Contacts of the helix formed by residues 348 - 355 (chain A) in PDB entry 1B3U
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 ILE 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A VAL* 5.4 1.1 - - - -
329A ILE* 3.7 27.1 - - + -
333A VAL* 4.6 1.6 - - + -
344A LEU* 2.9 29.9 + - + +
345A ALA* 4.2 3.3 - - - +
347A VAL* 1.3 79.9 - - - +
349A MET* 1.3 86.1 + - + +
350A GLY 3.3 0.7 + - - -
351A LEU* 3.3 36.2 + - + +
364A LEU* 4.6 5.7 - - + +
367A LEU* 4.3 23.6 - - + -
371A GLN* 3.5 26.5 - - - +
383A ILE* 4.2 11.4 - - + -
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Residues in contact with MET 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 ALA 5.3 1.0 + - - +
347A VAL 3.0 3.4 + - - -
348A ILE* 1.3 108.6 - - + +
350A GLY* 1.3 60.7 + - - +
351A LEU 2.9 6.1 - - - -
352A SER* 2.9 31.5 + - - -
364A LEU* 3.9 20.9 - - + +
365A LEU* 5.5 1.3 - - - -
368A PHE* 3.3 59.5 - - + +
383A ILE* 5.1 7.0 - - + +
386A ASN* 4.1 19.3 - - + +
389A CYS* 3.8 9.2 - - + +
390A VAL* 3.6 31.0 - - + -
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Residues in contact with GLY 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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306A LYS* 3.9 28.3 - - - +
310A GLU* 4.7 1.9 - - - +
347A VAL 2.8 13.4 + - - -
349A MET* 1.3 76.3 - - - +
351A LEU* 1.3 59.4 + - - +
352A SER 3.4 0.2 - - - -
353A PRO* 3.4 17.5 - - - +
354A ILE* 4.1 6.1 - - - +
386A ASN* 6.3 0.4 - - - +
389A CYS* 4.2 17.1 - - - +
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Residues in contact with LEU 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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305A VAL* 4.0 8.7 - - + -
306A LYS* 4.0 17.9 - - + -
309A CYS* 3.9 35.9 - - + -
321A ILE* 5.5 6.3 - - + -
326A LEU* 6.3 0.9 - - + -
329A ILE* 3.9 26.2 - - + -
348A ILE* 3.3 28.9 - - + +
349A MET 2.9 0.8 - - - -
350A GLY* 1.3 79.2 - - - +
352A SER* 1.3 63.9 + - - +
353A PRO 3.4 0.4 - - - -
354A ILE* 2.9 24.5 + - + +
355A LEU* 3.0 21.0 + - + +
364A LEU* 4.0 17.9 - - + -
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Residues in contact with SER 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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349A MET* 2.9 16.5 + - - -
351A LEU* 1.3 75.8 - - - +
353A PRO* 1.3 67.5 - - - +
354A ILE 3.0 0.5 + - - -
355A LEU 3.1 1.7 + - - -
356A GLY* 2.9 27.9 + - - -
360A THR* 3.2 34.7 + - - +
364A LEU* 3.7 10.2 - - - +
390A VAL* 3.8 23.3 - - - +
393A VAL* 3.9 13.2 - - - +
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Residues in contact with PRO 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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310A GLU* 6.0 1.1 - - - +
349A MET 4.0 1.8 - - - +
350A GLY 3.4 19.3 - - - +
352A SER* 1.3 95.0 - - - +
354A ILE* 1.3 61.6 + - + +
355A LEU 3.4 0.2 - - - -
356A GLY* 4.2 5.7 + - - +
389A CYS* 4.2 18.2 - - + +
392A GLU* 6.0 1.8 - - - +
393A VAL* 3.5 21.8 - - + -
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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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306A LYS* 4.3 5.6 - - + +
309A CYS* 4.3 0.9 - - + -
310A GLU* 3.7 48.2 - - + +
317A ARG* 3.9 30.5 - - + +
318A GLU* 4.3 10.4 - - - +
321A ILE* 3.8 26.2 - - + -
350A GLY 4.1 14.4 - - - +
351A LEU* 2.9 20.9 + - + +
353A PRO* 1.3 83.8 - - + +
355A LEU* 1.3 62.8 + - + +
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Residues in contact with LEU 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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318A GLU* 3.4 24.1 - - + +
321A ILE* 3.5 37.2 - - + -
322A MET* 4.0 30.1 - - + -
326A LEU* 5.4 4.3 - - + -
351A LEU* 3.0 21.4 + - + +
352A SER 4.0 2.2 - - - +
354A ILE* 1.3 84.1 - - + +
356A GLY* 1.3 60.6 + - - +
359A ASN* 3.0 38.9 + - + +
360A THR* 4.6 3.6 - - - +
363A HIS* 5.6 0.4 - - + -
364A LEU* 4.1 30.3 - - + -
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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