Contacts of the helix formed by residues 279 - 290 (chain E) in PDB entry 3TNP
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 GLU 279 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277E SER 4.4 2.0 - - - +
278E LEU* 1.3 77.0 - - - +
280E VAL* 1.3 67.9 + - - +
281E SER* 3.4 6.7 + - - +
282E GLU* 2.9 28.5 + - + +
283E ARG* 2.9 22.5 + - - +
392E ARG* 3.9 22.4 + - - +
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Residues in contact with VAL 280 (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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278E LEU 4.1 0.2 + - - -
279E GLU* 1.3 71.6 - - - +
281E SER* 1.3 66.0 + - - +
283E ARG* 3.1 29.8 + - - +
284E LEU* 3.0 43.8 + - + +
192F LYS 6.1 0.9 - - - +
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Residues in contact with SER 281 (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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279E GLU* 3.4 6.0 + - - +
280E VAL* 1.3 78.9 - - - +
282E GLU* 1.3 71.1 + - - +
284E LEU* 3.3 15.2 + - - +
285E LYS* 3.1 30.0 + - - +
192F LYS 5.7 4.0 - - - -
194F ARG* 4.6 1.5 + - - +
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Residues in contact with GLU 282 (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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278E LEU* 3.7 16.0 - - + +
279E GLU* 2.9 41.1 + - + +
281E SER* 1.3 88.9 + - - +
283E ARG* 1.3 64.0 + - - +
285E LYS* 3.3 15.8 + - - +
286E VAL* 3.3 16.8 + - - +
383E LEU* 3.6 33.8 - - + +
389E ILE* 5.2 1.4 - - - +
392E ARG* 3.3 33.0 + - - -
285F LYS* 4.9 6.9 + - - -
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Residues in contact with ARG 283 (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 GLU* 3.0 28.4 + - - +
269E ILE* 3.8 23.0 - - + +
270E GLU* 3.0 38.1 + - - +
275E LEU 5.1 2.8 + - - +
276E LYS* 5.3 3.6 + - - +
278E LEU* 3.6 47.4 + - + +
279E GLU 2.9 7.3 + - - +
280E VAL* 3.1 37.6 + - - +
282E GLU* 1.3 77.4 - - - +
284E LEU* 1.3 57.5 + - - +
286E VAL* 3.2 6.1 + - - +
287E VAL* 2.9 31.7 + - - +
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Residues in contact with LEU 284 (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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262E ARG* 5.2 2.0 - - - +
266E GLU* 3.9 26.0 - - - +
280E VAL* 3.0 31.1 + - + +
281E SER* 3.6 11.4 - - - +
282E GLU 3.3 0.2 - - - -
283E ARG* 1.3 72.5 - - - +
285E LYS* 1.3 60.9 + - - +
287E VAL* 3.1 9.6 + - + +
288E ASP* 2.9 34.0 + - - +
192F LYS 4.5 4.5 - - - +
193F GLY* 3.9 22.7 - - - -
194F ARG* 3.4 37.5 - - + +
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Residues in contact with LYS 285 (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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281E SER* 3.1 21.6 + - - +
282E GLU* 3.5 9.9 - - - +
283E ARG 3.3 0.2 - - - -
284E LEU* 1.3 77.7 - - - +
286E VAL* 1.3 60.2 + - - +
288E ASP* 3.6 21.8 - - - +
289E VAL* 3.8 5.5 + - - +
382E LEU* 3.8 37.9 + - + +
383E LEU* 4.9 6.3 - - + -
194F ARG* 3.6 6.9 - - - +
217F LYS* 6.4 2.7 - - - -
282F GLY 4.9 2.0 + - - -
283F ASN* 2.9 53.2 + - - +
284F LEU 4.2 7.9 + - - -
287F GLY* 6.2 0.2 - - - -
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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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269E ILE* 4.1 29.6 - - + -
275E LEU* 5.9 0.4 - - + -
278E LEU* 4.8 4.7 - - + -
282E GLU 3.3 5.8 + - - +
283E ARG* 3.2 10.0 + - - +
284E LEU 3.1 0.6 - - - -
285E LYS* 1.3 76.2 - - - +
287E VAL* 1.3 65.7 + - - +
289E VAL* 3.3 6.8 + - - +
290E ILE* 3.0 26.6 + - + +
311E PHE* 5.5 1.1 - - + -
374E MET* 4.3 24.2 - - + -
379E PHE* 4.2 17.0 - - + -
382E LEU* 4.7 4.0 - - + -
383E LEU* 3.6 31.9 - - + -
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Residues in contact with VAL 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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262E ARG* 3.6 47.4 - - + +
265E TYR* 4.4 13.7 - - + -
266E GLU* 3.9 40.6 - - + +
269E ILE* 5.0 5.6 - - + -
283E ARG 2.9 21.1 + - - +
284E LEU* 3.4 13.5 - - + +
286E VAL* 1.3 74.4 - - - +
288E ASP* 1.3 66.1 + - - +
289E VAL 3.2 0.9 + - - -
290E ILE* 3.7 18.2 + - - +
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Residues in contact with ASP 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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262E ARG* 2.7 47.3 + - - +
284E LEU 2.9 17.5 + - - +
285E LYS* 3.6 13.6 - - - +
286E VAL 3.3 0.4 - - - -
287E VAL* 1.3 74.4 - - - +
289E VAL* 1.3 66.2 + - + +
290E ILE 5.2 0.2 - - - +
194F ARG* 2.6 31.6 + - - -
213F LYS* 6.2 0.3 - - - +
214F GLY 5.5 0.4 - - - -
215F TYR* 6.2 0.4 - - - -
277F LEU* 4.0 21.9 - - + +
283F ASN* 5.2 5.9 + - - +
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Residues in contact with VAL 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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285E LYS 3.9 14.6 - - - +
286E VAL 3.6 8.7 - - - +
287E VAL 3.2 0.2 - - - -
288E ASP* 1.3 81.3 - - + +
290E ILE* 1.3 71.9 + - - +
291E GLY* 3.2 4.3 + - - -
374E MET* 3.8 22.5 - - + +
382E LEU* 4.1 3.6 - - + -
276F ASP* 5.0 1.1 - - - +
277F LEU* 3.8 31.2 - - + +
278F THR* 3.7 33.2 - - + +
283F ASN* 5.9 0.2 - - - +
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Residues in contact with ILE 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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265E TYR* 4.0 30.1 - - + -
269E ILE* 3.9 28.9 - - + -
286E VAL* 3.0 16.4 + - + +
287E VAL* 3.7 18.0 + - - +
288E ASP 5.2 0.3 - - - +
289E VAL* 1.3 79.7 - - - +
291E GLY* 1.3 67.1 + - - +
311E PHE* 5.0 1.6 - - + -
313E ILE* 4.6 4.7 - - + -
372E LEU* 4.0 26.7 - - + -
373E ALA 3.6 17.3 - - - +
374E MET* 4.0 23.6 - - + +
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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