Contacts of the helix formed by residues 274 - 288 (chain E) in PDB entry 1TKK
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 GLY 274 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E ALA* 3.4 15.0 - - - +
104E GLU* 3.4 11.2 - - - -
269E LEU* 2.9 25.2 + - - +
272E ALA* 3.2 3.3 - - - +
273E GLY* 1.3 80.8 - - - +
275E ILE* 1.3 66.5 + - - -
276E SER 3.5 0.9 - - - -
277E GLY 4.6 0.2 - - - -
278E ALA* 3.5 20.4 + - - +
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Residues in contact with ILE 275 (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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104E GLU* 2.8 8.5 + - - +
105E MET* 4.6 12.1 - - - -
108E TYR* 3.7 53.6 - - + +
119E LEU* 4.0 17.0 - - + -
123E LEU* 4.2 19.7 - - + -
269E LEU* 3.9 28.3 - - + -
274E GLY* 1.3 72.3 - - - -
276E SER* 1.3 57.9 + - - +
278E ALA* 3.2 5.2 + - - +
279E GLU* 2.9 30.6 + - + +
306E ALA* 4.4 8.3 - - + +
310E PHE* 4.5 16.6 - - + -
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Residues in contact with SER 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E LEU* 4.1 17.0 - - - +
90E GLN* 4.3 9.2 + - - +
104E GLU* 2.7 34.5 + - - -
108E TYR* 3.5 20.4 + - - -
275E ILE* 1.3 72.8 - - - +
277E GLY* 1.3 59.5 + - - +
279E GLU* 3.6 8.9 + - - +
280E LYS* 3.2 48.0 + - - +
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Residues in contact with GLY 277 (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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90E GLN* 6.0 0.6 - - - -
250E PRO* 4.0 19.5 - - - +
272E ALA* 3.9 21.2 + - - -
274E GLY 4.3 2.2 + - - -
275E ILE 3.4 0.2 - - - -
276E SER* 1.3 81.1 + - - +
278E ALA* 1.3 64.0 + - - +
279E GLU 3.1 0.2 - - - -
280E LYS* 3.2 3.9 + - - +
281E ILE* 3.0 29.0 + - - +
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Residues in contact with ALA 278 (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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267E ILE* 3.5 34.5 - - + +
268E LYS 5.0 0.2 - - - +
269E LEU* 4.0 11.0 - - + -
272E ALA* 3.6 7.1 - - + +
274E GLY 3.5 21.3 + - - +
275E ILE* 3.2 6.6 + - - +
277E GLY* 1.3 75.3 - - - +
279E GLU* 1.3 62.6 + - - +
281E ILE* 3.5 2.3 + - - +
282E ASN 3.2 17.0 + - - -
310E PHE* 3.4 22.8 - - + -
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Residues in contact with GLU 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E TYR* 4.7 10.4 + - - -
123E LEU* 3.7 20.9 - - - +
275E ILE* 2.9 17.8 + - + +
276E SER* 3.6 7.5 - - - +
277E GLY 3.1 0.2 - - - -
278E ALA* 1.3 79.1 - - - +
280E LYS* 1.3 58.6 + - + +
282E ASN* 3.4 4.1 + - - +
283E ALA* 3.0 27.4 + - + +
310E PHE* 3.6 15.0 - - + -
314E LYS* 2.6 38.6 + - - +
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Residues in contact with LYS 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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83E GLU* 5.7 3.9 + - - -
90E GLN* 6.3 1.4 - - - +
250E PRO* 4.0 23.8 - - + -
276E SER* 3.2 35.3 + - - +
277E GLY* 3.2 4.6 + - - +
279E GLU* 1.3 78.9 - - + +
281E ILE* 1.3 64.8 + - - +
283E ALA* 3.9 7.5 - - - +
284E MET* 3.3 30.0 + - + +
283F ALA* 4.0 33.1 - - + +
286F GLU* 4.0 20.2 + - + -
287F ALA* 6.5 0.2 - - + -
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Residues in contact with ILE 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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247E VAL* 4.5 5.2 - - + +
248E PHE 3.5 25.8 - - - +
249E THR 3.8 11.2 - - - +
250E PRO* 3.6 21.3 - - + -
253E ALA* 3.9 18.6 - - + +
257E LEU* 4.9 0.9 - - - +
265E ILE* 4.1 17.9 - - + -
267E ILE* 3.8 26.0 - - + -
