Contacts of the strand formed by residues 202 - 215 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A SER* 6.2 3.4 - - - +
196A ILE 3.6 11.7 - - - +
197A GLY* 4.0 8.5 - - - -
198A THR 2.8 26.7 - - - +
199A THR* 3.9 29.5 + - - +
201A LEU* 1.3 71.9 - - - +
203A LEU* 1.3 63.2 + - - +
204A VAL* 3.2 13.6 + - + +
297A TYR* 3.4 2.6 - - - -
298A GLU* 2.8 61.7 + - - +
299A SER 4.9 5.3 - - - -
300A SER* 4.7 8.7 - - - +
333A ARG* 5.0 12.3 - - - +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ILE* 3.4 37.8 + - + +
202A ARG* 1.3 68.1 - - - +
204A VAL* 1.3 61.3 + - - +
205A GLU 4.0 20.9 - - - +
206A PHE* 4.3 11.4 - - + -
227A ILE* 3.9 31.8 - - + +
296A GLN 3.9 4.7 - - - -
297A TYR* 3.7 26.2 - - + -
374A LEU* 4.7 2.9 - - + -
386A LEU* 3.5 25.9 - - + +
388A MET* 3.8 28.9 - - + -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ILE 5.7 0.2 - - - +
202A ARG* 3.2 21.0 + - + +
203A LEU* 1.3 78.2 - - - +
205A GLU* 1.3 64.1 + - + +
227A ILE* 5.1 0.6 - - - +
228A GLY* 3.4 25.6 - - - +
296A GLN* 3.1 35.9 + - - +
298A GLU* 3.7 34.8 - - + +
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.6 7.5 - - - +
204A VAL* 1.3 82.9 - - + +
206A PHE* 1.3 63.7 + - - +
207A SER* 3.4 17.8 - - - -
227A ILE 3.5 3.8 - - - +
228A GLY 5.3 1.1 - - - +
229A HIS* 3.9 21.5 + - + +
294A THR* 3.4 35.1 - - - +
295A SER* 3.4 4.0 - - - -
296A GLN* 2.8 67.7 + - + +
337A ARG* 4.6 2.1 + - - -
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 4.3 10.1 - - + -
205A GLU* 1.3 75.9 - - - +
207A SER* 1.3 69.9 + - - +
208A ALA* 5.0 1.6 - - + -
225A VAL* 3.8 26.5 - - + -
226A HIS* 3.4 2.6 - - - +
227A ILE* 2.9 62.5 + - + +
229A HIS* 4.0 1.7 + - - -
275A PHE* 3.8 16.8 - + - -
293A VAL* 4.3 22.7 - - + -
294A THR 3.5 4.5 - - - -
295A SER* 4.0 16.6 - - - +
344A P1L 4.9 16.4 - - + -
372A ILE* 6.5 0.7 - - + -
374A LEU* 4.4 16.6 - - + -
388A MET* 4.3 12.6 - - + -
390A CYS* 5.7 2.5 - - - -
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLU* 3.4 17.0 - - - -
206A PHE* 1.3 83.9 - - - +
208A ALA* 1.3 58.2 + - - +
209A PHE* 4.1 7.6 - - - -
221A LYS* 5.5 1.4 + - - -
223A LEU* 3.6 25.6 - - - +
225A VAL 3.6 8.0 + - - -
229A HIS* 4.3 11.3 - - - -
293A VAL* 3.2 6.1 - - - +
294A THR* 2.7 42.0 + - - -
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 5.3 1.6 - - + -
207A SER* 1.3 72.9 - - - +
209A PHE* 1.3 64.4 + - - +
223A LEU* 3.6 4.0 - - - +
224A PHE* 2.8 33.8 + - + -
225A VAL* 3.3 17.5 + - + +
292A GLY 3.4 4.9 - - - +
293A VAL* 3.8 17.9 - - + -
343A MET* 4.7 1.6 - - - -
344A P1L 3.9 30.7 - - + -
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Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 4.1 13.2 - - - -
208A ALA* 1.3 76.8 - - - +
