Contacts of the helix formed by residues 300 - 311 (chain E) in PDB entry 3K6G
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 300 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364C ARG* 2.7 51.7 + - + +
368C ILE* 3.9 13.0 - - + +
298E ALA* 4.0 4.8 - - - +
299E GLN* 1.3 82.4 - - + +
301E SER* 1.3 56.7 + - - +
302E GLU* 3.6 3.8 + - - +
303E ALA* 3.1 24.6 + - + +
304E ALA* 3.0 25.8 + - - +
310F GLN* 4.4 6.9 + - - +
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Residues in contact with SER 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E PHE* 3.5 4.9 - - - -
293E LYS* 3.4 36.8 + - - +
296E SER* 3.9 26.9 - - - -
298E ALA* 4.0 7.4 + - - -
299E GLN 3.8 2.8 + - - -
300E ASP* 1.3 72.3 - - - +
302E GLU* 1.3 67.1 + - - +
304E ALA* 4.0 8.1 - - - -
305E PHE* 2.9 25.3 + - - +
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Residues in contact with GLU 302 (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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364C ARG* 3.6 21.8 - - - +
289E LYS* 2.5 44.2 + - - -
293E LYS* 3.1 26.8 + - - +
300E ASP* 3.2 1.9 + - - +
301E SER* 1.3 82.9 + - - +
303E ALA* 1.3 62.8 + - - +
305E PHE* 3.3 4.4 + - - +
306E ALA* 3.1 23.4 + - + +
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Residues in contact with ALA 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 4.1 4.0 - - - +
300E ASP* 3.1 32.0 + - + +
302E GLU* 1.3 77.5 - - - +
304E ALA* 1.3 65.6 + - - +
306E ALA* 3.4 8.0 + - - +
307E LYS* 3.0 31.1 + - - +
310F GLN* 3.5 30.7 - - + +
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Residues in contact with ALA 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E PHE* 3.9 18.6 - - + -
298E ALA* 4.1 13.9 - - + -
300E ASP 3.0 16.7 + - - +
301E SER* 3.6 7.9 - - - +
302E GLU 3.3 0.2 - - - -
303E ALA* 1.3 77.4 - - - +
305E PHE* 1.3 62.0 + - - +
307E LYS* 3.3 11.8 + - - +
308E LEU* 3.1 25.7 + - + +
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Residues in contact with PHE 305 (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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333B THR* 3.8 23.8 - - + -
337B LEU* 3.8 26.2 - - + -
285E MSE 4.0 26.0 - - + -
286E MSE 4.9 1.1 - - + -
288E LEU* 4.2 3.1 - - + -
289E LYS* 3.6 57.0 - - + -
292E PHE* 3.8 30.0 - + + -
293E LYS* 5.4 0.7 - - + -
301E SER 2.9 16.1 + - - +
302E GLU* 3.7 6.7 - - - +
304E ALA* 1.3 74.0 - - - +
306E ALA* 1.3 67.4 + - - +
308E LEU* 3.1 8.4 + - + +
309E ASP* 3.0 21.4 + - + +
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Residues in contact with ALA 306 (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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302E GLU* 3.1 14.5 + - + +
303E ALA* 3.6 11.4 - - - +
305E PHE* 1.3 79.5 - - - +
307E LYS* 1.3 57.4 + - - +
309E ASP* 3.2 8.6 + - - +
310E GLN* 2.9 30.7 + - - +
306F ALA* 5.4 12.3 - - + -
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Residues in contact with LYS 307 (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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303E ALA* 3.0 20.8 + - - +
304E ALA* 3.3 13.2 - - - +
305E PHE 3.1 0.2 - - - -
306E ALA* 1.3 78.1 - - - +
308E LEU* 1.3 59.4 + - + +
310E GLN* 4.4 10.8 - - - +
311E LYS* 2.8 58.3 + - + +
310F GLN* 3.6 30.6 + - - +
311F LYS* 5.6 2.0 - - - +
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Residues in contact with LEU 308 (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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330B SER* 3.8 41.7 - - - +
333B THR* 4.1 12.3 - - + -
334B GLN* 3.2 26.8 + - + +
337B LEU* 3.9 11.1 - - + +
338B LYS* 2.9 21.0 + - - -
292E PHE* 3.7 34.1 - - + -
304E ALA* 3.1 16.5 + - + +
305E PHE* 3.1 10.1 + - - +
307E LYS* 1.3 77.9 - - + +
309E ASP* 1.3 58.7 + - - +
311E LYS* 3.2 7.5 - - + +
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Residues in contact with ASP 309 (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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337B LEU* 3.8 25.0 - - + +
338B LYS* 3.0 17.6 + - - +
364B ARG* 4.3 13.6 + - - +
367B ASP* 5.1 3.8 - - - +
393B ARG* 4.7 2.6 + - - -
397B ARG* 2.8 46.2 + - - -
285E MSE 3.7 15.2 - - + +
305E PHE* 3.0 15.0 + - + +
306E ALA* 3.6 10.8 - - - +
308E LEU* 1.3 76.9 - - - +
310E GLN* 1.3 60.9 + - - +
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Residues in contact with GLN 310 (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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364B ARG* 3.3 39.7 - - + +
306E ALA 2.9 15.8 + - - +
307E LYS* 3.7 13.8 - - - +
309E ASP* 1.3 78.3 - - - +
311E LYS* 1.3 95.9 + - + +
312E ASP 3.8 0.3 + - - -
300F ASP* 4.3 9.4 + - - +
303F ALA* 3.5 28.3 - - + +
307F LYS* 3.7 24.3 - - - +
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Residues in contact with LYS 311 (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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373A ASP* 5.3 13.8 + - + -
334B GLN* 2.9 22.6 + - - +
338B LYS* 2.8 23.6 + - - -
307E LYS* 2.8 37.9 + - + +
310E GLN* 1.3 106.4 - - + +
312E ASP* 1.3 64.3 + - - +
307F LYS* 4.7 7.4 - - - +
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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