.1 + - + +
312E LEU 3.3 18.4 + - - -
313E PHE* 3.0 31.7 + - + +
315E TYR* 3.0 52.7 - - - +
320E VAL* 5.2 17.2 - - + +
321E GLN 3.6 13.0 - - - +
322E SER* 3.8 4.0 - - - -
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Residues in contact with ASP 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ARG* 3.3 42.7 + - - -
235E PHE 3.4 3.8 - - - -
236E CYS* 3.8 15.9 - - - +
272E ARG* 1.3 92.5 + - - +
274E VAL* 1.3 61.9 + - - +
275E HIS* 5.0 11.9 + - + -
321E GLN* 2.9 35.4 + - + +
322E SER* 3.7 17.2 + - - -
323E PHE* 4.1 2.4 + - - +
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Residues in contact with VAL 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E ARG* 3.2 3.2 - - - +
235E PHE* 2.9 34.4 + - - +
272E ARG* 4.0 6.7 - - - +
273E ASP* 1.3 79.2 - - - +
275E HIS* 1.3 67.4 + - - +
278E SER* 4.2 3.8 - - - -
279E LEU* 3.8 27.3 - - + +
312E LEU* 3.8 37.5 - - + +
313E PHE* 3.8 35.2 - - + -
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Residues in contact with HIS 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E SER 5.8 0.2 - - - -
233E GLY 3.8 7.2 - - - +
234E ARG* 3.9 34.2 + - + -
273E ASP* 5.0 10.3 + - + -
274E VAL* 1.3 79.8 - - - +
276E ASN* 1.3 56.8 + - - +
277E ARG* 3.1 47.7 + - + +
278E SER* 2.8 33.9 + - - +
279E LEU* 3.7 3.2 + - - +
321E GLN* 4.1 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
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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