Contacts of the strand formed by residues 288 - 299 (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 GLY 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLU 4.0 0.2 - - - +
212A GLN* 3.8 1.0 - - - -
213A GLN* 3.4 29.5 + - - +
286A ASP 4.4 0.4 + - - -
287A ALA* 1.3 73.2 - - - +
289A ALA* 1.3 58.7 + - - +
290A PHE 4.4 0.2 + - - -
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Residues in contact with ALA 289 (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* 3.4 24.7 - - + -
211A GLU 3.1 6.3 - - - +
212A GLN* 4.1 14.4 - - - +
283A ILE* 5.7 2.9 - - + -
287A ALA 3.5 3.6 + - - +
288A GLY* 1.3 75.2 - - - -
290A PHE* 1.3 60.0 + - - +
291A TYR* 3.9 17.9 + - + +
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Residues in contact with PHE 290 (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* 3.7 17.3 - + - +
210A LEU* 3.5 3.7 - - - -
211A GLU* 3.0 43.8 + - + +
288A GLY 4.4 0.2 + - - -
289A ALA* 1.3 71.0 - - - +
291A TYR* 1.3 65.6 + - - +
292A GLY* 3.7 15.5 - - - -
340A ARG* 3.3 60.8 - - + +
342A PRO* 3.9 32.8 - - + -
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Residues in contact with TYR 291 (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 3.4 5.2 - - - -
210A LEU* 3.5 39.9 - - + +
224A PHE* 4.2 20.2 - + - -
283A ILE* 3.8 13.3 - - - +
289A ALA* 3.9 16.7 + - + +
290A PHE* 1.3 78.1 - - - +
292A GLY* 1.3 57.9 + - - +
342A PRO* 3.6 6.2 - - - +
343A MET* 3.1 37.6 + - + +
348A ILE* 3.7 48.8 - - + +
351A ILE* 4.5 11.9 - - + -
352A HIS* 2.8 30.9 + + - -
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Residues in contact with GLY 292 (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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208A ALA* 3.4 0.2 - - - -
209A PHE* 2.9 41.8 + - - +
290A PHE* 3.7 18.8 + - - -
291A TYR* 1.3 75.3 - - - +
293A VAL* 1.3 68.4 + - - +
341A SER 3.1 11.0 - - - -
343A MET* 3.8 4.7 - - - +
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Residues in contact with VAL 293 (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* 4.3 22.9 - - + -
207A SER 3.2 8.3 - - - +
208A ALA* 3.8 17.9 - - + -
209A PHE* 4.0 0.6 - - - -
292A GLY* 1.3 80.3 - - - +
294A THR* 1.3 65.9 + - - +
295A SER* 4.0 6.4 + - - +
321A LYS* 5.1 2.9 - - - +
323A GLU* 5.8 1.8 - - - +
338A ILE* 4.3 2.6 - - - +
340A ARG 4.2 0.2 + - - -
341A SER* 2.5 42.7 + - - +
343A MET* 3.7 17.7 - - + -
344A P1L 3.8 25.1 - - + -
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Residues in contact with THR 294 (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 27.1 - - - +
207A SER* 2.7 39.2 + - - -
209A PHE* 3.4 19.4 - - - -
221A LYS* 5.7 0.8 + - - -
293A VAL* 1.3 71.7 - - - +
295A SER* 1.3 59.0 + - - +
337A ARG* 3.7 27.6 - - - +
338A ILE 3.5 15.7 - - - +
339A ASN* 4.4 0.3 + - - -
340A ARG* 3.1 22.5 + - - +
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Residues in contact with SER 295 (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 12.6 - - - -
206A PHE* 4.0 18.8 - - - -
293A VAL* 4.0 6.9 + - - +
294A THR* 1.3 74.2 - - - +
296A GLN* 1.3 58.3 + - - +
297A TYR* 3.2 28.4 + - - -
323A GLU* 5.6 0.2 + - - -
337A ARG* 3.5 1.4 - - - -
338A ILE* 2.7 55.8 + - - +
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Residues in contact with GLN 296 (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* 3.9 2.4 - - - -
204A VAL* 3.1 33.2 + - + +
205A GLU* 2.8 40.3 + - + +
295A SER* 1.3 73.0 - - - +
297A TYR* 1.3 64.9 + - - +
298A GLU* 2.9 27.3 + - - -
330A GLU* 5.2 3.6 + - - -
333A ARG* 5.1 0.4 - - - +
335A VAL* 3.6 24.9 - - + +
336A TYR 3.7 2.5 - - - -
337A ARG* 4.0 24.8 + - + +
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Residues in contact with TYR 297 (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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201A LEU* 3.9 37.9 - - + -
202A ARG 3.4 4.3 - - - +
203A LEU* 3.7 38.4 - - + -
295A SER* 3.2 36.6 + - - -
296A GLN* 1.3 74.1 - - - +
298A GLU* 1.3 61.4 + - - +
305A VAL* 5.4 0.2 - - + -
307A CYS* 3.8 26.3 - - - +
335A VAL* 3.5 2.6 - - - +
336A TYR* 2.6 61.5 + - + +
338A ILE* 4.2 4.4 - - + +
374A LEU* 3.9 21.3 - - + +
376A VAL* 3.8 20.8 - - + +
386A LEU* 4.7 1.3 - - + -
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Residues in contact with GLU 298 (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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201A LEU* 4.8 0.2 - - - -
202A ARG* 2.8 50.4 + - - +
204A VAL* 3.7 32.2 - - + +
296A GLN* 2.9 23.8 + - - +
297A TYR* 1.3 76.2 - - - +
299A SER* 1.3 59.8 + - - +
333A ARG* 3.1 43.2 + - - -
334A PHE 3.7 3.6 - - - -
335A VAL* 3.7 15.0 - - + -
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Residues in contact with SER 299 (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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199A THR 3.9 3.5 + - - -
200A LYS 2.6 29.7 + - - -
201A LEU* 4.0 4.5 - - - +
202A ARG* 4.9 5.2 - - - +
298A GLU* 1.3 75.4 - - - +
300A SER* 1.3 62.2 + - - +
301A GLU* 3.1 18.4 + - - +
303A MET* 4.0 1.7 - - - +
333A ARG* 3.8 5.7 - - - +
334A PHE* 2.7 33.1 + - - +
336A TYR* 3.4 25.3 - - - -
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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