Contacts of the strand formed by residues 202 - 215 (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 ARG 202 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C ARG* 4.1 13.1 - - - +
195C SER* 2.9 46.1 + - - -
196C ILE 3.3 5.6 - - - +
197C GLY 2.8 40.4 + - - +
198C THR 3.2 20.8 + - - +
201C LEU* 1.3 73.8 - - - +
203C LEU* 1.3 59.4 + - - +
204C VAL* 3.5 7.6 + - + +
297C TYR* 3.2 8.1 - - - +
298C GLU* 2.9 39.7 + - + +
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Residues in contact with LEU 203 (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 SER* 3.0 7.4 - - - -
196C ILE* 2.8 50.7 + - + +
202C ARG* 1.3 68.6 - - - +
204C VAL* 1.3 59.1 + - - +
205C GLU 3.6 21.8 - - - +
206C PHE* 4.0 24.9 - - + -
227C ILE* 4.2 8.7 - - + +
295C SER* 4.2 3.8 - - - -
296C GLN 4.1 2.2 - - - +
297C TYR* 3.3 44.6 - - + +
374C LEU* 5.0 0.4 - - + -
386C LEU* 3.8 10.7 - - + +
388C MET* 3.4 30.5 - - + -
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Residues in contact with VAL 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ARG 5.4 0.3 + - - -
195C SER* 4.1 19.8 + - - -
202C ARG* 3.9 4.0 - - + +
203C LEU* 1.3 77.0 - - - +
205C GLU* 1.3 61.1 + - + +
227C ILE* 4.6 2.0 - - - -
228C GLY* 3.6 19.9 - - - +
296C GLN* 2.7 42.3 + - + +
298C GLU* 3.4 40.6 - - + +
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Residues in contact with GLU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LEU* 3.6 9.5 - - - +
204C VAL* 1.3 81.3 - - + +
206C PHE* 1.3 71.5 + - - +
207C SER* 3.5 11.3 + - - -
227C ILE 3.2 7.6 - - - +
228C GLY 4.7 3.4 - - - +
229C HIS* 2.7 38.8 + - + +
294C THR* 3.3 29.8 - - - +
295C SER* 3.3 3.8 - - - -
296C GLN* 3.0 37.5 + - + +
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Residues in contact with PHE 206 (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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203C LEU* 4.0 24.0 - - + -
205C GLU* 1.3 76.2 + - - +
207C SER* 1.3 67.6 + - - +
208C ALA 4.7 1.6 - - - -
225C VAL* 4.0 25.1 - - + -
226C HIS* 3.1 3.6 - - - +
227C ILE* 2.7 44.2 + - + +
275C PHE* 4.7 15.9 - + - -
293C VAL* 3.5 29.2 - - + -
294C THR 3.3 6.5 - - - -
295C SER* 3.8 19.7 - - - -
297C TYR* 5.6 0.2 - - - -
344C P1L 4.0 23.6 - - + -
374C LEU* 4.7 18.2 - - + -
388C MET* 6.1 1.8 - - - -
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Residues in contact with SER 207 (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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205C GLU* 3.5 14.8 + - - -
206C PHE* 1.3 81.4 - - - +
208C ALA* 1.3 59.9 - - - +
209C PHE* 3.9 9.4 - - - -
221C LYS* 5.6 1.6 + - - -
223C LEU* 4.5 12.2 - - - +
225C VAL 3.3 9.6 - - - -
226C HIS* 4.3 7.4 - - - -
229C HIS* 4.3 4.7 - - - -
293C VAL* 3.3 6.5 - - - +
294C THR* 2.8 48.3 + - - +
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Residues in contact with ALA 208 (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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207C SER* 1.3 72.5 - - - +
209C PHE* 1.3 56.6 + - - +
223C LEU* 3.4 5.0 - - - +
224C PHE* 2.7 36.0 + - + -
225C VAL* 3.1 15.4 + - + +
292C GLY 3.4 8.3 - - - +
293C VAL* 4.4 4.3 - - + +
343C MET* 4.7 2.7 - - - -
344C P1L 3.6 48.0 - - + -
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Residues in contact with PHE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C SER* 3.9 16.8 - - - -
