Contacts of the strand formed by residues 206 - 222 (chain I) in PDB entry 1K9O
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 ILE 206 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ASP* 3.3 5.6 - - - +
198I PHE* 2.8 44.7 + - + +
200I VAL* 3.7 17.3 - - + -
204I LYS* 5.4 9.4 - - + -
205I THR* 1.3 81.5 - - - +
207I LYS* 1.3 63.7 + - - +
208I VAL* 3.4 27.6 - - + -
385I GLU* 3.6 38.8 - - + +
386I PRO* 5.1 0.9 - - - +
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Residues in contact with LYS 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I MET* 6.0 0.9 - - - -
195I ASP* 3.8 38.5 - - + +
196I ARG* 3.6 4.3 - - - +
197I ASP* 3.3 30.6 + - - +
206I ILE* 1.3 81.2 - - - +
208I VAL* 1.3 64.1 + - - +
209I PRO* 4.7 1.6 - - - +
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Residues in contact with VAL 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I ASP* 3.6 3.6 - - - -
196I ARG 2.8 33.6 + - - +
197I ASP 5.0 0.4 - - - +
198I PHE* 3.9 16.8 - - + -
206I ILE* 3.4 33.9 - - + -
207I LYS* 1.3 74.5 - - - +
209I PRO* 1.4 68.6 - - + +
210I THR* 2.8 23.3 + - - +
282I PRO* 3.7 24.2 - - + -
386I PRO* 4.1 27.4 - - + +
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Residues in contact with PRO 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I THR* 4.2 15.0 - - + -
194I MET 3.6 4.9 - - - +
195I ASP* 3.2 20.8 - - - +
207I LYS 4.7 1.1 - - - +
208I VAL* 1.4 84.0 - - + +
210I THR* 1.3 58.7 + - - +
282I PRO* 3.5 3.6 - - - +
283I LYS* 3.2 39.9 + - + +
386I PRO* 5.9 2.2 - - + +
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Residues in contact with THR 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I THR* 3.5 5.3 - - - +
194I MET 2.7 28.4 + - - +
196I ARG* 3.5 26.0 + - + +
197I ASP 4.9 2.0 + - - +
208I VAL* 2.8 26.2 + - - +
209I PRO* 1.3 71.6 - - - +
211I MET* 1.3 63.4 + - - +
212I ILE* 3.7 7.1 + - - +
280I THR* 3.4 45.3 - - + +
281I LEU 3.8 7.6 - - - -
282I PRO* 4.0 5.6 - - + +
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Residues in contact with MET 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I TRP* 5.1 0.2 - - - +
188I PHE* 3.6 24.7 - - + -
193I THR* 3.7 11.2 - - - +
210I THR* 1.3 71.6 - - - +
212I ILE* 1.3 59.3 + - - +
279I ILE 3.4 1.9 - - - +
280I THR* 3.2 5.0 - - - -
281I LEU* 2.7 81.7 + - + +
282I PRO 3.8 6.7 - - - +
283I LYS* 3.5 22.4 - - + -
335I VAL* 3.8 19.3 - - + -
336I ASN 3.3 32.3 - - - +
337I GLU* 3.5 15.9 - - + -
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Residues in contact with ILE 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I PHE* 3.5 12.9 - - - +
189I VAL* 4.4 4.2 + - - +
192I ARG* 3.2 63.0 + - + +
193I THR* 4.7 1.2 + - - -
194I MET* 4.2 14.6 - - + -
196I ARG* 4.1 22.0 - - - +
210I THR 3.7 6.5 + - - +
211I MET* 1.3 77.2 - - - +
213I GLY* 1.3 61.7 + - - +
278I GLU* 3.5 28.0 - - + +
279I ILE 3.5 4.0 - - - +
280I THR* 3.9 17.7 - - + +
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Residues in contact with GLY 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I LYS 5.6 0.2 - - - -
188I PHE* 3.6 12.6 - - - -
212I ILE* 1.3 77.7 - - - +
214I LYS* 1.3 75.2 + - - -
215I LYS* 4.0 8.0 - - - +
278I GLU* 4.2 2.0 + - - -
279I ILE* 2.7 43.3 + - - +
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Residues in contact with LYS 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E VAL* 5.1 4.0 - - - +
186I ASP* 3.6 12.8 - - - +
189I VAL* 5.7 4.2 - - - +
192I ARG* 3.0 24.6 - - - +
213I GLY* 1.3 77.1 - - - -
215I LYS* 1.3 75.0 + - - +
