Contacts of the strand formed by residues 212 - 224 (chain C) in PDB entry 1KIA
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 LYS 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C ASP* 6.0 1.8 - - - -
208C THR* 3.3 4.5 - - - -
209C VAL* 3.0 64.1 + - + +
210C ASN* 5.5 1.6 - - + -
211C ASN* 1.3 77.5 - - - +
213C ALA* 1.3 71.0 + - - +
214C HIS* 3.2 41.5 + - - +
243C TYR* 5.8 5.8 - - - +
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Residues in contact with ALA 213 (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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181C LEU* 3.7 40.4 - - + -
206C VAL* 5.0 1.8 - - + -
207C LEU 4.1 1.1 - - - +
208C THR* 3.8 16.8 + - - +
211C ASN 4.1 0.8 + - - -
212C LYS* 1.3 80.9 - - - +
214C HIS* 1.3 59.4 + - - +
243C TYR* 4.8 9.0 + - - -
244C PRO* 3.9 15.0 - - + +
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Residues in contact with HIS 214 (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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145C ASP* 4.6 30.2 + - + +
146C SER* 5.0 4.6 - - - -
207C LEU* 2.8 29.4 + - + +
209C VAL* 3.7 22.2 - - + +
212C LYS* 3.1 33.7 + - - +
213C ALA* 1.3 73.7 - - - +
215C MET* 1.3 76.8 + - + +
243C TYR* 3.8 15.4 - - - -
244C PRO* 3.7 10.4 - - - +
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Residues in contact with MET 215 (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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144C PRO* 5.4 12.3 - - + -
205C SER 3.5 1.4 - - - +
206C VAL* 3.6 2.3 - - - +
207C LEU* 2.8 50.3 + - + -
214C HIS* 1.3 99.1 - - + +
216C VAL* 1.3 66.7 - - - +
217C THR* 3.8 22.7 - - - +
241C SER* 4.1 16.2 - - - -
242C TYR 3.6 11.7 - - - +
244C PRO* 3.8 4.3 - - - +
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Residues in contact with VAL 216 (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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177C TYR* 4.3 17.9 - - + -
180C ILE* 4.0 11.0 - - + -
181C LEU* 3.9 16.4 - - + -
204C THR* 3.7 28.7 - - + -
205C SER 3.4 3.4 - - - +
206C VAL* 4.6 3.4 - - + -
215C MET* 1.3 75.4 - - - +
217C THR* 1.3 62.7 - - - +
218C LEU* 4.3 11.2 - - + -
241C SER* 3.5 0.9 - - - -
242C TYR* 2.8 43.9 + - + +
244C PRO* 3.5 33.2 - - + -
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Residues in contact with THR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C THR 3.4 2.4 - - - +
205C SER* 2.8 51.8 + - - -
215C MET* 3.8 14.2 - - - +
216C VAL* 1.3 71.9 - - - +
218C LEU* 1.3 64.3 + - - +
219C ASP* 4.1 4.6 - - - +
239C ARG* 3.1 48.7 - - + +
240C LEU 3.5 4.5 - - - +
241C SER* 3.6 18.0 + - - +
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Residues in contact with LEU 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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175C ARG* 3.9 30.3 - - - +
180C ILE* 5.4 0.7 - - + -
186C ALA* 4.1 6.3 - - + -
202C ILE* 4.1 15.5 - - + -
203C THR 3.5 1.1 - - - -
204C THR* 3.5 42.2 - - + +
216C VAL* 4.3 7.6 - - + -
217C THR* 1.3 75.0 - - - +
219C ASP* 1.3 62.2 + - - +
220C TYR* 3.3 36.8 - - + +
239C ARG* 3.3 5.0 - - - +
240C LEU 2.8 33.8 + - - +
242C TYR* 3.7 18.6 - - + -
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Residues in contact with ASP 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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201C ASP* 3.6 4.9 - - - +
202C ILE* 3.4 3.8 + - - -
203C THR* 3.0 45.7 + - - +
205C SER* 4.4 7.3 + - - -
217C THR* 4.1 4.7 - - - +
218C LEU* 1.3 76.0 - - - +
220C TYR* 1.3 63.8 + - - +
221C THR* 4.3 1.3 + - - -
238C PHE 3.6 5.5 - - - +
239C ARG* 2.9 53.6 + - - +
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Residues in contact with TYR 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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33C TYR* 3.0 34.8 - + - -
199C THR* 5.0 0.7 - - + -
201C ASP 3.4 5.2 - - - +
202C ILE* 3.5 30.7 - - + -
218C LEU* 3.3 34.3 - - + +
219C ASP* 1.3 72.1 - - - +
221C THR* 1.3 66.2 + - - +
222C VAL* 4.0 5.6 - - + -
236C SER 4.4 0.4 - - - -
237C LYS* 3.3 8.8 - - - +
238C PHE* 2.8 70.6 + + + +
240C LEU* 3.4 23.6 - - + -
242C TYR* 2.6 25.2 + - - -
2294C ACT 2.8 14.4 + - + -
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Residues in contact with THR 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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199C THR* 3.5 1.3 - - - -
200C LYS* 2.7 37.5 + - + +
201C ASP* 2.7 37.8 + - + +
219C ASP 4.3 1.4 + - - -
220C TYR* 1.3 76.2 + - - +
222C VAL* 1.3 54.2 + - - +
235C PHE* 4.1 25.4 - - + -
236C SER 3.5 2.7 - - - -
237C LYS* 3.6 34.6 + - + -
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Residues in contact with VAL 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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29C VAL* 4.7 8.3 - - + +
32C LEU* 3.7 36.6 - - + +
33C TYR* 4.3 9.4 - - + +
198C LEU* 3.6 19.5 - - + +
199C THR* 4.1 17.9 - - + +
220C TYR* 4.4 3.1 - - + -
221C THR* 1.3 75.5 - - - +
223C GLN* 1.3 65.2 + - - +
224C VAL* 3.3 1.4 + - - +
235C PHE* 4.3 1.6 - - - -
236C SER* 2.8 39.1 + - - +
238C PHE* 3.7 31.6 - - + -
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Residues in contact with GLN 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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32C LEU* 4.3 0.3 - - - +
198C LEU* 2.7 59.9 + - + +
200C LYS* 3.1 25.9 + - - -
222C VAL* 1.3 72.7 - - - +
224C VAL* 1.3 70.3 + - - +
225C PRO* 3.3 3.4 - - - +
226C GLY* 4.1 12.7 + - - +
233C PRO* 4.4 16.1 - - - +
234C GLY 3.1 18.6 + - - +
235C PHE* 3.4 28.4 - - + -
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Residues in contact with VAL 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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28C ARG* 3.8 24.7 - - - +
29C VAL* 3.7 29.8 - - + -
32C LEU* 4.1 4.0 - - + -
222C VAL 3.3 2.0 + - - +
223C GLN* 1.3 72.4 - - - +
225C PRO* 1.3 83.8 - - + +
226C GLY 2.9 8.5 + - - -
227C ALA* 3.7 14.1 - - + +
234C GLY 3.0 20.7 + - - +
235C PHE 4.8 1.3 - - - -
236C SER* 3.9 10.3 - - - +
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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