208C ALA* 1.3 74.5 - - - +
210C LEU* 1.3 60.3 + - - +
211C GLU* 3.8 30.1 - - + -
221C LYS* 3.8 19.5 - - + -
222C HIS 3.0 14.6 - - - +
223C LEU* 3.9 13.2 - - + -
224C PHE* 3.6 11.6 - - - -
290C PHE* 3.9 21.5 - + - -
291C TYR* 3.5 4.3 - - - +
292C GLY* 3.0 55.3 + - - -
293C VAL 4.0 1.8 - - - -
294C THR* 3.5 27.1 - - - -
340C ARG* 4.0 19.7 - - + -
343C MET* 4.6 1.2 - - - +
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Residues in contact with LEU 210 (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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209C PHE* 1.3 73.2 - - - +
211C GLU* 1.3 72.8 + - - +
212C GLN* 3.6 30.5 + - + +
220C ASN* 3.9 1.2 + - - +
221C LYS* 3.5 1.2 - - - -
222C HIS* 2.8 38.7 + - + +
224C PHE* 3.6 21.0 - - + -
281C CYS* 4.6 9.6 - - + -
283C ILE* 3.8 29.6 - - + -
289C ALA* 3.9 9.4 - - + -
290C PHE 3.5 8.5 - - - +
291C TYR* 3.5 33.4 - - + +
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Residues in contact with GLU 211 (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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209C PHE* 3.8 17.7 - - + -
210C LEU* 1.3 71.2 - - - +
212C GLN* 1.3 66.0 + - - +
219C TYR* 2.3 44.4 + - + +
220C ASN 3.3 4.5 - - - +
221C LYS* 3.9 11.8 + - + -
288C GLY 3.6 0.2 - - - +
289C ALA* 3.2 5.5 - - - -
290C PHE* 2.8 45.4 + - + +
340C ARG* 2.8 45.5 + - - -
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Residues in contact with GLN 212 (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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210C LEU* 3.6 32.8 + - + +
211C GLU* 1.3 81.9 - - - +
213C GLN* 1.3 61.7 + - - +
214C ARG 3.8 1.4 + - - +
218C SER 3.8 0.3 - - - +
219C TYR* 3.4 8.5 - - - -
220C ASN* 2.7 60.3 + - + +
222C HIS* 6.0 0.8 - - - +
281C CYS* 5.4 1.6 - - - +
282C ASN 2.8 24.7 + - - +
283C ILE* 3.8 1.2 - - - +
284C GLN* 2.8 50.3 + - + +
287C ALA* 5.5 1.6 - - + -
288C GLY 3.1 8.7 - - - +
289C ALA* 4.4 5.5 - - + +
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Residues in contact with GLN 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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212C GLN* 1.3 72.6 - - - +
214C ARG* 1.3 65.1 + - - +
215C ASP* 2.5 34.9 + - - +
216C PRO* 4.2 8.8 + - + +
218C SER 2.5 22.3 + - - +
219C TYR* 4.1 18.4 - - + +
287C ALA* 3.7 3.6 - - - +
288C GLY* 2.8 31.5 + - - +
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Residues in contact with ARG 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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222A HIS* 5.0 2.8 + - - -
278A ASP* 5.2 2.2 + - - -
280A ASN* 3.1 42.7 + - - +
281A CYS* 5.6 2.6 - - - +
282A ASN* 5.7 2.4 - - - +
212C GLN 3.8 2.8 + - - -
213C GLN* 1.3 73.9 - - - +
215C ASP* 1.3 77.1 + - - +
218C SER* 3.4 33.2 + - - -
284C GLN* 3.7 29.5 + - - +
286C ASP 5.6 0.5 - - - +
287C ALA* 3.9 16.9 - - + +
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Residues in contact with ASP 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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278A ASP* 5.1 3.5 - - - +
398A GLU 4.5 8.9 - - - +
399A HIS* 3.5 14.8 - - - +
213C GLN* 2.5 37.6 + - - -
214C ARG* 1.3 106.6 + - - +
216C PRO* 1.3 69.2 - - + +
217C ASP* 2.8 32.5 + - - +
218C SER* 3.1 18.6 + - - -
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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