Contacts of the helix formed by residues 341 - 353 (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 ASP 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A LYS* 3.7 17.8 - - + +
313A ILE* 6.0 0.2 - - - +
339A PHE 3.8 3.0 + - - -
340A TYR* 1.3 81.7 - - - +
342A PRO* 1.3 73.6 - - - +
343A ALA* 2.7 40.9 + - - +
344A ASP* 2.9 40.8 + - - +
345A MET 3.7 1.7 + - - -
474A ARG* 3.4 23.6 + - - +
6B G 4.5 10.9 + - - +
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Residues in contact with PRO 342 (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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219A GLU* 4.8 2.2 - - - +
340A TYR* 3.7 36.3 - - + +
341A ASP* 1.3 88.1 - - - +
343A ALA* 1.3 53.3 + - - +
345A MET* 2.7 31.8 + - + +
346A ALA* 3.2 4.9 + - - +
376A GLU* 4.4 5.4 - - - +
474A ARG* 3.6 46.0 - - + +
477A ILE* 6.3 3.6 - - + -
484A GLN* 5.8 1.1 - - - +
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Residues in contact with ALA 343 (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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341A ASP* 2.7 27.1 + - - +
342A PRO* 1.3 74.2 - - - +
344A ASP* 1.3 62.0 + - - +
346A ALA* 3.2 11.9 + - - +
347A TRP* 3.0 21.1 + - - +
484A GLN* 4.6 19.8 - - - +
23B C 4.8 2.6 + - - +
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Residues in contact with ASP 344 (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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220A LYS* 2.8 31.1 + - - +
244A ASN* 6.0 1.1 - - - +
248A LYS* 4.9 2.1 + - - -
312A ASP* 3.9 15.4 - - + +
313A ILE* 4.1 18.5 + - + +
339A PHE 4.8 0.3 - - - +
341A ASP* 2.9 29.0 + - - +
343A ALA* 1.3 78.8 - - - +
345A MET* 1.3 61.6 + - - +
347A TRP* 3.5 7.0 + - + +
348A LEU* 3.2 26.3 + - + +
23B C 2.8 32.1 + - - +
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Residues in contact with MET 345 (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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313A ILE* 4.3 16.2 - - + -
340A TYR* 3.9 30.7 - - + +
341A ASP 3.7 0.2 + - - -
342A PRO* 2.7 18.0 + - + +
344A ASP* 1.3 70.1 - - - +
346A ALA* 1.3 61.3 + - - +
348A LEU* 3.0 6.1 + - - +
349A ARG* 2.8 70.9 + - - +
368A LEU* 3.7 45.5 - - + +
369A ASN* 4.6 0.4 - - - +
371A MET* 5.1 0.4 - - - -
372A GLY* 3.8 22.4 - - - -
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Residues in contact with ALA 346 (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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342A PRO 3.2 4.2 + - - +
343A ALA* 3.5 14.1 - - - +
345A MET* 1.3 79.4 - - - +
347A TRP* 1.3 63.0 + - - +
349A ARG* 3.3 13.2 + - - +
350A ARG* 3.0 24.8 + - - +
484A GLN* 5.5 9.2 - - - +
486A ILE* 5.5 16.6 - - + +
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Residues in contact with TRP 347 (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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244A ASN* 4.2 29.4 - - + -
245A SER* 6.1 0.2 - - - -
343A ALA 3.0 10.3 + - - +
344A ASP* 3.5 9.6 - - + +
345A MET 3.2 0.2 - - - -
346A ALA* 1.3 76.8 - - - +
348A LEU* 1.3 99.6 + - + +
350A ARG* 3.2 40.4 + - - +
351A CYS* 3.0 33.3 + - - -
23B C 3.4 80.5 - + + +
24B G 3.3 39.7 + + - -
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Residues in contact with LEU 348 (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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244A ASN* 4.4 7.2 - - - +
313A ILE* 3.7 31.2 - - + +
314A PRO 3.8 8.1 - - - +
315A ARG* 4.2 31.2 - - + +
344A ASP 3.2 15.0 + - - +
345A MET* 3.0 8.1 + - - +
347A TRP* 1.3 102.3 - - + +
349A ARG* 1.3 65.2 - - - +
351A CYS* 3.1 18.7 + - + +
352A LEU* 3.1 21.4 + - + +
368A LEU* 3.8 29.6 - - + -
24B G 5.5 0.7 - - - +
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Residues in contact with ARG 349 (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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345A MET* 2.8 46.7 + - - +
346A ALA* 3.6 10.0 - - - +
348A LEU* 1.3 74.6 - - - +
350A ARG* 1.3 64.1 + - - +
352A LEU* 3.1 5.4 + - - +
353A GLU* 3.1 37.4 + - - +
368A LEU* 3.5 20.2 - - + -
369A ASN* 3.2 28.7 + - - +
372A GLY* 5.5 2.0 - - - -
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Residues in contact with ARG 350 (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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346A ALA 3.0 12.9 + - - +
347A TRP* 3.2 49.8 + - - +
349A ARG* 1.3 77.5 - - - +
351A CYS* 1.3 74.8 + - - +
352A LEU 3.2 0.7 + - - -
353A GLU* 3.5 10.5 + - - +
354A GLU* 3.5 43.7 + - + +
486A ILE* 4.8 26.2 - - + +
23B C 4.3 22.8 - - - -
24B G 5.7 0.4 + - - -
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Residues in contact with CYS 351 (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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315A ARG* 6.0 0.2 - - - +
347A TRP* 3.0 39.9 + - - +
348A LEU* 3.1 13.4 + - + +
350A ARG* 1.3 93.9 - - - +
352A LEU* 1.3 66.2 + - + +
354A GLU* 3.7 18.0 + - - +
355A LYS* 3.5 14.8 + - - -
24B G 4.5 38.4 + - + +
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Residues in contact with LEU 352 (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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315A ARG* 4.1 26.7 - - + +
348A LEU* 3.1 19.3 + - + +
349A ARG* 3.5 9.0 - - - +
351A CYS* 1.3 77.0 - - + +
353A GLU* 1.3 60.0 + - + +
354A GLU 3.1 9.3 + - - -
355A LYS* 3.2 33.0 + - + +
361A GLN* 3.4 14.1 - - + +
364A GLU* 3.5 51.8 - - + +
365A ARG* 3.6 14.8 - - + +
368A LEU* 4.2 18.4 - - + -
24B G 4.9 0.2 - - - +
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Residues in contact with GLU 353 (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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349A ARG* 3.1 28.1 + - - +
350A ARG* 3.5 10.4 + - - +
352A LEU* 1.3 77.3 - - + +
354A GLU* 1.3 57.9 + - - +
355A LYS 4.5 2.9 - - - +
361A GLN* 3.8 20.2 - - - +
365A ARG* 4.4 14.6 + - - +
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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