272E ALA* 3.9 11.4 - - + -
277E GLY 3.0 21.7 + - - +
278E ALA* 3.6 6.5 - - - +
280E LYS* 1.3 75.0 - - - +
282E ASN* 1.3 60.4 + - - +
284E MET* 3.5 4.0 + - - +
285E ALA* 2.9 27.4 + - - +
292E CYS* 4.9 1.1 - - - -
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Residues in contact with ASN 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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267E ILE* 3.9 9.4 - - + -
278E ALA 3.2 13.3 + - - +
279E GLU* 3.8 4.8 - - - +
280E LYS 3.3 0.2 - - - -
281E ILE* 1.3 78.6 - - - +
283E ALA* 1.3 61.2 + - - +
286E GLU* 2.9 30.8 + - - +
292E CYS* 3.8 12.2 - - - -
310E PHE* 4.4 7.2 - - + -
314E LYS* 3.7 24.6 - - - +
316E ASN* 3.0 40.9 + - - +
317E ILE* 3.5 22.5 - - - +
83F GLU* 5.3 0.7 - - - +
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Residues in contact with ALA 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E GLU* 3.0 17.7 + - + +
280E LYS* 3.9 9.2 - - - +
282E ASN* 1.3 75.6 + - - +
284E MET* 1.3 65.2 + - + +
286E GLU* 3.2 12.9 + - - +
287E ALA* 3.1 22.3 + - - +
280F LYS* 4.0 35.6 - - + +
283F ALA* 6.1 2.9 - - + -
284F MET* 5.3 2.2 - - + -
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Residues in contact with MET 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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250E PRO* 3.6 27.6 - - + +
253E ALA* 4.6 3.1 - - - -
254E PHE* 3.7 36.3 - - + -
257E LEU* 3.7 10.5 - - + -
280E LYS* 3.3 17.8 + - + +
281E ILE 3.6 4.0 - - - +
283E ALA* 1.3 78.6 - - + +
285E ALA* 1.3 63.0 + - - +
287E ALA* 3.2 11.6 + - - +
288E CYS* 3.3 18.5 + - - -
254F PHE* 5.1 2.2 - - + -
283F ALA 4.5 2.0 - - - +
284F MET* 3.7 40.3 - - + +
287F ALA* 3.6 31.0 - - + -
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Residues in contact with ALA 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E LEU* 3.6 12.9 - - - +
265E ILE* 4.2 12.8 - - + -
281E ILE 2.9 21.5 + - - +
282E ASN 3.9 0.9 - - - +
284E MET* 1.3 73.0 - - - +
286E GLU* 1.3 61.1 + - - +
288E CYS 3.1 6.9 + - - -
290E VAL* 2.9 47.3 + - + +
292E CYS* 3.5 22.7 - - - -
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Residues in contact with GLU 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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282E ASN* 2.9 22.3 + - - +
283E ALA* 3.5 7.4 - - - +
284E MET 3.2 0.2 - - - -
285E ALA* 1.3 77.0 - - - +
287E ALA* 1.3 60.3 + - - +
288E CYS 3.2 0.2 - - - -
289E GLY* 3.3 12.9 + - - +
290E VAL 4.0 0.7 - - - +
315E ARG* 4.4 12.6 + - - +
316E ASN* 3.6 41.9 + - + +
83F GLU* 4.4 8.9 - - - +
87F HIS* 5.3 9.4 + - - -
280F LYS* 4.0 26.3 + - - +
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Residues in contact with ALA 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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283E ALA 3.1 11.5 + - - +
284E MET 3.2 8.9 + - - +
286E GLU* 1.3 76.2 - - - +
288E CYS* 1.3 60.9 + - - +
289E GLY 3.5 0.6 + - - -
250F PRO* 4.2 15.0 - - + -
251F ARG* 3.8 30.9 - - + +
254F PHE* 5.8 0.8 - - + +
280F LYS* 6.4 1.3 - - + -
284F MET* 3.8 23.1 - - + -
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Residues in contact with CYS 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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226A ASP* 5.1 8.5 - - - +
257E LEU* 4.1 24.9 - - + +
260E ARG* 5.2 7.9 + - - +
284E MET 3.5 12.8 - - - +
285E ALA 3.1 8.3 + - - +
287E ALA* 1.3 80.8 - - - +
289E GLY* 1.3 60.6 + - - +
290E VAL* 3.2 7.8 + - + +
251F ARG* 5.6 4.0 - - - +
254F PHE* 3.7 45.1 - - - -
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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