Contacts of the strand formed by residues 225 - 236 (chain D) in PDB entry 3U1K
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 GLN 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220D GLY* 3.2 5.7 - - - -
221D ALA* 2.8 40.2 + - + +
222D PRO 3.4 16.6 - - - +
223D LYS* 2.9 27.6 + - + +
224D SER* 1.3 83.9 + - - +
226D ILE* 1.3 60.3 + - - +
249D VAL* 5.2 0.7 - - - +
253D GLN* 5.0 0.2 + - - -
524D ILE* 5.4 0.9 - - - +
564D PRO 4.6 3.8 - - - +
565D GLY* 3.9 21.7 - - - +
566D ILE* 3.4 3.7 - - - -
567D PRO* 3.2 40.8 - - - +
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Residues in contact with ILE 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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218D VAL* 4.9 1.8 - - + -
219D ALA 3.9 4.7 - - - +
225D GLN* 1.3 73.8 - - - +
227D VAL* 1.3 61.7 - - - +
228D MET 4.0 6.1 - - - +
229D LEU* 3.7 31.0 - - + -
245D ILE* 3.8 20.6 - - + -
249D VAL* 3.7 33.0 - - + -
561D ILE* 3.6 18.5 - - + +
565D GLY* 3.2 2.0 - - - -
566D ILE 2.7 35.8 + - - +
568D ILE* 4.2 19.7 - - + -
571D VAL* 3.9 22.4 - - + -
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Residues in contact with VAL 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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136D ARG* 3.9 7.2 - - - +
137D SER* 3.6 24.2 - - - +
140D PRO* 3.7 28.3 - - + -
141D LEU* 4.6 7.6 - - + -
188D VAL* 4.4 8.3 - - + -
219D ALA* 2.9 13.1 + - + +
220D GLY 4.1 2.9 - - - -
221D ALA* 3.6 36.8 - - + +
226D ILE* 1.3 75.9 - - - +
228D MET* 1.3 59.4 + - - +
559D ALA 4.6 0.2 - - - +
561D ILE* 3.5 28.3 + - - +
565D GLY* 4.1 13.0 - - - +
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Residues in contact with MET 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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133D ILE* 3.6 14.6 - - + +
136D ARG* 3.7 33.7 - - + +
137D SER* 3.4 26.7 - - - +
170D ILE* 4.7 0.4 - - + -
217D VAL* 3.5 33.7 - - + +
218D VAL* 3.7 0.5 - - - -
219D ALA* 3.0 42.1 + - + +
226D ILE* 3.7 0.8 - - - +
227D VAL* 1.3 82.2 - - - +
229D LEU* 1.3 89.4 + - - +
230D GLU* 3.6 11.9 - - - +
559D ALA 4.1 6.1 - - - +
561D ILE* 4.9 0.4 - - - -
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Residues in contact with LEU 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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136D ARG* 5.4 0.3 + - - -
216D LEU* 4.4 5.8 - - + -
217D VAL 3.6 2.0 - - - +
218D VAL* 3.8 32.8 - - + -
226D ILE* 3.7 19.1 - - + -
228D MET* 1.3 87.2 - - - +
230D GLU* 1.3 64.3 + - - +
245D ILE* 4.2 14.8 - - + -
545D PHE* 4.3 2.5 - - + -
557D LEU* 3.8 26.7 - - + -
558D GLN* 3.7 1.7 - - - -
559D ALA* 2.9 49.7 + - + +
571D VAL* 3.8 29.6 - - + -
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Residues in contact with GLU 230 (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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133D ILE* 4.0 25.6 - - + -
136D ARG* 2.9 28.1 + - - -
215D ASN 3.7 1.4 - - - +
216D LEU* 3.4 1.4 - - - +
217D VAL* 2.8 43.1 + - + +
228D MET* 3.8 12.6 - - - -
229D LEU* 1.3 76.8 - - - +
231D ALA* 1.3 63.9 + - - +
456D LYS* 2.6 30.2 + - - +
557D LEU 3.5 5.8 - - - +
558D GLN* 3.3 26.2 + - - +
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Residues in contact with ALA 231 (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 LEU* 4.7 0.2 - - + -
215D ASN 3.2 7.4 - - - +
216D LEU* 3.8 12.6 - - + -
230D GLU* 1.3 78.9 - - - +
232D SER* 1.3 61.5 + - - +
241D PHE* 3.6 37.9 - - + -
456D LYS* 3.0 16.7 - - - -
556D ALA* 3.3 2.2 - - - -
557D LEU* 2.8 39.0 + - + +
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Residues in contact with SER 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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214D LEU* 3.5 1.8 - - - +
215D ASN* 2.7 53.1 + - - +
231D ALA* 1.3 73.8 - - - +
233D ALA* 1.3 62.3 + - - +
456D LYS* 3.9 29.0 + - - +
459D TYR* 5.8 4.2 - - - -
460D PRO* 6.0 0.7 - - - +
555D THR 3.5 6.8 + - - -
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Residues in contact with ALA 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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213D THR 3.6 7.2 - - - +
214D LEU* 3.5 21.1 - - + +
232D SER* 1.3 76.8 + - - +
234D GLU* 1.3 60.2 + - - +
235D ASN 2.8 8.7 + - - -
236D ILE* 3.9 14.1 - - + -
241D PHE* 4.6 6.1 - - + -
460D PRO* 3.2 19.2 - - - +
554D ILE 3.5 18.8 - - - +
555D THR* 2.9 15.3 + - - +
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Residues in contact with GLU 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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212D SER 4.7 5.4 - - - +
213D THR* 2.9 37.6 + - - +
233D ALA* 1.3 69.8 - - - +
235D ASN* 1.3 69.9 + - - +
236D ILE* 3.4 6.3 + - - +
421D LYS* 5.0 3.2 + - - -
459D TYR* 3.5 31.7 - - - -
460D PRO* 3.9 22.1 - - - +
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Residues in contact with ASN 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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233D ALA 2.8 13.1 + - - -
234D GLU* 1.3 74.4 - - - +
236D ILE* 1.3 60.2 + - - +
237D LEU* 6.0 0.2 - - - +
460D PRO* 4.1 7.8 - - + +
461D VAL* 5.4 3.1 - - + +
503D SER* 5.6 2.8 + - - -
504D SER* 5.8 1.6 - - - -
550D THR* 2.6 42.2 + - - +
552D LYS* 5.0 6.4 - - - +
553D GLY* 3.2 17.6 - - - +
554D ILE 3.0 10.3 - - - -
555D THR* 3.7 12.3 - - + +
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Residues in contact with ILE 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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195D ILE* 4.3 16.8 - - + -
213D THR* 3.4 37.7 - - + +
214D LEU* 4.1 16.2 - - + -
233D ALA* 3.9 9.6 - - + -
234D GLU 3.8 10.5 - - - +
235D ASN* 1.3 78.3 - - - +
237D LEU* 1.3 68.3 + - - +
238D GLN 3.6 0.2 + - - -
240D ASP* 4.4 6.3 - - + +
241D PHE* 4.0 40.2 - - + +
553D GLY* 3.1 4.9 - - - -
554D ILE* 2.9 26.7 + - + +
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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