Contacts of the strand formed by residues 234 - 241 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228D SER* 2.9 21.1 + - - -
229D VAL 4.2 0.3 + - - -
232D SER* 3.0 42.4 + - - +
233D GLY* 1.3 80.9 - - - +
235D PHE* 1.3 70.5 + - - +
236D CYS* 5.4 3.9 - - + +
273D ASP* 3.1 41.3 + - - -
274D VAL 3.1 18.4 - - - +
275D HIS* 3.8 24.4 + - + -
276D ASN* 3.5 8.2 + - - +
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Residues in contact with PHE 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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182D VAL* 4.1 20.0 - - + -
184D LYS* 5.6 2.5 - - + -
226D LEU* 3.6 34.5 - - + -
227D PHE 3.2 17.5 - - - +
228D SER* 3.5 17.9 - - - -
234D ARG* 1.3 81.0 - - - +
236D CYS* 1.3 61.4 + - - +
237D GLY 3.8 0.4 - - - -
272D ARG 3.6 1.1 - - - +
273D ASP* 3.4 2.8 - - - -
274D VAL 2.8 33.8 + - - +
276D ASN* 3.9 7.6 - - - -
279D LEU* 3.7 24.7 - - + -
292D VAL* 3.9 22.4 - - + -
293D THR* 4.1 23.3 - - + -
309D ILE* 6.4 0.9 - - + -
313D PHE* 3.8 19.7 - + + -
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Residues in contact with CYS 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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188D LEU* 5.0 7.4 - - + -
191D VAL* 4.1 19.1 - - - -
227D PHE* 2.8 31.9 + - - -
228D SER* 4.3 3.1 - - - -
229D VAL* 4.4 18.2 - - + +
234D ARG* 5.4 5.4 - - + +
235D PHE* 1.3 75.5 - - - +
237D GLY* 1.3 59.3 + - - +
268D TRP* 4.6 2.3 - - - -
271D VAL* 3.8 9.4 - - - +
272D ARG 3.3 25.7 + - - -
273D ASP* 4.0 14.1 - - - +
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Residues in contact with GLY 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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226D LEU* 3.6 1.4 - - - -
227D PHE* 2.8 30.3 + - - +
235D PHE 3.8 1.0 - - - -
236D CYS* 1.3 80.9 - - - +
238D VAL* 1.3 68.8 + - - +
268D TRP* 3.9 11.9 - - - -
270D VAL 3.1 13.2 - - - -
271D VAL* 4.4 0.4 - - - -
313D PHE* 3.8 14.6 - - - -
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Residues in contact with VAL 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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172D ILE* 5.9 0.9 - - + -
224D TYR* 4.1 15.3 - - + -
225D LEU 3.2 9.2 - - - +
226D LEU* 3.7 22.9 - - + -
237D GLY* 1.3 80.8 - - - +
239D ALA* 1.3 71.9 + - - +
268D TRP* 3.6 4.8 - - - -
269D ILE* 2.8 32.7 + - + -
270D VAL* 2.8 30.7 + - + +
310D LEU* 3.9 23.3 - - + -
313D PHE* 4.0 17.9 - - + -
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Residues in contact with ALA 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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224D TYR* 3.5 2.9 - - - -
225D LEU* 2.8 34.4 + - + +
227D PHE* 4.1 17.7 - - + -
238D VAL* 1.3 79.3 - - - +
240D GLU* 1.3 66.9 + - - +
266D VAL* 4.2 8.3 - - + -
267D ARG 3.2 15.3 - - - +
268D TRP* 3.8 23.8 - - + -
269D ILE* 4.2 0.9 - - - +
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Residues in contact with GLU 240 (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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222D LYS* 4.2 24.7 - - + +
223D ILE 3.4 9.0 - - - +
224D TYR* 3.9 23.6 + - + -
225D LEU* 4.5 3.6 - - - -
239D ALA* 1.3 74.4 - - - +
241D MSE 1.3 67.8 + - - +
242D SER* 5.8 0.9 - - - -
266D VAL* 3.2 9.5 - - - +
267D ARG* 2.8 69.5 + - + +
269D ILE* 3.2 35.2 - - + +
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Residues in contact with MSE 241 (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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210D LEU* 3.6 48.2 - - + +
211D SER* 5.6 0.2 - - - -
214D TYR* 3.8 30.6 - - + -
222D LYS* 4.6 14.4 + - - +
223D ILE* 3.0 34.5 + - + +
225D LEU* 3.3 37.5 - - + +
240D GLU* 1.3 80.9 - - - +
242D SER* 1.3 58.6 + - - +
243D SER 3.7 10.8 - - - +
244D ASN* 6.2 0.4 - - - -
264D PHE* 3.5 30.3 - - + -
265D LYS 3.9 2.2 - - - -
266D VAL* 4.5 2.0 - - - -
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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