Contacts of the strand formed by residues 230 - 235 (chain D) in PDB entry 4UI2
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 LYS 230 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ILE* 3.6 0.3 - - - -
220D PHE* 3.0 33.6 + - + +
227D THR* 4.1 2.0 - - - +
228D ASP* 3.5 28.2 + - - +
229D GLN* 1.3 79.7 + - - +
231D VAL* 1.3 69.2 + - - +
232D TYR 4.3 0.2 - - - -
243D PHE* 3.9 20.4 - - + -
245D ASP* 3.1 27.0 + - - +
247D THR* 3.1 23.1 + - - +
249D SER 3.1 22.8 + - - -
250D GLY* 3.8 8.5 - - - -
251D GLY 4.6 1.0 - - - +
258D LEU* 3.9 27.1 - - + -
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010A PRO* 5.4 6.1 - - + -
217D THR* 4.2 13.2 - - + -
218D ILE 3.3 10.5 - - - +
219D ILE* 4.2 16.6 - - + -
229D GLN* 4.2 20.2 - - + +
230D LYS* 1.3 83.6 - - - +
232D TYR* 1.3 68.7 + - - +
233D GLN* 5.0 1.3 - - + -
243D PHE* 3.3 10.0 - - - +
244D VAL* 3.0 52.8 + - + +
245D ASP* 5.7 0.4 + - - -
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Residues in contact with TYR 232 (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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216D ILE 4.6 2.7 - - - -
217D THR* 3.3 4.5 - - - +
218D ILE* 2.8 48.5 + - + +
220D PHE* 4.9 1.0 - - + -
231D VAL* 1.3 73.8 - - - +
233D GLN* 1.3 65.7 + - - +
234D ALA* 3.5 23.3 - - + -
239D LEU* 3.5 7.8 - - - +
240D PRO* 2.4 47.9 + - + +
242D ALA 3.2 25.1 - - - -
243D PHE* 3.8 7.4 - + + +
260D ILE* 3.3 20.9 - - + -
269D VAL* 3.5 14.8 - - + +
271D MET* 3.7 28.0 - - + -
282D VAL* 4.3 15.9 - - + -
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Residues in contact with GLN 233 (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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1010A PRO* 3.7 30.3 + - - +
1011A PRO 5.5 0.8 + - - +
1012A SER* 5.2 11.4 - - - -
215D LYS* 4.0 22.8 + - + +
216D ILE 3.3 6.7 - - - +
217D THR* 3.3 27.0 + - + +
231D VAL* 4.0 2.7 + - + -
232D TYR* 1.3 80.4 - - - +
234D ALA* 1.3 69.8 + - - +
235D VAL* 4.9 5.0 - - + +
238D ASP* 5.3 1.6 - - - +
240D PRO* 3.8 19.4 - - - +
242D ALA 5.2 0.4 + - - +
244D VAL* 4.3 21.4 - - + +
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Residues in contact with ALA 234 (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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215D LYS* 3.3 0.9 - - - +
216D ILE 3.0 31.8 + - - +
232D TYR* 3.5 22.7 - - + +
233D GLN* 1.3 74.9 - - - +
235D VAL* 1.3 70.1 + - - +
238D ASP* 3.4 11.0 - - - +
239D LEU* 3.5 25.8 - - + -
282D VAL* 4.3 7.0 - - + -
289D LEU* 3.5 5.5 - - + +
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Residues in contact with VAL 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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214D ASN 3.3 15.3 - - - +
215D LYS* 3.9 26.9 - - + -
233D GLN* 4.9 8.3 - - + +
234D ALA* 1.3 81.5 - - - +
236D THR* 1.3 73.3 + - - +
237D ASP 2.9 1.0 + - - -
238D ASP* 2.7 44.4 + - + +
284D GLN* 4.9 0.2 - - - +
289D LEU* 3.6 11.8 - - - +
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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