Contacts of the strand formed by residues 270 - 277 (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 PHE 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ILE* 4.9 0.2 - - + -
258A LEU* 4.1 14.8 - - + -
261A LEU* 3.3 40.8 - - + -
262A PHE* 3.5 43.1 - + + -
265A GLY 4.7 2.2 - - - -
266A PRO 3.3 24.2 - - - -
267A GLN 3.2 12.7 + - - +
268A ASN* 3.4 1.2 - - - -
269A ALA* 1.3 78.1 - - - +
271A PHE* 1.3 71.6 + - - +
384A THR* 4.0 21.3 - - + -
387A CYS* 3.5 31.0 - - + -
407A ARG* 4.0 2.4 - - - +
408A LEU* 3.2 25.9 + - + +
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Residues in contact with PHE 271 (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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195A SER 5.0 2.9 - - - -
196A ILE* 4.8 10.3 - - + -
197A GLY* 3.7 24.7 - - - -
239A LEU* 4.4 16.4 - - + -
268A ASN 3.5 26.9 - - - -
269A ALA* 3.5 9.9 - - - -
270A PHE* 1.3 80.0 - - - +
272A LEU* 1.3 60.1 + - - +
273A VAL* 5.1 0.4 - - + -
386A LEU* 3.6 27.1 - - + -
387A CYS 2.9 9.8 + - - +
388A MET* 4.4 11.9 - - + -
389A ALA 2.8 25.7 + - - -
405A ILE* 4.1 20.2 - - + -
406A TYR 3.4 15.0 - - - +
407A ARG* 4.3 13.7 - - + -
408A LEU* 3.5 10.7 - - - +
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Residues in contact with LEU 272 (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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242A VAL* 4.0 22.9 - - + -
247A ILE* 3.8 39.9 - - + -
251A PHE* 4.8 0.2 - - + -
271A PHE* 1.3 73.0 - - - +
273A VAL* 1.3 64.0 + - - +
389A ALA* 3.4 19.7 - - + +
391A VAL* 4.1 22.2 - - + -
405A ILE* 3.6 1.0 - - - +
406A TYR* 2.7 50.2 + - + +
408A LEU* 3.7 18.1 - - + +
91B LEU* 4.9 0.2 - - + -
95B PHE* 3.8 26.7 - - + -
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Residues in contact with VAL 273 (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* 6.4 0.4 - - + -
227A ILE* 4.5 2.9 - - + -
271A PHE* 5.1 0.9 - - + -
272A LEU* 1.3 81.2 - - - +
274A LYS* 1.3 65.5 + - - +
275A PHE* 3.5 41.1 - - + -
388A MET* 3.6 33.2 - - + -
389A ALA 2.7 12.1 + - - +
390A CYS* 3.5 2.4 - - - +
391A VAL* 3.0 28.2 + - - +
403A HIS* 4.4 3.8 - - + -
404A HIS 3.3 9.9 - - - +
405A ILE* 3.9 27.4 - - + -
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Residues in contact with LYS 274 (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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272A LEU 4.2 0.8 + - - -
273A VAL* 1.3 72.0 - - - +
275A PHE* 1.3 66.1 + - - +
276A TRP* 3.6 22.1 - - + -
391A VAL* 3.4 23.5 - - + +
392A PHE 4.3 0.9 - - - -
393A GLU* 3.0 51.7 + - - +
403A HIS* 3.2 4.9 - - - +
404A HIS* 2.8 39.2 + - + +
406A TYR* 4.2 6.8 - - + -
95B PHE* 2.7 65.5 + - + +
96B PHE* 4.1 5.5 - - - -
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A PHE* 3.8 18.2 - + - -
225A VAL* 3.6 32.5 - - + -
226A HIS 4.8 2.2 - - - -
227A ILE* 3.5 39.0 - - + -
273A VAL* 3.5 18.4 - - + -
274A LYS* 1.3 76.2 - - - +
276A TRP* 1.3 62.9 + - - +
277A ALA 3.7 0.2 - - - -
388A MET* 4.7 0.7 - - + -
390A CYS* 3.7 26.7 - - + -
391A VAL 2.7 11.9 + - - -
392A PHE* 3.3 39.8 - + + -
393A GLU 2.8 27.2 + - - +
402A GLN 3.8 2.7 - - - -
403A HIS* 3.7 15.0 - + + -
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Residues in contact with TRP 276 (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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225A VAL* 4.7 0.6 - - - +
274A LYS* 3.6 36.3 - - + -
275A PHE* 1.3 71.8 - - - +
277A ALA* 1.3 66.1 + - - +
393A GLU* 3.4 31.2 + - + -
394A VAL 4.3 2.9 - - - -
395A SER* 3.5 26.2 - - - +
396A ASN 5.3 1.1 - - - -
401A ALA* 3.3 9.2 - - - +
402A GLN* 2.8 54.8 + - + +
404A HIS* 3.5 32.5 - - - -
94B SER 3.7 8.3 - - - -
95B PHE 3.7 13.7 - - - -
96B PHE* 4.1 4.6 + - - -
97B LYS 4.0 2.0 - - - -
98B PRO* 3.5 45.5 - - + +
99B PRO* 4.1 1.8 - - + -
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Residues in contact with ALA 277 (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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224A PHE 3.4 6.7 - - - +
225A VAL* 3.8 18.8 - - + -
275A PHE 3.7 1.8 - - - -
276A TRP* 1.3 72.9 - - - +
278A ASP* 1.3 61.8 + - - +
279A LEU* 3.5 10.6 + - + -
344A P1L 4.0 28.5 - - + -
367A LEU* 6.2 0.7 - - + -
392A PHE* 4.8 6.1 - - + -
393A GLU 2.8 15.5 + - - +
394A VAL* 3.5 6.2 - - + +
395A SER* 2.6 27.1 + - - -
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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