Contacts of the strand formed by residues 217 - 224 (chain C) in PDB entry 1K9A
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 ASN 217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C ASP* 3.2 7.1 + - - -
214C TYR 2.7 44.3 + - - +
215C ARG* 3.2 21.4 + - - +
216C GLY* 1.3 78.0 - - - +
218C LYS* 1.3 68.3 + - - +
219C VAL* 3.3 7.9 + - + +
252C LEU* 5.8 2.9 - - + -
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Residues in contact with LYS 218 (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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198C LEU* 6.0 6.3 - - + -
211C LEU* 4.0 17.9 - - + +
212C GLY 3.4 6.5 - - - +
213C ASP* 4.7 4.5 - - + +
216C GLY 5.9 0.4 - - - +
217C ASN* 1.3 73.2 - - - +
219C VAL* 1.3 63.9 + - - +
267C GLU* 5.1 0.3 - - - -
268C TYR* 3.1 45.1 + - + +
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Residues in contact with VAL 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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195C LEU* 4.6 2.5 - - + -
211C LEU* 3.5 5.9 - - - +
212C GLY 2.7 49.1 + - - +
213C ASP 4.3 2.2 - - - +
214C TYR* 4.1 17.3 - - + -
217C ASN* 3.5 14.4 - - + +
218C LYS* 1.3 81.7 - - - +
220C ALA* 1.3 58.9 + - - +
221C VAL* 3.9 9.9 - - + -
252C LEU* 3.3 30.1 - - + -
265C VAL* 3.6 21.1 - - + -
266C THR 3.6 8.3 - - - +
267C GLU* 5.4 0.2 - - - -
268C TYR* 3.6 8.3 - - - +
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Residues in contact with ALA 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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201C ILE* 4.3 16.2 - - + -
209C VAL* 5.9 3.1 - - + -
210C MET 3.5 5.2 - - - -
219C VAL* 1.3 73.6 - - - +
221C VAL* 1.3 61.5 + - - +
222C LYS* 4.2 0.4 - - - -
264C ILE 3.6 0.9 - - - +
265C VAL* 3.4 3.8 - - - +
266C THR* 2.8 49.0 + - - +
267C GLU 4.4 1.6 - - - +
268C TYR* 3.9 14.4 - - + +
269C MET 5.4 0.7 - - - +
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Residues in contact with VAL 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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195C LEU* 4.1 9.4 - - + -
197C LEU* 4.0 26.2 - - + -
208C ASP 3.5 1.7 - - - +
209C VAL* 3.1 5.9 - - - +
210C MET* 2.7 44.6 + - + +
212C GLY 4.4 2.0 - - - +
219C VAL* 3.9 20.2 - - + +
220C ALA* 1.3 77.6 - - - +
222C LYS* 1.3 63.3 + - - +
223C CYS* 4.1 1.1 + - + -
263C TYR* 3.8 41.1 - - + -
264C ILE 3.5 2.2 - - - -
265C VAL* 4.3 11.7 - - + -
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Residues in contact with LYS 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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208C ASP* 3.2 33.4 + - - +
209C VAL* 3.3 21.0 - - + +
220C ALA 4.2 0.6 - - - -
221C VAL* 1.3 75.1 - - - +
223C CYS* 1.3 63.7 + - - +
224C ILE* 3.4 33.6 + - + -
229C THR* 5.6 3.7 - - - +
233C PHE* 3.2 50.3 - - + -
262C LEU 3.5 1.6 - - - +
263C TYR* 3.3 2.2 - - - -
264C ILE* 2.6 52.5 + - + +
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Residues in contact with CYS 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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208C ASP* 2.9 31.8 + - + +
221C VAL* 4.1 2.1 + - + +
222C LYS* 1.3 74.9 - - - +
224C ILE* 1.3 72.4 + - - +
225C LYS* 5.3 3.1 - - - -
257C GLU* 3.9 20.0 - - - -
261C GLY* 5.4 0.4 - - - -
262C LEU 3.4 7.2 - - - -
263C TYR* 3.6 32.8 - - + -
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Residues in contact with ILE 224 (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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79C LEU* 3.4 15.8 - - + +
222C LYS* 3.4 35.2 - - + +
223C CYS* 1.3 76.1 - - - +
225C LYS* 1.3 60.2 + - - +
227C ASP* 6.0 2.0 - - + -
229C THR* 6.2 1.1 - - + -
230C ALA* 4.0 19.5 - - + +
233C PHE* 4.2 13.2 - - + -
234C LEU* 3.4 44.2 - - + +
261C GLY* 3.6 1.1 - - - -
262C LEU* 2.8 43.5 + - + +
264C ILE* 4.7 11.2 - - + -
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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