Contacts of the helix formed by residues 385 - 395 (chain A) in PDB entry 3BMW
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 THR 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A GLU 2.7 23.2 + - - +
364A GLN* 3.6 25.1 - - - +
365A TYR* 3.9 18.6 - - + -
382A ASN* 3.8 20.0 - - + +
383A THR 3.5 1.2 - - - -
384A SER* 1.3 78.0 + - - +
386A THR* 1.3 64.8 + - - +
387A ALA 3.7 0.3 + - - -
388A TYR* 3.0 17.7 + - - +
389A ASN* 2.9 22.9 + - - -
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Residues in contact with THR 386 (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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340A ARG* 5.3 2.0 - - - +
343A GLU* 3.5 24.0 - - + +
365A TYR* 3.5 12.4 + - - -
384A SER 3.6 1.6 + - - -
385A THR* 1.3 71.7 - - - +
387A ALA* 1.3 57.3 + - - +
389A ASN* 3.1 5.7 + - - +
390A VAL* 2.8 30.9 + - + +
463A LEU* 3.8 25.1 - - + +
464A LEU* 3.7 22.2 - - + -
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU* 4.4 5.4 - - + -
346A LEU* 3.9 18.6 - - + +
362A THR 4.3 1.3 - - - +
363A GLU* 3.8 20.4 - - - +
365A TYR* 2.9 34.5 + - + +
385A THR 3.2 0.4 - - - -
386A THR* 1.3 73.1 - - - +
388A TYR* 1.3 66.0 + - - +
390A VAL* 3.2 9.9 + - - +
391A ILE* 3.1 28.4 + - - +
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Residues in contact with TYR 388 (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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64A GLY 4.1 1.4 + - - -
65A TYR* 2.7 62.0 + + - -
68A GLY* 3.2 30.1 - - - -
69A MET* 3.6 24.7 - - + +
363A GLU* 4.0 13.7 + - + +
382A ASN 4.1 9.0 - - - +
383A THR* 3.3 43.0 - - + +
385A THR* 3.0 24.7 + - - +
387A ALA* 1.3 75.9 - - - +
389A ASN* 1.3 62.9 + - - +
391A ILE* 3.3 6.0 + - - +
392A LYS* 2.9 27.8 + - + +
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Residues in contact with ASN 389 (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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383A THR 3.3 23.5 + - - +
384A SER* 3.6 11.5 + - - +
385A THR 2.9 20.6 + - - +
386A THR* 3.1 8.0 + - - +
388A TYR* 1.3 76.6 - - - +
390A VAL* 1.3 64.6 + - - +
392A LYS* 3.6 24.0 - - + +
393A LYS* 3.0 36.3 + - - +
463A LEU* 3.7 17.9 - - + +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU* 4.1 20.6 - - + +
346A LEU* 4.5 8.7 - - + -
347A ALA* 4.2 10.3 - - + +
350A LEU* 4.5 2.2 - - + -
386A THR* 2.8 21.3 + - + +
387A ALA* 3.2 11.4 + - - +
389A ASN* 1.3 76.4 - - - +
391A ILE* 1.3 63.5 + - + +
393A LYS* 3.4 0.7 + - - +
394A LEU* 3.0 44.5 + - + +
460A LEU* 4.3 7.2 - - + -
463A LEU* 3.8 14.6 - - + -
464A LEU* 3.9 29.2 - - + -
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Residues in contact with ILE 391 (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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16A VAL* 4.9 3.4 - - + -
69A MET* 3.3 39.7 - - + +
70A GLY 5.4 0.2 - - - -
71A VAL* 5.4 2.9 - - + -
346A LEU* 4.3 16.4 - - + -
350A LEU* 3.8 15.3 - - + -
358A ILE* 3.8 40.8 - - + -
363A GLU* 3.9 15.9 - - + -
387A ALA 3.1 16.4 + - - +
388A TYR 3.6 5.2 - - - +
390A VAL* 1.3 77.0 - - + +
392A LYS* 1.3 57.1 + - - +
395A ALA* 2.8 45.6 + - + +
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Residues in contact with LYS 392 (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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68A GLY* 2.9 36.6 + - - +
69A MET* 3.3 12.9 + - - +
70A GLY* 5.3 0.6 - - - +
388A TYR* 2.9 22.8 + - + +
389A ASN* 3.6 25.4 - - - +
391A ILE* 1.3 76.7 - - - +
393A LYS* 1.3 60.8 + - + +
396A PRO* 3.1 24.8 - - - +
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Residues in contact with LYS 393 (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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389A ASN* 3.0 24.9 + - - +
390A VAL 4.0 2.7 - - - +
392A LYS* 1.3 81.9 - - + +
394A LEU* 1.3 63.4 + - + +
396A PRO* 3.8 6.9 - - - +
397A LEU* 3.9 13.2 - - - +
459A VAL* 4.1 17.3 + - + +
460A LEU* 3.5 47.4 + - + +
461A GLY* 5.3 2.4 - - - +
463A LEU* 4.2 16.4 - - + -
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Residues in contact with LEU 394 (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 ALA* 3.7 42.6 - - + +
350A LEU* 4.0 23.0 - - + +
351A THR* 4.3 9.6 - - + +
390A VAL* 3.0 25.9 + - + +
393A LYS* 1.3 80.0 - - - +
395A ALA* 1.3 67.6 + - - +
396A PRO* 3.3 2.0 - - - -
397A LEU* 3.0 39.8 + - + +
398A ARG* 4.1 1.6 + - - +
459A VAL* 4.6 4.5 - - + -
460A LEU* 3.9 21.8 - - + -
489A VAL* 4.0 21.8 - - + -
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Residues in contact with ALA 395 (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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14A THR 4.9 1.7 - - - +
16A VAL* 3.6 26.7 - - + +
69A MET 4.1 1.8 - - - +
70A GLY 3.5 28.9 - - - +
72A THR* 6.1 1.1 - - - +
350A LEU* 4.5 4.8 - - + +
391A ILE* 2.8 29.9 + - + +
394A LEU* 1.3 73.3 - - - +
396A PRO* 1.4 64.0 - - + +
397A LEU 3.1 1.7 + - - -
398A ARG* 3.2 21.2 + - - +
399A LYS* 4.4 1.7 + - - +
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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