Contacts of the helix formed by residues 315 - 323 (chain E) in PDB entry 3K75
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 315 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E TYR* 3.5 24.3 - - - -
313E VAL* 3.1 21.1 - - - +
314E ASP* 1.3 80.1 - - - +
316E GLU* 1.3 64.5 + - - +
317E GLN* 3.2 19.8 + - - +
318E ASP* 3.2 28.2 + - - -
319E ILE* 3.6 1.0 - - - +
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Residues in contact with GLU 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E ARG* 3.1 39.6 + - - +
266E TYR* 4.1 20.3 - - + +
269E VAL* 3.7 9.3 - - + +
270E LEU* 3.8 12.7 - - + -
315E SER* 1.3 71.2 - - - +
317E GLN* 1.3 70.6 + - - +
319E ILE* 2.8 22.9 + - + +
320E PHE* 3.1 22.5 + - + -
327E TYR* 3.3 20.5 + - + -
333E ARG* 2.7 36.8 + - - -
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Residues in contact with GLN 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E SER* 3.2 20.4 + - - +
316E GLU* 1.3 79.7 - - - +
318E ASP* 1.3 57.0 + - - +
320E PHE* 2.6 30.3 + - - +
321E ASP* 2.7 24.4 + - - +
327E TYR* 2.9 49.6 + - + -
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Residues in contact with ASP 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PRO* 5.1 0.5 - - - +
312E PRO 4.5 2.0 - - - +
313E VAL* 3.7 13.9 - - + -
314E ASP* 2.7 31.7 + - - +
315E SER* 3.2 22.6 + - - +
316E GLU 3.2 0.2 - - - -
317E GLN* 1.3 76.3 - - - +
319E ILE* 1.3 61.3 + - - +
321E ASP* 3.2 10.6 + - - +
322E TYR* 2.9 39.8 + - + -
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Residues in contact with ILE 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E TYR 3.6 24.2 - - - +
267E CYS* 3.8 17.5 - - - -
270E LEU* 3.6 31.6 - - + -
282E MET* 3.9 7.9 - - + -
293E ILE* 4.0 15.3 - - + -
298E ILE* 4.2 14.6 - - + -
313E VAL* 3.5 23.6 - - + -
315E SER 3.6 7.0 - - - +
316E GLU* 2.8 12.3 + - - +
318E ASP* 1.3 75.8 - - - +
320E PHE* 1.3 60.7 + - - +
322E TYR* 3.9 9.4 + - - +
323E ILE* 3.6 23.9 + - - +
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Residues in contact with PHE 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E LEU* 4.4 6.7 - - + -
278E PHE* 3.8 24.0 - + - -
282E MET* 3.8 21.3 - - + -
316E GLU* 3.1 32.1 + - + -
317E GLN* 2.6 16.5 + - - +
319E ILE* 1.3 72.3 - - - +
321E ASP* 1.3 61.9 + - - +
323E ILE* 3.5 4.9 - - - +
324E GLN 3.1 4.7 + - - -
325E TRP* 2.9 64.2 + + + +
326E ARG 3.7 10.1 - - - -
327E TYR* 3.6 41.3 - + + -
328E ARG* 3.9 18.2 - - + -
333E ARG* 4.3 9.9 - - - -
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Residues in contact with ASP 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PRO* 3.8 19.1 - - + +
97C SER* 3.7 9.4 + - - -
100C ARG* 3.6 22.4 + - - +
136C TYR* 3.6 4.9 - - - -
317E GLN* 2.7 26.8 + - - +
318E ASP* 3.6 12.8 - - - +
320E PHE* 1.3 73.5 - - - +
322E TYR* 1.3 70.2 + - - +
323E ILE 3.1 1.6 - - - -
324E GLN* 2.7 23.5 + - - +
325E TRP 5.5 0.3 - - - +
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Residues in contact with TYR 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE* 4.4 5.6 - + - -
92C SER* 5.9 0.7 - - - -
95C SER* 5.2 7.0 - - - -
96C PRO* 3.8 23.5 - - + +
135C PRO* 5.4 0.5 - - - +
136C TYR* 2.9 36.1 + - - -
291E PHE* 3.7 16.4 - + + -
298E ILE* 3.6 28.9 - - + -
311E LEU* 3.6 39.9 - - + -
312E PRO* 2.7 47.8 + - - +
313E VAL* 3.9 8.1 - - + -
318E ASP* 2.9 30.3 + - + +
319E ILE* 4.0 2.5 - - - +
320E PHE 3.5 0.2 - - - -
321E ASP* 1.3 80.0 - - - +
323E ILE* 1.3 58.8 + - - +
324E GLN* 3.4 1.9 + - - +
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Residues in contact with ILE 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E MET* 4.2 32.8 - - + -
285E HIS* 3.5 24.4 + - + -
286E ALA* 3.9 33.0 - - + +
289E LYS* 3.7 14.0 - - + +
291E PHE* 4.0 22.7 - - + -
293E ILE* 4.6 1.3 - - + -
298E ILE* 4.2 7.9 - - + -
319E ILE 3.6 12.5 + - - +
320E PHE* 3.5 12.6 - - - +
322E TYR* 1.3 75.5 - - - +
324E GLN* 1.3 71.4 + - - +
325E TRP* 3.1 24.6 + - + -
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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