Contacts of the helix formed by residues 359 - 369 (chain A) in PDB entry 1LB6
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 ASN 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A GLY* 1.3 73.6 + - - +
360A PHE* 1.3 63.8 + - - +
361A GLY 3.3 2.9 - - - -
362A MET* 3.2 33.4 + - + +
363A HIS* 3.5 10.6 - - - +
491A ASP* 3.1 21.1 + - - +
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Residues in contact with PHE 360 (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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357A ILE* 4.0 22.4 - - + +
358A GLY 3.0 2.9 + - - -
359A ASN* 1.3 75.2 - - - +
361A GLY* 1.3 67.8 + - - +
363A HIS* 2.9 23.6 + + + +
364A LEU* 3.0 41.9 + - + +
375A ILE* 5.7 0.4 - - + -
393A LEU* 5.1 6.3 - - + -
395A LEU* 4.3 25.4 - - + -
407A ILE* 4.9 1.8 - - + -
479A LEU* 4.8 0.4 - - + -
482A LEU* 3.8 22.0 - - + -
488A ILE* 3.5 24.7 - - + -
491A ASP* 3.1 20.7 + - - +
492A THR 4.7 0.2 - - - +
493A LEU* 3.8 35.4 - - + -
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Residues in contact with GLY 361 (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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359A ASN 3.3 0.2 - - - -
360A PHE* 1.3 72.8 - - - +
362A MET* 1.3 59.8 + - - +
364A LEU* 3.3 8.6 + - - -
365A LYS* 2.8 46.5 + - - +
488A ILE* 6.0 0.2 - - - +
491A ASP* 2.7 22.9 + - - -
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Residues in contact with MET 362 (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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359A ASN* 3.2 26.0 + - + +
360A PHE 3.0 0.6 - - - -
361A GLY* 1.3 74.9 - - - +
363A HIS* 1.3 83.4 + - + +
365A LYS* 3.3 9.5 + - + +
366A CYS* 3.1 28.4 + - + +
491A ASP* 4.9 0.8 + - - -
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Residues in contact with HIS 363 (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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357A ILE* 4.1 17.6 - - + +
358A GLY 3.8 15.8 + - - -
359A ASN* 3.5 19.6 + - + +
360A PHE* 2.9 19.3 + + + +
362A MET* 1.3 94.6 - - + +
364A LEU* 1.3 64.6 + - - +
366A CYS* 3.2 7.9 + - - +
367A GLN* 3.0 20.8 + - - +
373A VAL* 3.5 30.2 - - + +
375A ILE* 4.0 24.5 - - + +
395A LEU* 4.1 9.2 - - + -
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Residues in contact with LEU 364 (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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360A PHE* 3.0 46.0 + - + +
361A GLY* 3.6 13.5 - - - +
362A MET 3.3 0.2 - - - -
363A HIS* 1.3 77.3 - - - +
365A LYS* 1.3 70.8 + - - +
367A GLN* 3.2 6.0 + - - +
368A GLU* 3.0 39.5 + - - +
395A LEU* 4.1 7.9 - - + -
479A LEU* 3.8 30.5 - - + -
482A LEU* 4.8 6.1 - - + -
488A ILE* 5.8 2.7 - - + -
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Residues in contact with LYS 365 (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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361A GLY* 2.8 40.6 + - - +
362A MET* 3.7 8.1 - - + +
363A HIS 3.3 0.2 - - - -
364A LEU* 1.3 84.7 - - - +
366A CYS* 1.3 63.0 + - - +
368A GLU* 3.3 21.1 + - - +
369A GLU* 3.1 23.9 + - - +
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Residues in contact with CYS 366 (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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362A MET* 3.1 20.2 + - + +
363A HIS* 3.4 11.4 - - - +
364A LEU 3.2 0.2 - - - -
365A LYS* 1.3 76.5 - - - +
367A GLN* 1.3 63.0 + - - +
369A GLU* 2.9 22.5 + - - +
371A LYS* 3.2 46.6 + - - -
372A PRO 3.9 15.5 - - - -
373A VAL* 3.9 6.5 - - + -
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Residues in contact with GLN 367 (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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363A HIS 3.0 13.4 + - - +
364A LEU* 3.5 8.4 + - - +
366A CYS* 1.3 76.0 - - - +
368A GLU* 1.3 75.8 + - - +
370A GLU* 2.9 15.8 + - - -
371A LYS 3.9 10.3 - - - +
373A VAL* 3.7 7.3 - - + +
395A LEU* 3.9 24.5 - - + +
396A GLN 2.8 29.7 - - - +
397A LEU* 4.5 1.7 - - + +
398A PRO* 3.2 30.1 - - + +
405A ASN* 2.9 25.2 + - - +
479A LEU* 3.6 20.0 - - - +
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Residues in contact with GLU 368 (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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364A LEU* 3.0 30.3 + - - +
365A LYS* 3.6 21.4 + - - +
366A CYS 3.2 0.2 - - - -
367A GLN* 1.3 85.2 + - - +
369A GLU* 1.3 56.8 + - - +
370A GLU* 3.0 15.1 + - - +
398A PRO* 4.2 7.8 - - + +
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Residues in contact with GLU 369 (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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365A LYS 3.1 11.2 + - - +
366A CYS* 2.9 19.2 + - - +
368A GLU* 1.3 75.1 - - - +
370A GLU* 1.3 70.0 + - - +
371A LYS* 3.0 44.9 + - + +
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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