Contacts of the helix formed by residues 346 - 357 (chain A) in PDB entry 3L4U
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 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A LEU* 3.5 4.9 - - - +
308A ARG* 3.4 12.4 + - - -
339A TYR* 4.9 2.6 + - - -
344A PHE 3.3 0.2 + - - -
345A LYS* 1.3 80.2 - - - +
347A PHE* 1.3 64.6 + - - +
348A PRO* 3.3 8.6 - - - +
349A GLU* 3.0 24.1 + - - +
350A PHE 3.0 18.0 + - - -
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Residues in contact with PHE 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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304A LEU* 3.4 15.1 - - + +
307A MET* 4.8 2.9 - - - -
326A ALA* 4.2 18.8 - - + -
330A TYR* 4.0 27.6 - + + -
339A TYR* 3.8 20.2 - + + -
344A PHE* 3.1 32.3 + + - +
345A LYS 3.3 0.2 - - - -
346A GLY* 1.3 74.7 - - - +
348A PRO* 1.4 64.6 - - + +
350A PHE* 3.2 30.1 + + - +
351A VAL* 3.0 32.5 + - + +
361A LEU* 4.1 18.8 - - + -
363A ILE* 4.9 1.8 - - + -
435A VAL* 3.8 29.8 - - + -
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Residues in contact with PRO 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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339A TYR* 3.5 27.1 - - + +
346A GLY* 3.5 5.6 - - - -
347A PHE* 1.4 93.5 - - + +
349A GLU* 1.3 61.4 + - + +
351A VAL* 3.5 9.7 + - + +
352A ASN* 3.2 27.3 + - - +
434A GLN* 3.5 26.2 - - - +
435A VAL* 4.9 3.6 - - + -
436A GLU 6.0 0.2 - - - +
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Residues in contact with GLU 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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308A ARG* 4.3 8.6 + - - +
346A GLY* 3.0 23.2 + - - +
348A PRO* 1.3 76.8 - - + +
350A PHE* 1.3 65.4 + - - +
352A ASN* 3.3 14.5 + - - +
353A GLU* 3.1 30.3 + - - +
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Residues in contact with PHE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 3.6 17.9 - - + -
307A MET* 3.8 24.9 - - - -
308A ARG* 3.5 47.3 - - + +
311A VAL* 3.9 32.1 - - + -
324A GLN* 4.5 1.3 - - + -
346A GLY 3.0 7.4 + - - +
347A PHE* 3.2 23.1 + + - +
349A GLU* 1.3 75.8 - - - +
351A VAL* 1.3 60.7 + - + +
353A GLU* 3.0 19.1 + - + +
354A LEU* 2.9 58.1 + - + +
361A LEU* 4.9 3.4 - - + -
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PHE* 3.0 24.6 + - + +
348A PRO* 3.6 10.5 - - + +
350A PHE* 1.3 75.4 - - + +
352A ASN* 1.3 63.1 + - - +
354A LEU* 3.3 8.3 + - - +
355A HIS* 2.9 55.5 + - + +
361A LEU* 3.6 31.0 - - + -
435A VAL* 3.9 15.0 - - + -
436A GLU* 3.5 23.3 - - + +
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Residues in contact with ASN 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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348A PRO 3.2 16.2 + - - +
349A GLU* 3.4 15.4 - - - +
351A VAL* 1.3 77.4 - - - +
353A GLU* 1.3 58.0 + - + +
355A HIS* 3.2 7.8 + - - +
356A ASN* 2.8 30.4 + - - +
436A GLU* 4.4 15.1 - - - +
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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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308A ARG* 3.3 31.1 + - - -
312A GLU* 6.1 0.4 - - - +
349A GLU* 3.1 18.7 + - - +
350A PHE* 3.0 17.9 + - + +
352A ASN* 1.3 71.5 - - + +
354A LEU* 1.3 68.5 + - - +
356A ASN* 3.3 7.0 + - - +
357A ASN* 3.0 36.6 + - - +
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Residues in contact with LEU 354 (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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311A VAL* 4.3 10.8 - - + -
324A GLN* 4.1 18.6 - - + -
350A PHE* 2.9 49.5 + - + +
351A VAL* 3.3 11.4 + - + +
353A GLU* 1.3 75.1 - - - +
355A HIS* 1.3 67.0 + - + +
357A ASN* 3.1 8.9 + - - +
358A GLY 3.3 0.2 + - - -
359A GLN* 3.0 60.4 + - + +
360A LYS 4.2 6.5 - - - +
361A LEU* 3.8 32.8 - - + -
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Residues in contact with HIS 355 (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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351A VAL* 2.9 31.9 + - + +
352A ASN* 3.7 8.4 + - - +
354A LEU* 1.3 81.0 - - + +
356A ASN* 1.3 56.8 + - - +
358A GLY* 3.0 19.4 + - - -
359A GLN 3.4 19.2 - - - +
360A LYS* 4.7 3.1 - - + -
361A LEU* 4.6 1.8 + - - +
436A GLU* 3.1 38.5 + - + -
438A ASP* 2.8 33.9 + - - -
745A LEU* 5.2 2.8 - - - +
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Residues in contact with ASN 356 (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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352A ASN 2.8 16.9 + - - +
353A GLU* 3.7 9.1 - - - +
354A LEU 3.3 0.2 - - - -
355A HIS* 1.3 76.2 - - - +
357A ASN* 1.3 67.3 + - - +
358A GLY 3.2 1.2 + - - -
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Residues in contact with ASN 357 (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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312A GLU* 4.7 4.0 - - - +
315A ARG* 3.1 51.7 + - - +
353A GLU* 3.0 25.1 + - - +
354A LEU* 3.1 3.9 + - - +
356A ASN* 1.3 86.1 + - - +
358A GLY* 1.3 61.3 + - - +
359A GLN* 3.3 11.9 + - - +
743A THR* 3.5 15.6 - - - +
2001A NAG 5.2 6.1 + - - -
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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