Contacts of the strand formed by residues 230 - 236 (chain B) in PDB entry 3K1L
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 VAL 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B PRO* 3.7 1.0 - - - +
226B LEU* 2.8 37.0 + - + -
227B LYS* 3.2 18.8 + - + +
228B ASP 3.1 10.5 + - - +
229B ARG* 1.3 84.6 - - + +
231B TYR* 1.3 71.5 + - - +
250B ILE* 4.3 7.6 - - + -
251B ILE 3.4 8.7 - - - +
252B GLY* 4.9 0.4 - - - -
253B PRO* 4.3 3.1 - - + -
256B GLU* 3.7 41.5 - - + +
260B LEU* 3.7 23.1 - - + -
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Residues in contact with TYR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.5 32.8 - - + -
223B LEU* 3.9 15.9 - - + -
224B PHE 3.6 5.8 - - - +
225B PRO* 4.0 20.4 - - + -
227B LYS 5.9 0.2 - - - -
229B ARG* 4.4 18.7 - - - -
230B VAL* 1.3 81.2 - - - +
232B LEU* 1.3 60.5 + - - +
250B ILE* 3.7 1.9 - - - -
251B ILE* 2.6 60.3 + - + +
326B LEU* 3.5 45.7 - - + +
337B LYS* 3.6 19.1 + - - -
375B PHE* 4.8 4.3 - + - -
378B LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 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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222B ARG 3.9 0.5 - - - +
223B LEU* 3.6 2.5 - - - +
224B PHE* 2.8 62.3 + - + +
226B LEU* 4.3 15.9 - - + -
230B VAL* 4.3 0.4 + - + -
231B TYR* 1.3 75.2 - - - +
233B LYS* 1.3 63.7 + - - +
234B LEU 3.8 1.4 + - - -
248B LEU* 3.6 33.2 - - + -
249B LYS 3.5 11.7 - - - +
250B ILE* 5.0 5.8 - - + -
281B LEU* 4.3 7.4 - - + -
285B PHE* 3.6 37.2 - - + -
290B PHE* 4.3 9.4 - - + -
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Residues in contact with LYS 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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221B THR* 4.0 24.5 - - + -
222B ARG 3.6 9.4 - - - +
223B LEU* 3.5 23.8 - - + +
232B LEU* 1.3 72.9 - - - +
234B LEU* 1.3 63.6 + - - +
235B THR* 3.7 16.0 + - + +
247B SER 3.6 4.7 - - - +
249B LYS* 2.9 43.8 + - + +
251B ILE* 4.3 12.8 - - + +
377B ALA* 3.3 28.9 + - + +
378B LEU* 4.7 8.1 + - + +
379B LEU 4.6 0.6 + - - -
380B ASN* 4.9 3.0 + - - +
381B ASP* 3.8 25.4 + - - +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASN* 6.6 0.2 - - + -
200B PHE* 3.8 24.0 - - + -
203B ILE* 3.3 34.8 - - + -
221B THR* 3.6 1.9 + - - -
222B ARG* 2.8 40.9 + - + +
224B PHE* 4.2 12.1 - - + -
232B LEU* 3.8 2.8 + - - +
233B LYS* 1.3 73.1 - - - +
235B THR* 1.3 72.0 + - - +
236B ILE* 4.4 3.8 - - + -
246B MET* 3.7 29.4 - - + -
247B SER 3.6 5.6 - - - +
248B LEU* 3.9 18.1 - - + +
277B ILE* 4.0 18.6 - - + -
281B LEU* 5.2 0.7 - - + -
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Residues in contact with THR 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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200B PHE* 5.8 0.2 - - - -
220B LYS 3.8 4.2 + - - -
221B THR* 3.6 15.7 + - - -
233B LYS* 3.7 22.9 - - + +
234B LEU* 1.3 79.4 - - - +
236B ILE* 1.3 66.6 + - - +
237B ALA* 4.0 2.9 + - - +
245B SER 3.8 1.0 - - - +
246B MET* 3.6 1.4 - - - -
247B SER* 2.9 59.6 + - - +
249B LYS* 4.9 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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196B PHE* 4.0 19.5 - - + +
199B ASN* 5.2 2.7 - - + -
200B PHE* 3.4 35.2 - - + -
220B LYS* 3.0 34.0 + - - +
234B LEU* 4.4 9.9 - - + -
235B THR* 1.3 77.1 + - - +
237B ALA* 1.3 63.3 + - - +
238B ASP 3.7 22.0 - - - +
239B PRO 4.5 0.2 - - - -
242B CYS* 3.7 37.2 - - - +
245B SER* 3.8 4.0 - - - +
246B MET* 4.7 3.1 - - - -
277B ILE* 4.4 14.4 - - + -
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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