Contacts of the helix formed by residues 278 - 290 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A GLY 3.5 3.6 + - - -
277A LYS* 1.3 72.0 - - - +
279A LYS* 1.3 56.0 + - - +
281A ILE* 4.0 25.1 - - - +
282A ASP* 2.8 61.6 + - - +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLU 4.6 5.1 + - - -
240A TYR* 4.0 19.4 - - - -
241A ASP* 2.7 38.5 + - - -
252A ARG* 4.1 17.3 + - - +
277A LYS* 4.2 12.5 - - + +
278A GLN* 1.3 79.7 - - - +
280A TYR* 1.3 80.0 + - + +
282A ASP* 3.7 5.1 + - - +
283A ASP* 3.3 25.3 + - - +
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLU* 2.8 42.4 + - - +
240A TYR* 3.5 48.7 - + - -
268A TYR 3.5 17.9 - - - +
271A LEU* 3.6 30.7 - - + -
272A ALA* 3.5 12.3 - - - +
275A THR* 3.1 29.8 - - + -
277A LYS* 3.1 21.0 + - + +
279A LYS* 1.3 89.9 + - + +
281A ILE* 1.3 60.4 + - - +
282A ASP 3.2 0.4 - - - -
283A ASP* 3.2 2.9 + - - +
284A ALA* 2.9 31.5 + - - +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ALA* 4.1 14.6 - - + +
276A GLY* 3.6 25.6 - - - +
277A LYS 3.3 8.2 + - - +
278A GLN* 3.7 33.2 - - - +
280A TYR* 1.3 77.5 - - - +
282A ASP* 1.3 57.9 + - - +
285A ASN* 2.9 48.9 + - - +
329A TYR* 3.4 21.8 + - + +
332A VAL* 6.5 0.4 - - + -
333A ILE* 5.2 7.6 - - + -
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLN* 2.8 48.6 + - - +
279A LYS* 3.9 6.3 - - - +
280A TYR 3.2 0.4 - - - -
281A ILE* 1.3 78.3 - - - +
283A ASP* 1.3 62.2 + - - +
285A ASN* 3.7 5.5 - - - +
286A ARG* 3.1 39.0 + - - +
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Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A TYR* 2.7 28.1 + - - +
252A ARG* 2.9 40.3 + - - +
254A TYR* 5.1 0.5 - - - +
268A TYR* 3.9 18.3 - - + -
279A LYS 3.3 11.5 + - - +
280A TYR 3.2 5.4 + - - +
282A ASP* 1.3 74.8 - - - +
284A ALA* 1.3 66.1 + - - +
286A ARG* 3.0 33.8 + - - +
287A TRP* 3.1 23.2 + - - +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A TYR* 3.9 18.3 - - + +
269A VAL* 4.0 19.7 - - + -
272A ALA* 5.0 0.2 - - + -
280A TYR 2.9 19.8 + - - +
283A ASP* 1.3 75.4 - - - +
285A ASN* 1.3 64.5 + - - +
287A TRP* 3.4 5.1 + - - +
288A LEU* 3.0 27.0 + - - +
329A TYR* 3.6 30.1 - - + +
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ILE* 2.9 34.2 + - - +
282A ASP* 3.7 6.7 - - - +
284A ALA* 1.3 75.7 - - - +
286A ARG* 1.3 59.2 + - - +
289A ASP* 2.8 37.9 + - - +
329A TYR* 3.1 31.9 + - - -
333A ILE* 3.6 9.8 - - - +
338A ARG* 3.6 33.5 + - - +
342A TYR* 3.4 12.6 + - - -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LEU* 3.7 33.6 - - - +
252A ARG 3.6 23.0 + - - +
254A TYR* 3.5 36.5 - - + +
282A ASP* 3.1 30.0 + - - +
283A ASP* 3.0 35.1 + - - +
285A ASN* 1.3 74.7 - - - +
287A TRP* 1.3 62.7 + - - +
289A ASP* 4.4 1.1 - - - -
290A TYR* 3.0 22.0 + - - +
295A VAL* 3.6 25.1 - - + +
296A ASN* 5.9 1.3 - - - +
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Residues in contact with TRP 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TYR* 3.5 30.0 - - + +
256A TRP 3.0 20.8 + - - -
257A THR* 3.3 20.2 - - - -
258A ILE* 4.4 2.7 - - + -
265A TYR* 3.4 59.1 - + + -
268A TYR* 4.5 7.4 - + + -
269A VAL* 4.1 7.9 - - + -
283A ASP 3.1 9.1 + - - +
284A ALA* 3.7 8.1 - - - +
286A ARG* 1.3 79.2 - - - +
288A LEU* 1.3 84.9 + - + +
290A TYR* 3.1 14.6 + - - +
291A TRP* 3.3 19.8 + + - +
322A THR* 4.1 11.2 - - + -
325A VAL* 3.6 39.7 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A VAL* 4.9 1.1 - - + -
284A ALA 3.0 17.1 + - - +
287A TRP* 1.3 101.4 - - + +
289A ASP* 1.3 60.1 + - - +
291A TRP* 3.4 5.3 + - + +
292A THR* 2.9 29.7 + - - +
322A THR* 3.9 28.9 - - + -
325A VAL 4.8 0.2 - - - +
326A ALA* 4.0 31.4 - - + +
329A TYR* 3.6 33.4 - - + -
342A TYR* 3.5 27.3 - - + -
345A PHE* 5.2 2.7 - - + -
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASN* 2.8 21.9 + - - +
286A ARG* 4.9 0.7 - - - -
287A TRP 3.1 0.2 - - - -
288A LEU* 1.3 73.9 - - - +
290A TYR* 1.3 59.6 + - - +
292A THR* 2.9 3.9 + - - -
293A VAL* 2.9 20.0 + - + +
294A GLY* 2.6 29.4 + - - -
295A VAL* 3.6 21.0 - - + +
338A ARG* 3.0 21.4 + - - -
341A ARG* 2.8 22.9 + - - -
342A TYR* 2.8 21.1 + - - -
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Residues in contact with TYR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TYR* 3.5 25.6 - + + +
255A ARG* 3.6 48.5 + - + +
286A ARG 3.0 12.9 + - - +
287A TRP 3.1 7.8 + - - +
289A ASP* 1.3 76.4 - - - +
291A TRP* 1.3 72.1 + + - +
294A GLY* 4.0 7.2 - - - -
295A VAL* 3.9 13.2 - - + +
298A GLN* 3.5 25.1 - - + -
299A ARG* 3.4 31.7 + - - +
300A VAL* 3.0 49.3 + - + -
301A PRO* 4.9 4.0 - - - +
310A LEU* 5.2 1.5 - - + +
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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