Contacts of the helix formed by residues 271 - 284 (chain A) in PDB entry 4TMU
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 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A GLY 4.2 0.6 + - - -
270A LEU* 1.3 74.2 - - - +
272A HIS* 1.3 61.5 + - - +
273A GLU* 3.2 23.6 - - - +
274A VAL* 2.9 37.5 + - + +
275A ARG* 3.0 11.0 + - - +
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Residues in contact with HIS 272 (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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270A LEU 3.7 3.4 + - - -
271A GLU* 1.3 71.9 - - - +
273A GLU* 1.3 56.5 + - - +
274A VAL 3.4 0.2 - - - -
275A ARG* 4.0 36.5 + - + +
276A ALA* 3.2 25.6 + - - +
27B G 6.0 3.7 - - + +
28B C 5.0 13.4 + - - -
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Residues in contact with GLU 273 (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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271A GLU* 3.2 21.0 - - - +
272A HIS* 1.3 75.9 - - - +
274A VAL* 1.3 71.1 + - + +
276A ALA* 3.6 6.9 + - - +
277A SER* 3.1 26.7 + - - -
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Residues in contact with VAL 274 (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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270A LEU* 4.5 20.9 - - + -
271A GLU* 2.9 31.3 + - + +
273A GLU* 1.3 81.8 - - + +
275A ARG* 1.3 66.4 + - - +
277A SER* 3.0 7.6 + - - -
278A VAL* 2.9 33.0 + - + +
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Residues in contact with ARG 275 (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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266A TYR* 3.0 63.5 + - + +
267A HIS 3.6 19.3 - - - +
268A ALA* 3.5 29.8 + - - +
270A LEU* 3.7 21.5 + - + +
271A GLU 3.0 14.7 + - - +
272A HIS* 4.0 36.4 + - + +
274A VAL* 1.3 76.1 - - - +
276A ALA* 1.3 59.4 + - - +
278A VAL* 3.3 1.0 + - - +
279A GLN* 2.9 27.3 + - - +
295A ALA* 4.0 9.8 + - - +
27B G 2.9 27.9 + - - -
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Residues in contact with ALA 276 (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 HIS 3.2 17.0 + - - +
273A GLU* 3.8 8.1 - - - +
274A VAL 3.1 0.6 - - - -
275A ARG* 1.3 79.4 - - - +
277A SER* 1.3 56.9 + - - +
279A GLN* 3.9 6.8 - - - +
280A GLU* 2.9 31.8 + - - +
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Residues in contact with SER 277 (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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273A GLU 3.1 14.2 + - - -
274A VAL* 3.0 11.3 + - - -
276A ALA* 1.3 74.7 - - - +
278A VAL* 1.3 58.4 + - - +
280A GLU* 3.7 5.3 - - - +
281A LYS* 2.7 68.7 + - - +
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Residues in contact with VAL 278 (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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264A ALA* 4.1 15.0 - - + -
265A ALA 4.0 16.4 - - - +
266A TYR* 3.9 22.2 - - + -
270A LEU* 5.8 0.4 - - + -
274A VAL* 2.9 29.7 + - + +
275A ARG* 3.7 4.3 - - - +
277A SER* 1.3 77.8 - - - +
279A GLN* 1.3 58.4 + - - +
281A LYS* 3.3 6.6 + - - +
282A PHE* 2.9 29.3 + - - +
287A LEU* 4.0 19.4 - - + +
290A VAL* 4.1 19.3 - - + -
296A PHE* 5.2 0.2 - - + -
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Residues in contact with GLN 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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76A SER* 5.7 2.6 + - - -
80A ASP* 5.8 0.4 + - - -
266A TYR* 4.3 13.0 + - + -
275A ARG 2.9 16.7 + - - +
276A ALA* 3.9 6.3 - - - +
278A VAL* 1.3 75.9 - - - +
280A GLU* 1.3 59.7 + - - +
282A PHE* 3.2 5.6 + - - +
283A GLN* 2.8 56.2 + - + +
296A PHE* 4.3 23.6 - - + -
299A GLY 3.2 26.3 + - - -
300A ILE* 4.1 10.8 - - + +
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Residues in contact with GLU 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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276A ALA 2.9 20.0 + - - +
277A SER* 3.7 6.1 - - - +
279A GLN* 1.3 77.7 - - - +
281A LYS* 1.3 59.1 + - + +
283A GLN* 3.3 10.9 + - - +
284A ARG* 2.9 45.3 + - + +
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Residues in contact with LYS 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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277A SER* 2.7 47.4 + - - +
278A VAL* 3.7 10.3 - - - +
280A GLU* 1.3 70.0 - - + +
282A PHE* 1.3 67.7 + - - +
284A ARG* 2.9 13.7 + - - +
285A ASP 3.0 10.2 + - - -
286A ASP* 3.0 37.1 + - + +
287A LEU* 3.9 21.8 - - + -
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Residues in contact with PHE 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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238A SER* 3.2 18.6 - - - -
239A GLY 3.5 20.2 - - - -
240A ILE* 3.9 20.2 - - + -
278A VAL 2.9 18.3 + - - +
279A GLN* 3.4 6.1 - - - +
281A LYS* 1.3 75.9 - - - +
283A GLN* 1.3 64.4 + - + +
285A ASP* 3.3 8.0 + - - -
287A LEU* 3.6 20.9 - - + +
288A GLN 3.1 24.2 - - - -
290A VAL* 3.4 21.8 - - + -
296A PHE* 3.9 20.0 - + - -
300A ILE* 5.2 3.6 - - + -
302A LYS* 3.2 47.6 + - + -
305A VAL* 4.0 13.0 - - + -
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Residues in contact with GLN 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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279A GLN* 2.8 54.4 + - + +
280A GLU* 3.5 13.5 - - - +
281A LYS 3.1 0.2 - - - -
282A PHE* 1.3 80.1 - - + +
284A ARG* 1.3 56.4 + - - +
285A ASP* 3.1 8.7 + - - +
299A GLY 4.8 0.4 + - - -
300A ILE* 4.4 5.2 - - - +
301A ASN* 3.0 42.9 + - - +
302A LYS* 3.6 26.7 + - + +
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Residues in contact with ARG 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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280A GLU* 2.9 33.8 + - - +
281A LYS* 2.9 3.8 + - - +
283A GLN* 1.3 73.8 - - + +
285A ASP* 1.3 66.3 + - - +
286A ASP* 3.1 32.4 + - - +
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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