Contacts of the strand formed by residues 223 - 229 (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 ILE 223 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D ARG* 3.3 9.6 - - + +
181D PHE* 3.8 23.8 - - + -
210D LEU 4.3 3.1 - - - +
213D ALA* 3.4 21.1 - - + +
214D TYR* 3.4 39.2 - - + +
217D LEU* 3.5 20.2 - - + +
222D LYS* 1.3 76.5 - - - +
224D TYR* 1.3 63.7 + - - +
225D LEU* 3.9 4.8 - - + +
240D GLU* 3.4 3.2 - - - -
241D MSE 3.0 63.3 + - + +
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Residues in contact with TYR 224 (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* 4.6 10.6 - - + +
173D HIS 3.4 10.7 + - - -
174D VAL* 3.7 24.8 - - + +
175D PRO* 3.3 21.5 - - - +
178D SER* 3.8 14.8 - - - -
179D ARG 3.1 9.3 + - - -
180D PHE* 3.5 32.7 - + + -
181D PHE 2.9 27.0 + - - +
222D LYS* 3.9 12.7 - - + +
223D ILE* 1.3 76.0 - - - +
225D LEU* 1.3 64.2 + - - +
226D LEU* 4.6 10.0 - - + +
238D VAL* 4.1 16.8 - - + -
239D ALA 3.5 1.8 - - - +
240D GLU* 3.9 31.4 + - + -
269D ILE* 4.0 8.7 - - + -
310D LEU* 4.7 6.3 - - + -
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Residues in contact with LEU 225 (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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181D PHE* 3.5 13.0 - - + -
183D ILE* 3.8 22.0 - - + -
200D TRP* 5.2 0.4 - - + -
210D LEU* 4.3 0.7 - - + -
223D ILE* 3.9 7.4 - - + +
224D TYR* 1.3 80.1 - - - +
226D LEU* 1.3 63.8 + - - +
227D PHE* 3.7 23.4 - - + -
237D GLY 3.7 0.2 - - - +
238D VAL* 3.2 6.4 - - - -
239D ALA 2.8 38.5 + - - +
240D GLU 4.5 0.4 - - - -
241D MSE 3.3 44.2 - - + +
264D PHE* 3.8 20.0 - - + -
266D VAL* 4.0 15.3 - - + -
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Residues in contact with LEU 226 (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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180D PHE* 5.1 4.0 - - + -
181D PHE 2.9 17.1 + - - +
182D VAL* 4.5 1.8 - - - -
183D ILE 2.9 22.3 + - - +
224D TYR* 4.6 7.4 - - + +
225D LEU* 1.3 82.4 - - - +
227D PHE* 1.3 62.6 + - - +
235D PHE* 3.6 24.1 - - + -
237D GLY 3.6 4.3 - - - +
238D VAL* 3.7 27.8 - - + -
292D VAL* 5.8 0.4 - - + -
301D ILE* 3.6 26.0 - - + -
306D SER* 5.0 8.7 - - - +
309D ILE* 4.4 26.2 - - + -
310D LEU* 4.4 10.8 - - + -
313D PHE* 5.1 4.0 - - + -
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Residues in contact with PHE 227 (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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183D ILE* 3.4 29.8 - - + -
185D SER* 5.6 0.9 - - - -
191D VAL* 3.9 15.7 - - + -
194D SER* 4.5 0.9 - - - -
200D TRP* 3.7 43.3 - + + -
225D LEU* 3.7 32.3 - - + -
226D LEU* 1.3 71.2 - - - +
228D SER* 1.3 57.5 + - - +
235D PHE* 3.2 9.0 - - - +
236D CYS* 2.8 43.8 + - - -
237D GLY 2.8 14.9 + - - +
239D ALA* 4.1 10.5 - - + -
266D VAL* 5.6 0.7 - - + -
268D TRP* 3.5 41.5 - + + -
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Residues in contact with SER 228 (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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183D ILE 2.9 5.9 + - - -
184D LYS* 2.7 44.2 + - - +
185D SER* 3.1 21.6 + - - -
191D VAL* 6.0 0.9 - - - -
227D PHE* 1.3 78.1 - - - +
229D VAL* 1.3 60.8 + - - +
234D ARG 2.9 24.4 + - - -
235D PHE* 3.5 26.1 - - - +
236D CYS* 4.3 2.2 - - - -
276D ASN* 5.4 0.3 + - - -
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Residues in contact with VAL 229 (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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184D LYS* 3.6 6.7 + - - -
185D SER 3.4 11.0 - - - +
186D SER 4.7 2.5 - - - +
187D SER 4.3 3.6 - - - +
188D LEU* 3.9 51.4 - - + +
191D VAL* 4.2 13.0 - - + -
228D SER* 1.3 75.0 + - - +
230D ASN* 1.3 79.1 + - - +
231D ALA 3.2 0.7 + - - -
232D SER* 2.8 35.2 + - - +
233D GLY 4.8 0.2 + - - -
234D ARG 4.2 0.4 + - - -
236D CYS* 4.4 10.4 - - + -
2T A 4.1 0.2 + - - -
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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