Contacts of the strand formed by residues 317 - 324 (chain B) in PDB entry 1KF9
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 THR 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B LYS* 3.5 38.5 - - + +
311B LEU 3.6 4.7 - - - +
312B THR* 4.4 7.4 + - - +
315B GLY 4.5 2.4 - - - +
316B GLY* 1.3 71.2 - - - -
318B VAL* 1.3 64.5 + - - +
319B ASP 3.4 23.3 - - - +
320B GLU* 4.5 3.6 - - + -
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Residues in contact with VAL 318 (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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233B PRO* 2.9 45.1 - - + +
311B LEU* 2.5 27.3 + - + +
312B THR 5.6 0.2 - - - -
313B SER* 3.5 31.2 - - - +
315B GLY 5.2 3.1 - - - +
316B GLY 3.5 1.5 + - - +
317B THR* 1.3 78.0 - - - +
319B ASP* 1.3 65.5 + - + +
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Residues in contact with ASP 319 (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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234B LYS* 3.1 15.3 - - - +
235B PHE* 2.6 44.0 + - + +
310B LYS* 3.4 1.7 - - - -
311B LEU* 2.7 40.1 + - + -
317B THR* 3.4 7.3 - - - +
318B VAL* 1.3 83.4 - - + +
320B GLU* 1.3 77.5 + - - +
321B LYS* 5.2 1.2 - - - +
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Residues in contact with GLU 320 (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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235B PHE* 4.4 0.8 - - - -
280B TRP* 3.8 9.3 - - - -
308B CYS* 3.8 6.6 - - - +
309B ILE 3.1 37.4 + - - +
310B LYS* 2.4 38.4 + - + -
317B THR* 4.5 4.9 - - + -
319B ASP* 1.3 88.4 + - - +
321B LYS* 1.3 65.1 + - - +
322B CYS* 4.4 12.3 - - - -
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Residues in contact with LYS 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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235B PHE* 4.2 17.5 - - + -
237B LYS* 4.7 7.5 - - - +
238B CYS* 3.7 35.8 + - - +
308B CYS* 3.0 2.1 - - - -
309B ILE* 2.5 63.6 + - + +
319B ASP* 5.2 1.6 - - - +
320B GLU* 1.3 74.8 - - - +
322B CYS* 1.3 70.2 + - - +
323B PHE* 3.7 18.4 - - + +
328B ILE* 4.1 16.2 - - - +
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Residues in contact with CYS 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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42A HIS* 3.7 13.4 + - - +
45A TRP* 4.1 13.2 - - + -
46A TRP* 3.9 19.3 - - + -
307B TYR 3.2 4.0 - - - +
308B CYS* 2.1 48.0 - - - -
320B GLU* 4.0 13.2 - - - -
321B LYS* 1.3 84.4 - - - +
323B PHE* 1.3 67.1 + - - +
327B GLU* 4.4 0.2 - - - +
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Residues in contact with PHE 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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45A TRP* 3.6 12.1 - - - -
238B CYS* 4.1 14.6 - - - -
246B PHE* 3.7 28.5 - + - -
248B CYS* 4.2 5.2 - - - -
306B PRO* 3.2 5.2 - - - +
307B TYR* 2.4 61.8 + + + +
309B ILE* 4.1 18.6 - - + -
321B LYS* 3.7 22.0 - - + +
322B CYS* 1.3 79.9 - - - +
324B SER* 1.3 78.4 + - - +
325B VAL* 4.4 2.0 - - - -
327B GLU* 3.1 20.6 - - - +
328B ILE* 3.1 42.2 - - + -
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Residues in contact with SER 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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45A TRP* 4.5 8.9 - - - -
164A TYR* 4.9 7.3 - - - -
304B TRP* 4.6 8.6 - - - -
305B ILE 3.1 31.2 - - - -
307B TYR* 4.5 0.7 - - - +
323B PHE* 1.3 82.5 - - - +
325B VAL* 1.3 65.0 + - - +
326B ASP* 3.4 3.9 + - - +
327B GLU* 3.1 36.1 + - - +
328B ILE 4.0 0.2 + - - -
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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