Contacts of the helix formed by residues 278 - 290 (chain B) in PDB entry 1TF4
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 GLN 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B GLY 3.5 3.8 + - - -
277B LYS* 1.3 72.4 - - - +
279B LYS* 1.3 56.2 + - - +
281B ILE* 3.7 26.6 - - - +
282B ASP* 2.8 61.1 + - - +
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Residues in contact with LYS 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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237B GLU 4.6 5.7 + - - -
240B TYR* 3.9 19.6 - - + -
241B ASP* 2.7 38.2 + - - -
252B ARG* 4.2 17.5 + - - +
277B LYS* 3.0 12.1 + - + +
278B GLN* 1.3 79.4 - - - +
280B TYR* 1.3 78.8 + - + +
282B ASP* 3.7 4.7 + - - +
283B ASP* 3.3 25.3 + - - +
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Residues in contact with TYR 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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237B GLU* 2.7 44.4 + - - +
240B TYR* 3.5 49.6 - + - -
268B TYR 3.4 17.3 - - - +
271B LEU* 3.6 30.1 - - + -
272B ALA* 3.5 11.9 - - - +
275B THR* 3.1 28.7 - - - -
277B LYS* 3.1 21.0 + - + +
279B LYS* 1.3 89.8 + - + +
281B ILE* 1.3 61.2 + - - +
282B ASP 3.2 0.4 - - - -
283B ASP* 3.1 2.9 + - - +
284B ALA* 2.9 31.7 + - - +
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Residues in contact with ILE 281 (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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272B ALA* 4.1 16.2 - - + +
276B GLY* 3.6 26.2 - - - +
277B LYS 3.3 7.6 + - - +
278B GLN* 3.3 34.5 + - - +
280B TYR* 1.3 76.5 - - - +
282B ASP* 1.3 57.3 + - - +
285B ASN* 2.9 48.6 + - - +
329B TYR* 3.3 19.5 + - + +
332B VAL* 6.4 0.9 - - + -
333B ILE* 5.1 8.3 - - + -
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLN* 2.8 48.1 + - - +
279B LYS* 3.9 6.7 - - - +
281B ILE* 1.3 77.9 - - - +
283B ASP* 1.3 62.7 + - - +
285B ASN* 3.7 5.4 - - - +
286B ARG* 3.1 38.7 + - - +
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TYR* 2.7 28.6 + - - +
252B ARG* 2.9 38.1 + - - +
254B TYR* 5.1 0.5 - - - +
268B TYR* 3.9 18.6 - - + -
279B LYS 3.3 12.8 + - - +
280B TYR 3.1 5.4 + - - +
282B ASP* 1.3 74.8 - - - +
284B ALA* 1.3 64.3 + - - +
286B ARG* 3.0 34.2 + - - +
287B TRP* 3.1 23.7 + - - +
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Residues in contact with ALA 284 (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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268B TYR* 3.9 16.7 - - + +
269B VAL* 4.0 18.6 - - + +
280B TYR 2.9 20.0 + - - +
283B ASP* 1.3 72.7 - - - +
285B ASN* 1.3 64.9 + - - +
287B TRP* 3.4 5.2 + - - +
288B LEU* 3.0 28.2 + - - +
329B TYR* 3.5 31.9 - - + +
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Residues in contact with ASN 285 (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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281B ILE* 2.9 32.9 + - - +
282B ASP* 3.7 6.3 - - - +
284B ALA* 1.3 74.2 - - - +
286B ARG* 1.3 58.8 + - - +
289B ASP* 2.8 37.8 + - - +
329B TYR* 3.0 32.0 + - - -
333B ILE* 3.4 11.5 - - - +
338B ARG* 3.6 31.6 + - - +
342B TYR* 3.4 11.7 + - - -
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Residues in contact with ARG 286 (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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251B LEU* 3.7 33.7 - - - +
252B ARG 3.6 24.2 + - - +
254B TYR* 3.5 37.4 - - + +
282B ASP* 3.1 30.7 + - - +
283B ASP* 3.0 34.1 + - - +
285B ASN* 1.3 75.9 - - - +
287B TRP* 1.3 64.2 + - - +
289B ASP* 3.3 1.7 + - - -
290B TYR* 3.0 21.5 + - - +
295B VAL* 3.5 24.8 - - + +
296B ASN* 5.9 1.6 - - - +
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Residues in contact with TRP 287 (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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254B TYR* 3.5 27.9 - - + +
256B TRP 3.0 24.6 + - - -
257B THR* 3.3 21.1 - - - -
258B ILE* 4.4 2.2 - - + -
265B TYR* 3.4 53.1 - + + -
268B TYR* 4.5 7.2 - + + -
269B VAL* 4.1 8.7 - - + -
283B ASP 3.1 10.4 + - - +
284B ALA* 3.7 8.3 - - - +
286B ARG* 1.3 78.1 - - - +
288B LEU* 1.3 85.3 + - + +
290B TYR* 3.1 14.6 + - - +
291B TRP* 3.3 19.9 + + - +
322B THR* 4.1 10.1 - - + -
325B VAL* 3.6 44.2 - - + -
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Residues in contact with LEU 288 (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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269B VAL* 4.9 1.3 - - + -
284B ALA 3.0 13.0 + - - +
287B TRP* 1.3 103.0 - - + +
289B ASP* 1.3 59.6 + - - +
291B TRP* 3.5 5.4 + - + +
292B THR* 2.9 29.9 + - + +
322B THR* 3.9 28.5 - - + +
325B VAL 4.8 0.4 - - - +
326B ALA* 3.9 31.4 - - + +
329B TYR* 3.5 33.0 - - + -
342B TYR* 3.5 26.9 - - + -
345B PHE* 5.2 2.2 - - + -
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Residues in contact with ASP 289 (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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285B ASN* 2.8 22.0 + - - +
286B ARG* 3.6 5.6 + - - +
288B LEU* 1.3 73.6 - - - +
290B TYR* 1.3 59.2 + - - +
292B THR* 2.9 3.9 + - - -
293B VAL* 2.8 20.0 + - + +
294B GLY* 2.6 28.3 + - - -
295B VAL* 3.6 15.9 - - + +
338B ARG* 2.8 23.7 + - - -
341B ARG* 2.8 23.0 + - - -
342B TYR* 2.7 23.2 + - - -
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Residues in contact with TYR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.5 24.9 - + + +
255B ARG* 3.6 51.9 + - + +
286B ARG 3.0 12.7 + - - +
287B TRP 3.4 8.3 - - - +
289B ASP* 1.3 77.2 - - - +
291B TRP* 1.3 70.9 + + - +
292B THR 3.5 0.3 + - - -
294B GLY* 4.0 8.3 - - - -
295B VAL* 3.9 12.0 - - + +
298B GLN* 3.5 21.3 - - + -
299B ARG* 3.4 31.3 + - - +
300B VAL* 3.0 49.0 + - + +
301B PRO* 4.9 3.6 - - - +
310B LEU* 5.4 1.9 - - + +
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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