276I GLU* 5.5 3.4 - - + +
277I VAL 3.4 6.3 - - - +
278I GLU* 3.3 27.6 - - + +
346I ASN* 5.3 12.4 + - - +
356I ILE 5.1 2.7 - - - +
358I TYR* 3.3 42.6 - - + -
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Residues in contact with LYS 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I TRP* 4.8 5.4 - - + -
186I ASP* 3.0 36.9 + - + +
187I LYS 3.4 16.8 + - - -
188I PHE* 3.5 30.6 - - + -
213I GLY* 4.0 18.2 - - - +
214I LYS* 1.3 93.2 + - - +
216I ASP* 1.3 61.0 - - - +
217I VAL* 3.2 28.3 + - + +
232I MET* 4.7 13.9 - - + -
233I SER 6.0 1.1 - - - +
276I GLU* 3.6 4.2 - - - +
277I VAL 2.9 30.8 + - - +
279I ILE* 4.3 13.9 - - + -
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Residues in contact with ASP 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I LYS* 5.8 7.9 - - + +
186I ASP* 6.2 0.8 - - - +
215I LYS* 1.3 70.2 - - - +
217I VAL* 1.3 61.0 + - - +
233I SER* 5.0 8.8 + - - -
275I THR 3.7 5.8 - - - +
276I GLU* 3.0 38.5 + - - +
348I PHE* 5.9 2.8 - - - -
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Residues in contact with VAL 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LYS* 3.2 30.9 + - + +
216I ASP* 1.3 74.4 - - - +
218I ARG* 1.3 67.7 + - - +
219I TYR* 4.5 2.7 - - + +
230I ILE* 3.7 22.9 - - + -
231I GLU 3.3 11.0 - - - +
232I MET* 3.5 27.8 - - + -
274I ASN* 3.6 3.7 - - - +
275I THR* 2.8 49.2 + - + +
277I VAL* 4.7 4.9 - - + -
279I ILE* 4.3 10.8 - - + -
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Residues in contact with ARG 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I VAL* 1.3 73.9 - - - +
219I TYR* 1.3 60.1 + - - +
230I ILE* 3.5 2.3 - - - -
231I GLU* 2.8 60.2 + - + +
269I GLU* 4.2 20.0 + - - +
272I LEU* 3.3 50.5 + - + +
273I TYR 3.0 7.9 - - - +
274I ASN* 3.2 28.3 - - - +
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Residues in contact with TYR 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217I VAL* 3.9 4.4 - - + -
218I ARG* 1.3 74.5 - - - +
220I ALA* 1.3 80.6 + - - +
221I ASP* 4.4 9.0 - - + -
228I LYS* 3.0 47.5 + - + +
229I MET 3.4 4.7 - - - -
230I ILE* 4.0 30.1 - - + -
272I LEU* 3.7 0.7 - - - -
273I TYR* 2.6 70.6 + + + -
275I THR* 3.5 25.1 - - + -
277I VAL* 5.2 3.6 - - + -
361I VAL* 3.7 29.5 - - + +
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Residues in contact with ALA 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I TYR* 1.3 84.3 - - - +
221I ASP* 1.3 60.8 + - - +
222I VAL* 3.6 5.4 + - + -
228I LYS* 3.4 3.6 - - - +
229I MET* 2.6 43.2 + - + +
268I ALA 4.0 9.6 - - - +
271I ARG* 3.7 9.2 - - + +
272I LEU* 3.3 36.1 - - + +
273I TYR* 4.5 2.0 - - - -
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Residues in contact with ASP 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I TYR* 4.4 10.5 + - + -
220I ALA* 1.3 71.2 - - - +
222I VAL* 1.3 59.0 + - - +
223I PRO* 3.3 8.5 - - - +
227I ALA 4.0 5.6 - - - +
228I LYS* 3.3 28.5 + - - +
247I ASN* 5.2 7.5 + - - +
271I ARG* 2.8 38.6 + - - +
273I TYR* 5.1 3.6 - - + -
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Residues in contact with VAL 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220I ALA* 4.1 15.0 - - + +
221I ASP* 1.3 75.2 + - - +
223I PRO* 1.3 62.4 - - + +
224I GLU* 3.9 12.8 - - + +
225I LEU* 3.8 36.1 - - + +
226I ASP* 2.9 22.2 + - - -
227I ALA 2.8 24.5 + - - +
229I MET* 4.3 9.4 - - + -
244I ILE* 6.0 0.7 - - + -
247I ASN* 5.9 0.7 - - - -
268I ALA* 4.0 36.8 - - + +
271I ARG* 4.2 8.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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