210A LEU* 1.3 60.1 - - - +
211A GLU* 3.9 23.6 - - + -
221A LYS* 3.5 27.4 - - + -
222A HIS 3.0 13.5 - - - +
223A LEU* 3.7 14.1 - - + -
224A PHE* 3.6 11.3 - - - -
290A PHE* 3.7 37.5 - + - -
291A TYR* 3.4 4.5 - - - +
292A GLY 2.9 49.0 + - - +
293A VAL 4.3 0.4 - - - -
294A THR* 3.4 27.4 - - - -
340A ARG* 4.2 13.2 - - + -
343A MET* 4.5 0.4 - - - +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 1.3 73.7 - - - +
211A GLU* 1.3 62.4 + - - +
212A GLN* 3.8 27.3 + - + +
220A ASN* 3.9 3.0 + - - +
221A LYS* 3.4 1.7 - - - -
222A HIS* 2.8 43.5 + - + +
224A PHE* 3.7 15.4 - - + -
281A CYS* 4.4 12.3 - - + -
283A ILE* 4.1 16.2 - - + -
289A ALA* 3.4 31.0 - - + -
290A PHE 3.5 9.2 - - - +
291A TYR* 3.5 36.3 - - + +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 3.9 17.2 - - + -
210A LEU* 1.3 70.1 - - - +
212A GLN* 1.3 65.9 + - - +
219A TYR* 2.6 41.2 + - + +
220A ASN 3.2 4.0 - - - +
221A LYS* 4.3 9.1 + - + +
288A GLY 4.0 0.6 - - - +
289A ALA* 3.1 9.2 - - - +
290A PHE* 3.0 42.2 + - + +
340A ARG* 2.5 46.6 + - - -
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Residues in contact with GLN 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 3.8 24.6 - - + +
211A GLU* 1.3 81.5 - - - +
213A GLN* 1.3 61.6 + - - +
214A ARG 3.8 1.8 + - - -
218A SER 4.0 0.3 - - - +
219A TYR* 3.5 6.0 - - - -
220A ASN* 2.7 50.2 + - + +
281A CYS* 5.6 1.6 - - - +
282A ASN 3.2 26.5 + - - -
283A ILE* 3.4 10.0 - - - +
284A GLN* 3.1 54.5 + - - +
287A ALA* 4.3 3.9 - - + +
288A GLY 3.8 3.6 - - - -
289A ALA* 4.1 10.8 - - + +
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Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLN* 1.3 72.0 - - - +
214A ARG* 1.3 66.0 + - - +
215A ASP* 3.2 21.6 + - - +
216A PRO* 4.1 11.5 - - + +
218A SER 3.2 16.7 + - - +
219A TYR* 3.6 28.2 - - - +
287A ALA* 3.5 13.4 - - - +
288A GLY* 3.4 17.7 + - - +
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLN 3.8 1.4 + - - -
213A GLN* 1.3 73.9 - - - +
215A ASP* 1.3 79.4 + - - +
218A SER* 2.7 33.5 + - - -
284A GLN* 3.4 23.1 + - - +
286A ASP* 3.7 27.9 - - - +
287A ALA* 3.5 11.7 - - - -
222C HIS* 4.6 4.8 + - - -
278C ASP* 5.5 1.4 + - - -
280C ASN* 3.4 38.3 + - - +
281C CYS* 5.4 1.0 - - - +
399C HIS* 3.5 21.3 + - - +
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Residues in contact with ASP 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN* 3.2 19.9 - - - +
214A ARG* 1.3 104.2 + - - +
216A PRO* 1.4 74.7 - - + +
217A ASP* 3.0 25.4 + - - +
218A SER* 2.9 31.9 + - - +
278C ASP* 4.9 5.0 - - - +
280C ASN* 5.3 1.9 + - - -
399C HIS* 3.5 34.6 + - + -
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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