Contacts of the strand formed by residues 225 - 236 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B GLY* 3.3 4.9 - - - -
221B ALA* 2.7 38.5 + - + -
222B PRO 3.4 17.0 - - - +
223B LYS* 2.9 27.2 + - + +
224B SER* 1.3 81.9 + - - +
226B ILE* 1.3 60.6 + - - +
249B VAL* 5.6 0.4 - - - +
524B ILE* 5.4 0.5 - - - +
564B PRO 4.5 3.6 - - - +
565B GLY* 3.8 20.5 - - - +
566B ILE* 3.0 27.0 - - - -
567B PRO* 3.0 22.7 - - - +
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B VAL* 5.0 1.3 - - + -
219B ALA 3.9 4.5 - - - +
225B GLN* 1.3 73.5 - - - +
227B VAL* 1.3 61.9 + - - +
228B MET 3.9 9.0 - - - +
229B LEU* 3.5 32.3 - - + -
245B ILE* 3.8 28.5 - - + -
249B VAL* 3.9 21.8 - - + -
561B ILE* 3.5 18.7 - - + +
565B GLY* 3.1 2.4 - - - -
566B ILE 2.7 36.6 + - - +
568B ILE* 4.1 17.3 - - + -
571B VAL* 3.6 28.0 - - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 3.8 15.8 - - - +
137B SER* 3.4 27.6 - - - +
140B PRO* 4.1 13.0 - - + -
141B LEU* 5.1 4.9 - - + -
188B VAL* 4.6 7.6 - - + -
219B ALA* 3.0 15.5 + - + +
220B GLY 3.7 4.5 - - - +
221B ALA* 3.6 34.1 - - + +
226B ILE* 1.3 74.8 - - - +
228B MET* 1.3 60.5 - - + +
561B ILE* 3.4 29.3 + - - +
564B PRO 5.1 0.9 - - - -
565B GLY* 4.1 13.9 - - - +
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Residues in contact with MET 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 3.4 37.7 - - + +
136B ARG* 3.5 40.4 - - + +
137B SER* 3.7 21.3 - - - +
170B ILE* 4.8 0.4 - - + -
217B VAL* 3.7 21.5 - - + +
219B ALA* 3.0 38.7 + - + +
226B ILE* 3.7 2.7 - - - +
227B VAL* 1.3 82.1 - - - +
229B LEU* 1.3 96.7 + - - +
230B GLU* 3.7 6.3 - - - -
559B ALA 4.0 7.0 - - - +
561B ILE* 4.7 0.7 - - - -
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B LEU* 4.4 7.4 - - + -
217B VAL 3.4 2.7 - - - -
218B VAL* 3.8 30.5 - - + -
226B ILE* 3.5 27.4 - - + -
228B MET* 1.3 84.9 - - - +
230B GLU* 1.3 63.3 + - - +
245B ILE* 4.3 15.5 - - + -
545B PHE* 4.2 11.4 - - + -
557B LEU* 4.0 25.4 - - + -
558B GLN* 3.6 1.6 - - - -
559B ALA* 2.8 43.4 + - + +
561B ILE* 5.4 0.4 - - + -
571B VAL* 4.1 24.0 - - + -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 4.0 21.1 - - + -
136B ARG* 3.2 15.9 + - - +
215B ASN 3.6 1.4 - - - +
216B LEU* 3.5 0.7 - - - +
217B VAL* 2.7 39.7 + - + +
228B MET* 3.7 13.0 - - + -
229B LEU* 1.3 74.0 - - - +
231B ALA* 1.3 61.6 + - - +
456B LYS* 2.8 29.7 + - - +
557B LEU 3.4 5.4 - - - -
558B GLN* 2.9 46.5 + - - +
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ASN 3.0 10.1 - - - +
216B LEU* 3.7 13.9 - - + -
230B GLU* 1.3 77.6 - - - +
232B SER* 1.3 60.3 + - - +
241B PHE* 3.7 37.0 - - + -
456B LYS* 3.2 18.1 - - - -
556B ALA* 3.3 1.1 - - - -
557B LEU* 2.8 36.8 + - + +
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU* 3.5 3.5 - - - +
215B ASN* 2.8 49.6 + - - +
231B ALA* 1.3 75.6 - - - +
233B ALA* 1.3 63.8 + - - +
456B LYS* 3.9 29.2 - - - -
555B THR 3.3 10.8 - - - -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B THR 3.3 13.2 - - - +
214B LEU* 3.7 15.9 - - + +
232B SER* 1.3 76.7 - - - +
234B GLU* 1.3 60.9 + - - +
235B ASN 2.9 9.2 + - - -
236B ILE* 3.9 14.4 - - + -
241B PHE* 4.5 7.2 - - + -
460B PRO* 3.4 12.1 - - - +
554B ILE 3.5 17.7 - - - +
555B THR* 3.1 18.6 + - - +
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B SER 4.5 4.7 - - - +
213B THR* 2.8 41.4 + - + +
233B ALA* 1.3 68.0 - - - +
235B ASN* 1.3 72.9 + - - +
236B ILE* 3.3 6.1 + - - +
421B LYS* 4.9 3.8 + - - -
459B TYR* 3.4 32.5 - - - -
460B PRO* 3.9 25.6 - - - +
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Residues in contact with ASN 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ALA 2.9 12.1 + - - -
234B GLU* 1.3 75.8 - - - +
236B ILE* 1.3 63.4 + - - +
237B LEU* 5.8 0.7 - - - +
460B PRO* 4.2 6.7 - - + +
461B VAL* 5.5 3.1 - - + +
503B SER* 5.8 1.0 + - - -
504B SER* 5.5 2.4 - - - -
550B THR* 2.6 43.9 + - - +
552B LYS* 4.5 9.6 - - - +
553B GLY* 3.2 19.8 - - - +
554B ILE 3.2 8.1 - - - -
555B THR* 3.9 10.5 - - + +
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B ILE* 4.1 23.6 - - + -
213B THR* 3.6 35.7 - - - +
214B LEU* 4.2 11.7 - - + -
233B ALA* 3.9 9.4 - - + -
234B GLU 3.8 13.0 - - - +
235B ASN* 1.3 77.0 - - - +
237B LEU* 1.3 66.4 + - - +
238B GLN 3.6 0.2 + - - -
240B ASP* 4.2 6.5 - - + +
241B PHE* 3.7 42.4 - - + +
553B GLY* 3.2 3.4 - - - -
554B ILE* 2.8 30.1 + - - +
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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