Contacts of the helix formed by residues 380 - 397 (chain A) in PDB entry 2JJD
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 380 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 3.6 16.2 - - - -
306A VAL* 5.8 0.4 - - - -
378A VAL* 3.7 0.4 - - - +
379A GLN* 1.3 79.4 - - - +
381A ASP* 1.3 63.7 + - - +
382A MET* 3.8 8.3 - - - -
383A GLN* 3.1 29.1 + - - +
384A TYR 3.1 17.8 + - - -
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Residues in contact with ASP 381 (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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136A ARG* 4.7 21.3 - - + +
139A PHE* 3.7 24.6 - - + -
140A ASN* 5.9 0.2 - - - +
380A THR* 1.3 71.8 - - - +
382A MET* 1.3 62.8 + - - +
384A TYR* 3.1 4.4 + - - +
385A THR* 3.1 24.1 + - - -
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Residues in contact with MET 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLY* 5.7 3.6 - - - -
306A VAL* 3.2 30.4 - - + +
380A THR* 3.2 8.1 - - - -
381A ASP* 1.3 78.8 - - - +
383A GLN* 1.3 60.4 + - - +
385A THR* 4.0 6.7 + - - -
386A PHE* 3.4 14.7 + - - +
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Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TRP* 4.8 7.1 - - + +
306A VAL* 3.9 16.4 - - + -
340A GLY* 3.6 28.3 - - - -
341A ARG* 3.7 10.5 - - - +
344A THR* 3.5 17.0 - - + +
378A VAL* 3.6 6.5 - - + +
379A GLN* 2.7 35.4 + - - +
380A THR* 3.1 23.3 + - - +
381A ASP 3.2 0.6 - - - -
382A MET* 1.3 78.1 - - - +
384A TYR* 1.3 63.9 + - - +
386A PHE* 3.1 13.2 + - - +
387A ILE* 3.2 17.3 + - - +
1693A CL 3.9 14.1 - - - +
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Residues in contact with TYR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG 6.2 1.6 - - - -
138A GLU* 2.5 48.8 + - + +
139A PHE* 3.7 39.9 - + + -
142A LEU* 3.8 21.8 - - + -
363A VAL* 3.4 22.9 - - + +
364A PHE* 3.3 23.2 - - - +
367A VAL* 4.1 11.0 - - + -
378A VAL* 4.0 6.3 - - + +
380A THR 3.1 6.0 + - - +
381A ASP 3.1 8.5 + - - +
383A GLN* 1.3 74.1 - - - +
385A THR* 1.3 68.7 + - - +
386A PHE 3.3 0.3 + - - -
387A ILE* 3.5 16.0 + - + +
388A TYR* 3.5 24.8 - + - -
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Residues in contact with THR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASP 3.1 14.5 + - - -
382A MET* 4.1 7.6 - - - -
384A TYR* 1.3 77.7 - - - +
386A PHE* 1.3 57.0 + - - +
388A TYR* 2.9 28.4 + - - +
389A GLN* 3.1 20.3 + - - +
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Residues in contact with PHE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TRP* 4.6 14.6 - + - -
306A VAL* 3.5 24.0 - - + -
307A PRO* 3.6 37.0 - - + -
308A PHE 5.5 0.4 - - - -
309A THR 4.3 1.8 - - - -
310A PRO* 3.8 31.9 - - + -
313A MET* 4.4 15.0 - - + -
344A THR* 5.0 6.3 - - + -
348A ILE* 3.9 23.1 - - + -
382A MET 3.4 14.1 + - - +
383A GLN* 3.1 14.0 + - - +
385A THR* 1.3 75.5 - - - +
387A ILE* 1.3 66.8 + - - +
389A GLN* 3.4 20.4 + - - +
390A ALA* 3.1 19.8 + - - +
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Residues in contact with ILE 387 (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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344A THR* 4.3 20.0 - - - +
347A VAL* 3.4 45.5 - - + -
348A ILE* 4.1 15.4 - - + +
363A VAL* 3.7 28.5 - - + -
367A VAL* 4.6 1.8 - - + -
378A VAL* 4.2 17.0 - - + -
383A GLN 3.2 12.3 + - - +
384A TYR* 3.6 13.9 - - + +
386A PHE* 1.3 77.5 - - - +
388A TYR* 1.3 59.1 + - - +
390A ALA* 3.6 2.3 + - - +
391A LEU* 3.0 34.2 + - + +
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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
----------------------------------------------------------
115A ILE* 3.8 25.8 - - + +
120A LEU* 4.2 12.3 - - + +
124A ILE* 3.4 31.5 - - + +
127A ARG* 3.4 15.9 + - - -
138A GLU* 3.0 19.1 + - - -
361A VAL* 4.9 4.7 - - + -
363A VAL* 3.7 40.3 + - + +
364A PHE* 4.6 1.0 + - - +
384A TYR* 3.5 39.0 - + - -
385A THR* 2.9 12.6 + - - +
387A ILE* 1.3 77.9 - - - +
389A GLN* 1.3 59.8 + - + +
391A LEU* 3.2 8.4 + - + +
392A LEU* 2.9 29.8 + - - +
