Contacts of the helix formed by residues 386 - 394 (chain A) in PDB entry 3R2W
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 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A SER* 5.9 3.8 - - - +
110A MET* 3.8 9.9 - - - -
384A VAL* 4.3 3.5 - - - +
385A LYS* 1.3 86.0 - - + +
387A THR* 1.3 62.5 + - - +
388A SER* 3.4 21.9 + - - -
389A ASP* 2.8 33.6 + - - +
390A LEU* 3.5 2.8 + - - +
426A THR* 5.8 7.2 - - + -
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Residues in contact with THR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 3.9 8.0 - - - +
386A THR* 1.3 74.8 - - - +
388A SER* 1.3 67.4 + - - +
389A ASP 3.2 0.2 - - - -
390A LEU* 3.3 24.8 + - - +
391A LEU 3.4 9.2 + - - -
421A LEU* 3.9 10.0 - - + +
422A GLY 5.4 1.6 - - - +
425A PHE* 2.7 29.8 - - + +
426A THR* 3.4 27.2 + - + +
428A VAL* 4.7 3.2 - - - -
431A TYR* 3.2 36.0 - - - +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR* 2.8 13.7 + - - -
387A THR* 1.3 79.2 - - - +
389A ASP* 1.3 68.0 + - - +
390A LEU 3.3 0.2 - - - -
391A LEU* 3.6 1.5 + - - +
392A LEU* 3.4 17.5 + - - +
419A VAL* 3.5 39.5 + - - +
420A LYS* 4.4 0.7 - - - -
421A LEU* 3.4 35.9 + - - +
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A PRO 2.8 23.5 - - - +
384A VAL* 3.9 18.4 - - + +
385A LYS* 3.0 16.1 + - - +
386A THR* 2.8 18.0 + - - +
388A SER* 1.3 78.8 - - - +
390A LEU* 1.3 66.4 + - - +
392A LEU* 3.4 15.9 + - + +
393A VAL* 3.0 25.6 + - - +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 3.8 23.1 - - + -
119A ILE* 4.6 6.5 - - + -
120A GLY 4.4 8.3 - - - +
121A VAL* 4.4 16.6 - - + -
127A PHE* 4.9 0.2 - - + -
384A VAL* 3.8 22.7 - - + -
386A THR 3.5 2.4 + - - +
387A THR* 3.3 22.8 + - - +
389A ASP* 1.3 76.0 - - - +
391A LEU* 1.3 67.2 + - - +
393A VAL* 3.0 9.0 + - + +
394A MET* 2.8 54.1 + - + +
428A VAL* 4.5 14.1 - - + -
431A TYR* 4.2 9.6 - - + +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A THR 3.4 3.2 + - - -
388A SER 3.6 7.6 + - - +
389A ASP 3.3 0.4 - - - -
390A LEU* 1.3 80.1 - - - +
392A LEU* 1.3 52.6 + - - +
394A MET* 3.4 5.5 + - - +
395A SER* 2.5 30.7 + - - -
419A VAL* 4.4 9.6 - - + -
421A LEU* 4.1 7.6 - - + -
431A TYR* 3.1 21.2 + - + +
435A PHE* 3.4 40.4 - - + -
438A ILE* 3.5 25.1 - - + -
439A PRO* 4.0 3.4 - - + -
441A MET* 3.5 29.4 - - + -
447A LEU* 4.1 21.8 - - + -
461A LEU* 5.5 1.1 - - + -
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Residues in contact with LEU 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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388A SER 3.4 11.1 + - - +
389A ASP* 3.4 21.5 + - - +
390A LEU 3.1 0.2 - - - -
391A LEU* 1.3 78.1 - - - +
393A VAL* 1.3 57.7 + - + +
395A SER* 2.4 19.9 + - - -
397A LEU* 3.7 30.1 - - + +
398A TYR* 3.7 21.9 - - + +
416A VAL* 3.7 26.5 - - + -
417A PRO* 3.6 25.6 - - + +
419A VAL* 4.2 18.4 - - + +
441A MET* 4.0 4.2 - - + +
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 4.0 22.9 - - + +
122A ARG* 2.8 22.6 + - + -
244A LEU* 3.7 25.4 - - + -
382A LEU* 5.0 5.6 - - + -
384A VAL* 4.8 4.0 - - + -
389A ASP 3.0 12.2 + - - +
390A LEU* 3.2 18.8 - - + +
392A LEU* 1.3 80.6 - - - +
394A MET* 1.3 65.3 + - + +
395A SER 3.2 1.3 + - - -
398A TYR* 3.6 23.1 - - + +
405A LEU* 3.8 24.5 - - + -
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Residues in contact with MET 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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120A GLY 3.6 23.8 - - - +
121A VAL 3.4 23.1 - - - +
122A ARG* 3.8 23.0 + - + +
124A GLU* 5.5 3.6 - - - +
390A LEU* 2.8 52.4 + - + +
391A LEU 4.0 2.5 - - - +
393A VAL* 1.3 70.5 - - - +
395A SER* 1.3 57.5 + - - +
431A TYR* 3.4 30.5 - - + +
432A LEU* 5.2 7.9 - - + -
438A ILE* 3.5 37.4 - - + +
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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