Contacts of the helix formed by residues 320 - 328 (chain B) in PDB entry 1KY9
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 SER 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271B GLU* 3.1 22.7 - - - -
287B GLY 3.9 4.0 - - - -
288B ALA* 4.2 4.9 - - - -
318B ILE* 3.5 3.0 - - - +
319B SER* 1.3 84.4 + - - +
321B PHE* 1.3 69.7 + - - +
322B ALA* 3.5 10.4 - - - +
323B ALA* 2.9 31.3 + - - +
324B LEU* 3.1 10.2 + - - +
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ILE* 3.0 39.9 - - + -
268B MSE 4.4 3.6 - - - -
269B GLY* 3.3 35.0 - - - -
270B THR* 3.7 19.3 - - + +
271B GLU* 2.5 16.8 + - + +
288B ALA* 3.7 25.1 - - + +
289B PHE 4.7 0.9 - - - -
320B SER* 1.3 67.9 - - - +
322B ALA* 1.3 54.2 + - - +
324B LEU* 2.8 10.8 + - + +
325B ARG* 2.7 70.6 + - + +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B GLU* 3.6 3.2 + - - +
320B SER* 2.9 13.2 - - - +
321B PHE* 1.3 82.5 - - - +
323B ALA* 1.3 64.9 + - - +
325B ARG* 3.1 9.2 + - - +
326B ALA* 3.0 24.2 + - - +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B PRO 5.4 1.3 - - - +
318B ILE* 4.8 8.3 - - + -
319B SER* 4.5 12.6 - - - +
320B SER* 2.9 27.6 + - - +
322B ALA* 1.3 76.4 - - - +
324B LEU* 1.3 57.0 + - - +
326B ALA* 3.5 5.6 + - - +
327B GLN* 3.0 37.1 + - + +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 4.4 14.8 - - + -
267B ILE* 5.4 6.1 - - + -
288B ALA* 3.8 23.1 - - + -
310B ILE* 4.2 26.9 - - + -
313B LEU* 4.5 8.7 - - + -
318B ILE* 3.8 21.5 - - + +
320B SER 3.1 6.2 + - - +
321B PHE* 2.8 23.0 + - + +
323B ALA* 1.3 71.1 - - - +
325B ARG* 1.3 66.4 + - - +
326B ALA 3.1 1.6 - - - -
327B GLN* 3.1 5.0 + - - -
328B VAL* 2.9 53.4 + - + +
339B LEU* 5.1 0.4 - - + -
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ARG* 2.6 78.9 + - - +
321B PHE* 2.7 53.6 + - + +
322B ALA* 3.7 7.8 - - - +
324B LEU* 1.3 72.8 - - - +
326B ALA* 1.3 58.4 + - - +
328B VAL* 3.0 18.0 - - + +
329B GLY 3.5 3.1 + - - -
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ARG* 5.0 4.3 - - - +
196B GLU* 4.3 21.9 - - - +
322B ALA 3.0 16.0 + - - +
323B ALA* 3.7 6.1 - - - +
325B ARG* 1.3 75.9 - - - +
327B GLN* 1.3 64.2 + - + +
329B GLY* 3.2 13.6 + - - +
330B THR* 3.6 11.4 + - - -
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU* 3.0 43.3 + - + +
316B LYS* 4.7 19.7 + - - +
317B PRO 4.3 5.4 - - - +
318B ILE* 3.6 18.7 - - - +
323B ALA* 3.0 23.3 + - + +
324B LEU* 3.1 4.9 + - - +
326B ALA* 1.3 71.6 - - - +
328B VAL* 1.3 63.4 + - - +
329B GLY 3.0 5.4 - - - -
330B THR* 3.1 14.6 + - - -
331B MSE 2.9 28.9 - - + +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ARG* 4.4 5.2 - - - +
262B ARG* 5.9 0.2 - - - +
263B GLY 3.5 22.8 + - - +
264B GLU* 5.9 1.1 - - - -
265B LEU* 4.3 23.1 - - + +
313B LEU* 4.3 2.5 - - + -
324B LEU* 2.9 41.8 + - + +
325B ARG* 3.0 23.6 - - + +
327B GLN* 1.3 76.3 - - - +
329B GLY* 1.3 58.8 + - - +
330B THR 3.2 2.3 + - - -
331B MSE 3.7 21.6 + - - +
337B LEU* 4.0 22.7 - - + -
352B LEU* 4.7 3.1 - - + +
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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