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Residues in contact with GLN 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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124A ILE* 5.4 9.9 - - + -
306A VAL* 5.3 2.8 - - - +
308A PHE 4.6 10.6 + - - +
310A PRO* 4.0 14.6 - - + +
385A THR* 3.1 20.9 + - - +
386A PHE* 3.4 25.2 + - - +
388A TYR* 1.3 75.7 - - - +
390A ALA* 1.3 57.1 + - - +
392A LEU* 3.3 9.6 + - + +
393A GLU* 2.9 30.0 + - - +
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PRO* 3.8 24.8 - - + +
313A MET* 6.1 0.4 - - + -
314A LEU* 3.5 14.5 - - + +
348A ILE* 3.6 37.5 - - + -
386A PHE 3.1 13.0 + - - +
387A ILE 3.7 1.3 - - - +
389A GLN* 1.3 76.5 - - - +
391A LEU* 1.3 58.7 + - - +
393A GLU* 3.4 0.8 + - - -
394A TYR* 2.9 31.5 + - - +
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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
----------------------------------------------------------
120A LEU* 4.3 4.9 - - + -
348A ILE* 4.4 6.3 - - + +
351A MET* 3.4 44.2 - - + +
352A MET* 3.9 13.7 - - + +
355A MET* 3.2 38.0 - - + +
361A VAL* 3.6 16.8 - - + -
363A VAL* 3.7 18.4 - - + -
387A ILE* 3.0 27.7 + - + +
388A TYR* 3.2 8.9 + - + +
390A ALA* 1.3 77.0 - - + +
392A LEU* 1.3 60.3 + - - +
394A TYR* 3.4 4.1 + - - +
395A TYR* 3.1 17.5 + - - +
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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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120A LEU* 3.8 25.9 - - + +
121A GLU* 4.0 36.8 - - + +
124A ILE* 4.5 22.0 - - + -
388A TYR 2.9 15.8 + - - +
389A GLN* 3.6 7.6 - - + +
391A LEU* 1.3 73.0 - - - +
393A GLU* 1.3 66.9 + - - +
395A TYR* 2.9 4.0 + - + +
396A LEU* 2.8 63.1 + - + +
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Residues in contact with GLU 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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310A PRO* 4.2 20.7 - - + +
311A ILE* 5.1 11.4 - - - +
314A LEU* 3.9 15.7 - - + -
389A GLN 2.9 17.3 + - - +
390A ALA 3.5 4.9 - - - +
392A LEU* 1.3 75.4 - - - +
394A TYR* 1.3 56.5 + - - +
396A LEU* 5.0 1.3 - - - -
397A TYR* 3.1 44.8 + - + +
398A GLY 3.3 4.2 + - - -
660A GLN* 4.2 7.0 + - - +
663A LYS* 2.0 39.8 + - - -
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Residues in contact with TYR 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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314A LEU* 3.9 19.7 - - + +
352A MET* 3.3 55.5 - - + +
355A MET* 4.1 19.7 - - + -
356A HIS* 2.9 39.7 + + - -
390A ALA 2.9 18.6 + - - +
391A LEU* 3.7 4.7 - - - +
392A LEU 3.1 0.2 - - - -
393A GLU* 1.3 75.3 - - - +
395A TYR* 1.3 58.3 + - - +
398A GLY* 3.0 33.6 - - - +
399A ASP 5.5 0.2 - - - -
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Residues in contact with TYR 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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117A VAL* 3.7 55.3 + - + +
118A GLU* 4.4 5.2 + - - -
120A LEU* 4.7 4.3 - - + -
121A GLU 6.3 0.2 - - - -
355A MET* 4.2 16.2 - - + -
391A LEU 3.1 10.9 + - - +
392A LEU* 2.9 14.4 + - + +
394A TYR* 1.3 79.1 - - - +
396A LEU* 1.3 93.9 + - + +
397A TYR 3.3 0.9 + - - -
398A GLY* 3.9 3.6 + - - -
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Residues in contact with LEU 396 (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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121A GLU* 3.2 35.0 - - + +
392A LEU* 2.8 49.7 + - + +
393A GLU* 5.5 0.4 - - - +
395A TYR* 1.3 92.5 - - + +
397A TYR* 1.3 94.8 + - + +
432A LYS* 4.5 8.5 - - - +
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Residues in contact with TYR 397 (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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393A GLU* 3.1 25.3 + - - +
395A TYR 4.2 0.9 - - - -
396A LEU* 1.3 107.7 - - + +
398A GLY* 1.3 71.6 + - - +
399A ASP 3.0 4.1 + - - +
400A THR* 3.6 18.8 - - - +
432A LYS* 4.0 34.5 + - + -
435A ASN* 5.3 7.1 + - - +
436A VAL* 5.7 5.5 - - + +
659A PHE* 3.9 22.4 - + + -
660A GLN* 4.0 16.6 - - - +
663A LYS* 3.1 32.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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