Contacts of the helix formed by residues 346 - 357 (chain A) in PDB entry 4L1O
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 SER 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A TYR* 4.6 2.9 - - - -
344A VAL* 3.5 5.9 - - - +
345A ARG* 1.3 82.4 - - - +
347A LEU* 1.3 65.2 + - - +
348A GLU* 3.5 16.5 + - - +
349A GLU* 3.1 27.7 + - - +
350A ALA* 3.0 20.1 + - - +
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Residues in contact with LEU 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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217A TYR* 3.7 30.6 + - + +
346A SER* 1.3 72.5 - - - +
348A GLU* 1.3 71.7 + - - +
350A ALA* 3.2 3.0 + - - +
351A ILE* 3.0 33.3 + - + +
372A VAL* 4.2 36.8 - - + +
375A LYS* 3.9 26.2 - - + -
376A MET* 3.7 29.8 - - + -
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Residues in contact with GLU 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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346A SER* 3.1 12.9 - - - +
347A LEU* 1.3 90.8 + - - +
349A GLU* 1.3 60.7 + - - +
351A ILE* 3.3 11.1 + - + +
352A GLN* 3.1 23.4 + - - +
375A LYS* 4.3 24.8 + - - +
379A 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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343A CYS 4.8 2.1 - - - +
344A VAL* 4.1 17.1 - - + +
345A ARG* 2.8 47.3 + - - +
346A SER* 3.1 20.0 + - - +
348A GLU* 1.3 77.3 - - - +
350A ALA* 1.3 57.4 + - - +
352A GLN* 3.5 14.5 + - + +
353A PHE* 3.0 29.0 + - + +
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Residues in contact with ALA 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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217A TYR* 3.6 36.6 - - + -
250A LEU* 4.2 7.6 - - + +
344A VAL* 4.1 13.6 - - + +
346A SER 3.0 8.3 + - - +
347A LEU 3.2 9.2 + - - +
349A GLU* 1.3 75.6 - - - +
351A ILE* 1.3 59.0 + - - +
353A PHE* 3.4 6.4 + - - +
354A ILE* 3.1 36.7 + - - +
376A MET* 4.1 6.1 - - + -
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Residues in contact with ILE 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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347A LEU* 3.0 36.8 + - + +
348A GLU* 3.3 8.9 + - - +
350A ALA* 1.3 73.7 - - - +
352A GLN* 1.3 60.6 + - - +
354A ILE* 3.3 3.4 + - - +
355A ASN* 2.9 52.8 + - - +
375A LYS* 4.1 12.1 - - + +
376A MET* 4.1 32.3 - - + +
379A GLU* 3.6 37.5 - - + +
380A THR* 4.3 10.1 - - + -
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Residues in contact with GLN 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 GLU 3.1 15.4 + - - +
349A GLU* 3.7 14.8 - - - +
351A ILE* 1.3 76.8 - - - +
353A PHE* 1.3 57.9 + - - +
355A ASN* 3.1 7.0 + - - +
356A GLN* 2.8 63.1 + - - +
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Residues in contact with PHE 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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248A TYR* 3.5 32.8 - + - -
250A LEU* 3.8 22.9 - - + -
325A PRO* 3.8 26.5 - - + -
330A MET* 3.9 11.2 - - + -
342A VAL* 4.2 9.4 - - + -
344A VAL* 4.9 8.5 - - + -
349A GLU* 3.0 19.5 + - + +
350A ALA* 3.5 8.3 - - - +
352A GLN* 1.3 78.6 - - - +
354A ILE* 1.3 63.9 + - - +
356A GLN* 3.5 19.4 + - - +
357A ARG* 3.4 44.5 + - - -
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Residues in contact with ILE 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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215A PRO* 3.9 23.3 - - + -
217A TYR* 5.3 1.1 - - + -
248A TYR* 4.4 4.7 - - - +
250A LEU* 3.9 23.1 - - + -
350A ALA 3.1 19.0 + - - +
351A ILE* 3.8 4.7 - - - +
353A PHE* 1.3 76.2 - - - +
355A ASN* 1.3 64.1 + - - +
357A ARG* 3.3 21.4 + - - +
358A GLU 4.7 2.8 - - - +
359A LYS* 5.9 0.3 - - - -
360A PRO* 4.9 13.8 - - + +
363A LEU* 3.9 27.6 - - + -
376A MET* 4.0 21.5 - - + -
380A THR* 4.3 18.6 - - + -
381A SER 5.5 2.0 - - - +
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Residues in contact with ASN 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 ILE* 2.9 29.7 + - - +
352A GLN* 3.7 6.8 - - - +
354A ILE* 1.3 75.9 - - - +
356A GLN* 1.3 63.1 + - - +
357A ARG 3.4 7.6 - - - +
379A GLU* 2.9 29.2 + - - +
380A THR* 3.5 20.3 - - - +
381A SER 4.5 1.9 + - - -
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Residues in contact with GLN 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 GLN* 2.8 51.9 + - - +
353A PHE* 3.5 11.6 + - - +
355A ASN* 1.3 76.9 - - - +
357A ARG* 1.3 61.6 + - + +
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Residues in contact with ARG 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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213A LYS* 4.1 12.9 - - - +
248A TYR* 4.2 9.1 + - - +
325A PRO* 3.0 40.2 + - - +
326A GLN* 5.0 1.6 + - - -
330A MET* 2.8 31.7 + - - +
331A GLN* 3.4 10.6 - - - +
353A PHE* 3.4 44.6 + - - +
354A ILE* 3.3 13.9 + - - +
355A ASN 3.2 10.5 - - - +
356A GLN* 1.3 83.8 - - + +
358A GLU* 1.3 69.8 + - - +
359A LYS* 3.8 3.1 + - - +
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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