Contacts of the helix formed by residues 273 - 280 (chain B) in PDB entry 3EHN
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 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B PRO 2.6 27.9 + - - -
53B ILE* 3.4 7.3 - - - +
62B PRO* 3.9 11.0 - - - -
63B GLY* 3.4 40.1 - - - +
66B LEU* 3.0 25.8 - - - +
71B LEU* 4.3 2.9 - - - +
271B LEU 3.0 5.5 + - - -
272B ASN* 1.3 71.8 + - - +
274B MET* 1.3 59.3 + - - +
275B LEU 3.4 0.4 - - - -
276B ALA* 4.1 7.4 + - - +
353B LEU* 4.1 3.3 - - - +
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Residues in contact with MET 274 (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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66B LEU* 3.8 18.2 - - + -
71B LEU* 3.7 27.8 - - + +
81B PHE* 3.9 16.4 - - + -
272B ASN* 2.6 24.9 + - - +
273B SER* 1.3 72.1 - - - +
275B LEU* 1.3 63.2 + - - +
276B ALA 3.2 1.2 + - - -
277B SER* 3.6 2.6 + - - -
278B VAL* 3.1 32.4 + - + +
284B THR* 5.2 0.4 - - + -
345B PRO* 4.0 28.5 - - + -
347B VAL* 4.1 21.8 - - + -
353B LEU* 4.8 8.7 - - + -
460B TYR* 4.7 2.2 - - - +
461B PRO* 4.7 17.9 - - + -
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Residues in contact with LEU 275 (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 LEU* 4.1 13.0 - - + -
272B ASN 3.9 8.5 - - - +
273B SER 3.4 0.6 - - - -
274B MET* 1.3 76.0 - - - +
276B ALA* 1.3 65.6 + - - +
278B VAL* 4.4 3.6 - - - -
279B ASN* 2.9 37.7 + - + +
280B GLU* 3.3 12.3 + - + +
347B VAL* 3.4 40.8 - - + +
348B ASP* 3.4 8.5 - - - +
349B SER* 3.1 39.3 - - - +
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Residues in contact with ALA 276 (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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60B THR* 4.0 24.5 - - + -
63B GLY* 3.9 29.6 - - - -
272B ASN 4.9 0.2 + - - -
273B SER* 4.1 3.8 + - - +
274B MET 3.2 0.4 - - - -
275B LEU* 1.3 79.5 - - - +
277B SER* 1.3 59.0 + - - +
280B GLU* 2.9 36.6 + - - +
281B TYR* 2.9 20.8 + - + -
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Residues in contact with SER 277 (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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63B GLY 5.2 1.6 - - - -
67B GLN* 2.7 31.1 + - - +
71B LEU* 3.7 19.3 - - - -
72B ILE* 4.6 0.5 - - - +
273B SER 4.8 0.2 + - - -
274B MET 3.6 2.4 + - - -
275B LEU 3.4 0.2 - - - -
276B ALA* 1.3 79.5 - - - +
278B VAL* 1.3 59.8 + - - +
281B TYR* 4.0 9.2 - - - -
282B ASN 3.4 2.0 + - - -
283B GLU* 2.9 33.6 + - - +
284B THR* 2.5 33.2 + - - -
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Residues in contact with VAL 278 (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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71B LEU* 5.4 0.2 - - + -
274B MET* 3.1 28.4 + - + +
275B LEU* 4.2 1.6 - - - +
277B SER* 1.3 79.0 - - - +
279B ASN* 1.3 81.9 + - - +
282B ASN* 3.5 9.9 + - - -
284B THR* 4.0 20.6 - - + +
285B ARG* 2.9 29.1 + - - +
344B ARG* 4.3 17.7 - - + -
345B PRO* 3.6 33.2 - - + +
347B VAL* 4.5 5.8 - - + -
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Residues in contact with ASN 279 (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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275B LEU* 2.9 43.2 + - + +
278B VAL* 1.3 88.6 - - - +
280B GLU* 1.3 70.3 + - - +
282B ASN* 3.8 17.6 + - - +
344B ARG* 3.0 25.0 + - - +
347B VAL* 4.6 4.6 + - - +
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Residues in contact with GLU 280 (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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60B THR* 4.5 11.9 - - + +
275B LEU* 3.7 6.8 - - + +
276B ALA* 2.9 30.9 + - - +
279B ASN* 1.3 84.3 - - - +
281B TYR* 1.3 74.6 + - + +
282B ASN* 4.5 4.0 - - - +
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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