Contacts of the helix formed by residues 285 - 295 (chain E) in PDB entry 6CXI
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 ASP 285 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ARG* 2.9 30.9 + - - -
62C GLY* 3.0 26.8 - - - +
63C ILE* 4.8 1.7 - - - +
201C THR* 6.1 4.7 - - - +
267D GLY 5.4 2.1 - - - +
170E LEU* 4.5 8.3 - - - +
172E HIS* 5.3 5.3 + - - -
283E LYS 5.1 1.7 - - - +
284E CYS* 1.3 74.5 - - - +
286E VAL* 1.3 66.7 + - + +
287E ASP 4.5 3.6 - - - +
288E ILE* 3.1 33.6 - - + +
289E ARG* 3.1 9.2 - - - +
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Residues in contact with VAL 286 (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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199C PHE* 6.1 0.7 - - + -
203C ALA* 6.4 1.6 - - + -
204C GLU* 3.4 35.4 - - + +
241C LEU* 5.6 2.7 - - + -
242C PRO* 3.2 18.8 - - + +
243C ASP* 3.3 44.7 - - + +
285E ASP* 1.3 73.7 - - + +
287E ASP* 1.3 67.2 + - + +
289E ARG* 3.3 38.3 + - - +
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Residues in contact with ASP 287 (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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58C GLN 4.3 2.6 - - - +
59C SER 4.1 9.9 - - - +
61C ARG* 3.6 34.4 + - + +
62C GLY* 3.5 31.7 + - - +
203C ALA* 5.1 4.9 - - + -
242C PRO* 4.5 16.4 - - + +
165E TYR* 4.3 1.7 + - - -
285E ASP* 3.3 1.0 - - + -
286E VAL* 1.3 85.8 - - + +
288E ILE* 1.3 64.3 + - - +
289E ARG 3.5 0.5 + - - -
290E LYS* 2.9 42.7 + - - +
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Residues in contact with ILE 288 (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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62C GLY* 3.9 22.2 - - - -
63C ILE* 4.3 6.1 - - + +
163E PRO* 5.9 0.2 - - + -
164E ILE 5.7 0.2 - - - -
165E TYR* 3.3 57.2 - - + +
170E LEU* 3.5 32.1 - - + -
284E CYS* 4.1 4.5 - - + -
285E ASP* 3.1 26.5 - - + +
287E ASP* 1.3 75.9 - - - +
289E ARG* 1.3 60.7 + - - +
290E LYS* 3.3 3.1 - - - +
291E ASP* 2.8 22.7 - - - +
292E LEU* 3.0 26.8 - - + +
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Residues in contact with ARG 289 (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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243C ASP* 3.2 33.1 + - - +
281E ILE* 3.5 30.0 + - + +
282E MET* 2.7 50.6 + - - +
284E CYS 3.1 16.2 + - - -
285E ASP 3.1 16.5 + - - +
286E VAL* 3.3 32.8 - - - +
287E ASP 3.3 0.6 - - - -
288E ILE* 1.3 78.1 - - - +
290E LYS* 1.3 63.5 + - - +
292E LEU* 3.0 21.6 + - + +
293E TYR* 3.1 24.8 - - + -
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Residues in contact with LYS 290 (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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59C SER 4.7 7.7 + - - -
242C PRO* 3.8 28.0 + - + +
165E TYR* 4.9 5.5 + - - -
287E ASP* 2.9 39.2 + - - +
288E ILE* 4.8 2.2 - - - +
289E ARG* 1.3 79.6 - - - +
291E ASP* 1.3 72.4 + - + +
293E TYR* 4.2 4.0 + - - +
294E ALA* 4.5 7.6 + - - +
324E MET* 3.4 44.6 - - + +
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Residues in contact with ASP 291 (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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148E THR* 3.0 35.7 - - - +
149E GLY* 4.5 0.2 - - - -
165E TYR* 4.1 8.7 - - - -
288E ILE* 2.8 31.9 - - - +
290E LYS* 1.3 87.1 - - + +
292E LEU* 1.3 64.7 + - - +
293E TYR 3.4 1.1 - - - -
294E ALA* 4.0 6.1 - - + +
295E ASN* 2.8 41.8 + - - +
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Residues in contact with LEU 292 (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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148E THR* 5.0 1.1 - - + -
149E GLY* 3.2 30.7 - - - +
150E ILE* 3.1 37.3 - - + +
163E PRO* 4.1 8.7 - - + -
164E ILE 4.0 10.3 - - - +
281E ILE* 4.4 19.1 - - + -
284E CYS* 4.0 30.3 - - + -
288E ILE* 3.0 31.6 - - + +
289E ARG* 3.0 18.6 + - - +
291E ASP* 1.3 81.5 + - - +
293E TYR* 1.3 60.7 + - - +
295E ASN 3.4 8.5 + - - -
296E THR* 3.4 1.6 + - - -
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Residues in contact with TYR 293 (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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243C ASP 5.9 0.9 - - - -
278E PHE* 4.2 10.3 - + - -
281E ILE* 3.4 40.0 - - + +
282E MET* 3.4 28.8 - - - +
289E ARG* 3.1 34.3 - - + -
290E LYS 4.6 3.8 - - - +
291E ASP 3.4 0.4 - - - -
292E LEU* 1.3 77.9 - - - +
294E ALA* 1.3 57.7 + - - +
296E THR* 3.2 17.7 + - - -
316E ILE* 3.9 16.1 - - + +
320E ALA* 3.3 30.7 - - + -
321E PRO* 4.3 13.2 - - + +
324E MET* 4.4 13.7 - - + -
326E ILE* 3.3 33.8 - - + +
327E LYS 3.3 9.2 - - - +
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Residues in contact with ALA 294 (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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146E ARG* 4.7 0.5 + - - -
290E LYS 4.5 8.2 + - - +
291E ASP* 3.7 7.4 + - + +
292E LEU 3.4 0.2 - - - -
293E TYR* 1.3 75.5 - - - +
295E ASN* 1.3 69.2 + - - +
324E MET* 6.4 0.2 - - + -
325E LYS 3.9 16.8 - - - +
327E LYS* 2.9 48.4 - - + +
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Residues in contact with ASN 295 (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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141E LEU* 6.2 0.3 - - - +
146E ARG* 2.8 38.5 + - - +
148E THR* 2.7 22.2 - - - +
149E GLY* 3.3 18.3 - - - -
150E ILE 3.5 9.0 + - - +
291E ASP* 2.8 36.5 + - - +
292E LEU 3.4 4.0 + - - +
293E TYR 3.3 0.6 - - - -
294E ALA* 1.3 89.5 + - - +
296E THR* 1.3 63.1 + - - +
297E VAL* 3.4 14.9 + - - +
327E LYS* 5.8 0.2 - - - +
329E ILE* 5.6 2.2 - - - -
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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