Contacts of the strand formed by residues 218 - 227 (chain C) in PDB entry 3KYS
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 SER 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ASN* 5.8 1.8 - - - -
221A LYS 3.6 3.1 - - - -
222A HIS* 4.2 6.6 + - - +
212C GLN 4.4 0.2 - - - -
213C GLN* 2.5 36.4 + - - +
214C ARG* 3.4 48.7 + - - -
215C ASP* 3.1 19.8 + - - +
216C PRO 3.5 1.4 + - - -
217C ASP* 1.3 79.0 + - - +
219C TYR* 1.3 57.4 + - - +
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Residues in contact with TYR 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TYR* 3.7 36.6 - + - -
220A ASN* 3.4 10.1 + - - +
221A LYS* 3.0 42.8 + - + +
211C GLU* 2.3 52.4 + - + +
212C GLN 3.4 8.3 - - - -
213C GLN* 4.1 18.2 - - - +
218C SER* 1.3 75.2 - - - +
220C ASN* 1.3 68.0 + - - +
221C LYS* 3.7 19.4 + - + +
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Residues in contact with ASN 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A SER* 6.0 2.5 - - - -
219A TYR 2.9 16.3 + - - +
220A ASN* 3.6 16.3 - - - +
210C LEU 4.5 0.8 + - - +
211C GLU* 3.3 6.2 - - - +
212C GLN* 2.7 59.6 + - + +
219C TYR* 1.3 78.5 - - - +
221C LYS* 1.3 70.6 + - - +
222C HIS* 4.8 8.3 - - - +
281C CYS* 6.2 1.6 - - - +
282C ASN 6.0 1.8 - - - +
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Residues in contact with LYS 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASP 3.6 0.9 - - - +
218A SER* 3.5 3.8 - - - -
219A TYR* 2.7 51.5 + - + +
207C SER* 5.6 1.6 + - - -
209C PHE* 3.8 37.8 - - + -
210C LEU 3.5 4.0 - - - +
211C GLU* 3.9 16.5 + - + -
219C TYR* 3.7 29.5 + - + +
220C ASN* 1.3 79.5 + - - +
222C HIS* 1.3 63.2 + - - +
223C LEU* 4.6 13.9 - - + +
294C THR* 5.8 1.0 + - - -
340C ARG* 5.4 1.6 - - - +
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Residues in contact with HIS 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ARG* 4.6 1.2 + - - -
217A ASP* 3.2 13.4 + - + -
218A SER* 4.1 10.4 + - - +
209C PHE* 3.0 7.7 - - - +
210C LEU* 2.8 45.8 + - + +
212C GLN* 6.0 0.9 - - - +
220C ASN* 4.8 9.4 - - - +
221C LYS* 1.3 74.3 - - - +
223C LEU* 1.3 72.1 + - - +
224C PHE* 3.7 21.7 - + - -
278C ASP* 2.8 52.9 + - - -
280C ASN 3.7 14.6 + - - -
281C CYS* 3.6 27.5 - - + +
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Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PRO 3.7 20.0 - - - +
217A ASP* 2.8 36.7 + - + +
207C SER* 4.5 13.7 - - - +
208C ALA 3.4 5.2 - - - +
209C PHE* 3.9 18.8 - - + -
221C LYS* 4.6 16.6 - - + +
222C HIS* 1.3 91.5 + - - +
224C PHE* 1.3 62.1 + - - +
225C VAL 4.5 3.1 - - - +
226C HIS* 3.7 23.8 - - + -
229C HIS* 3.9 22.7 - - + +
278C ASP* 3.7 1.7 - - - +
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Residues in contact with PHE 224 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C ALA* 2.7 25.1 + - + +
209C PHE* 3.6 28.5 - - - -
210C LEU* 3.6 21.1 - - + -
222C HIS* 3.7 14.6 - + - -
223C LEU* 1.3 73.6 - - - +
225C VAL* 1.3 63.7 + - - +
276C TRP 4.4 1.2 - - - +
277C ALA* 3.3 1.6 - - + -
278C ASP* 2.8 44.8 + - - +
279C LEU* 4.4 10.3 - - + -
281C CYS* 3.9 17.0 - - - -
283C ILE* 5.5 0.2 - - + -
291C TYR* 4.3 8.3 - + - -
343C MET* 5.0 2.0 - - - -
344C P1L 3.9 25.1 - - + -
351C ILE* 4.1 39.9 - - + -
401C ALA* 4.5 3.4 - - - +
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C PHE* 4.0 15.3 - - + -
207C SER* 3.3 0.9 - - - -
208C ALA* 3.1 30.8 + - + +
223C LEU* 4.5 1.0 - - - +
224C PHE* 1.3 83.7 + - - +
226C HIS* 1.3 69.1 + - - +
275C PHE* 3.6 41.1 - - + -
276C TRP 4.7 1.6 - - - +
277C ALA* 3.7 23.1 - - + -
344C P1L 3.7 32.1 - - + -
392C PHE* 4.4 2.5 - - + -
401C ALA* 4.8 3.8 - - - -
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Residues in contact with HIS 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PRO* 4.8 11.7 + - + +
217A ASP* 3.2 28.2 + - - -
206C PHE 3.1 11.4 - - - +
207C SER* 4.3 1.3 - - - -
223C LEU* 3.7 14.3 - - + +
225C VAL* 1.3 81.9 - - - +
227C ILE* 1.3 62.9 + - - +
229C HIS* 3.7 50.2 + - + +
275C PHE* 4.8 1.2 - - - -
401C ALA* 3.3 32.8 + - + +
403C HIS* 3.4 24.8 + + - +
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Residues in contact with ILE 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ARG 3.8 19.3 - - - +
196C ILE* 3.8 30.3 - - + -
203C LEU* 4.2 19.1 - - + +
204C VAL 5.4 1.3 - - - +
205C GLU* 3.2 5.0 - - - -
206C PHE* 2.7 45.9 + - + +
226C HIS* 1.3 78.6 - - - +
228C GLY* 1.3 63.6 + - - +
229C HIS* 3.5 7.3 - - - -
273C VAL* 4.5 3.6 - - + -
275C PHE* 3.6 32.3 - - + -
388C MET* 4.4 5.8 - - - -
403C HIS* 3.8 24.5 - - + +
405C ILE* 5.1 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