Contacts of the helix formed by residues 380 - 397 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B PHE* 3.7 7.1 - - - -
304B PHE 6.2 0.2 - - - +
378B VAL* 4.1 0.3 - - - +
379B GLN* 1.3 88.9 - - + +
381B ASP* 1.3 60.3 + - - +
382B MET* 4.0 10.8 - - - +
383B GLN* 2.9 38.1 + - - +
384B TYR* 2.9 24.4 + - - +
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Residues in contact with ASP 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE 5.7 0.2 - - - +
136B ARG* 5.0 14.8 - - + -
139B PHE* 3.6 31.7 - - + -
380B THR* 1.3 71.3 - - - +
382B MET* 1.3 61.8 + - - +
384B TYR* 3.1 7.0 + - - +
385B THR* 3.0 31.7 + - + +
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Residues in contact with MET 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE 4.8 4.0 - - - +
305B GLY* 4.0 18.2 - - - -
306B VAL* 3.6 44.8 - - + +
380B THR* 3.1 10.7 - - - +
381B ASP* 1.3 78.3 - - - +
383B GLN* 1.3 57.6 + - - +
385B THR* 3.5 8.1 + - - -
386B PHE* 3.0 27.5 + - - +
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Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B TRP* 4.4 8.2 - - + +
305B GLY 5.2 2.3 + - - +
306B VAL* 4.0 17.3 - - + -
340B GLY* 3.8 3.7 - - - +
341B ARG* 3.8 30.3 - - - +
344B THR* 3.4 26.3 - - + +
378B VAL* 3.7 5.1 - - + +
379B GLN* 2.9 35.6 + - - +
380B THR* 2.9 29.8 + - - +
382B MET* 1.3 77.3 - - - +
384B TYR* 1.3 65.8 + - - +
386B PHE* 3.3 4.6 + - - +
387B ILE* 3.1 25.6 + - - +
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Residues in contact with TYR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 4.4 14.1 - + - -
138B GLU* 2.5 46.4 + - + +
139B PHE* 3.7 39.9 - + + -
142B LEU* 3.8 21.8 - - + -
363B VAL* 3.8 21.4 - - + +
364B PHE* 3.4 24.8 + - - +
367B VAL* 4.3 8.7 - - + -
378B VAL* 4.1 8.2 - - + +
380B THR 2.9 6.8 + - - +
381B ASP* 3.1 9.4 + - - +
383B GLN* 1.3 76.3 - - - +
385B THR* 1.3 63.8 + - + +
387B ILE* 3.2 27.6 + - + +
388B TYR* 3.6 15.2 + + - -
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Residues in contact with THR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 3.3 48.2 - - + -
381B ASP* 3.0 15.9 + - + +
382B MET* 3.5 10.4 + - - -
384B TYR* 1.3 73.2 - - + +
386B PHE* 1.3 62.2 + - - +
387B ILE 3.3 0.2 - - - -
388B TYR* 3.3 11.9 + - - +
389B GLN* 2.9 40.2 + - - +
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B TRP* 4.9 7.2 - + - -
306B VAL* 3.4 25.6 - - + -
307B PRO* 3.6 47.3 - - + -
309B THR 4.1 6.7 - - - -
310B PRO* 4.3 17.7 - - + -
313B MET* 4.1 21.3 - - + -
344B THR* 4.5 10.1 - - - -
348B ILE* 3.8 24.9 - - + -
382B MET 3.0 20.2 + - - +
383B GLN* 3.4 10.5 - - - +
384B TYR 3.2 0.2 - - - -
385B THR* 1.3 73.5 + - - +
387B ILE* 1.3 65.7 + - - +
389B GLN* 3.7 15.7 - - + +
390B ALA* 2.9 23.5 + - + +
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Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B THR* 4.2 19.3 - - - +
347B VAL* 3.4 43.1 - - + -
348B ILE* 4.1 15.4 - - + +
363B VAL* 3.7 30.1 - - + -
367B VAL* 4.6 1.6 - - + -
378B VAL* 4.0 22.4 - - + -
383B GLN 3.1 16.0 + - - +
384B TYR* 3.2 12.3 + - + +
386B PHE* 1.3 74.7 - - - +
388B TYR* 1.3 58.7 + - - +
390B ALA* 3.7 2.1 - - - +
391B LEU* 3.0 34.5 + - + +
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Residues in contact with TYR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 3.6 26.6 - - + +
120B LEU* 4.1 12.3 - - + +
124B ILE* 3.5 29.3 - - + +
127B ARG* 3.5 13.7 + - - -
135B PHE* 3.4 27.4 - + + -
138B GLU* 3.1 23.1 + - - -
361B VAL* 5.2 4.3 - - + -
362B ASP* 5.5 0.2 - - - -
363B VAL* 3.6 42.8 + - + +
364B PHE* 4.4 1.9 + - - +
384B TYR* 3.8 18.8 - + - -
385B THR 3.3 8.0 + - - +
386B PHE 3.2 0.6 - - - -
387B ILE* 1.3 77.0 - - - +
389B GLN* 1.3 58.5 + - - +
391B LEU* 3.1 8.8 + - + +
392B LEU* 2.8 29.8 + - - +
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Residues in contact with GLN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 5.2 10.5 - - + -
135B PHE* 6.5 0.2 - - + -
306B VAL* 5.0 4.5 - - - +
307B PRO 5.6 0.3 - - - +
308B PHE 5.6 1.7 - - - +
310B PRO* 4.0 14.5 - - + +
385B THR* 2.9 27.2 + - - +
386B PHE* 3.3 25.5 + - + +
388B TYR* 1.3 75.0 - - + +
390B ALA* 1.3 57.2 + - - +
392B LEU* 3.2 9.3 + - + +
393B GLU* 2.9 30.0 + - - +
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Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PRO* 3.6 23.7 - - + +
313B MET* 6.0 0.4 - - + -
314B LEU* 3.5 13.1 - - + +
348B ILE* 3.6 32.8 - - + -
386B PHE* 2.9 20.5 + - + +
387B ILE 3.7 1.6 - - - +
389B GLN* 1.3 75.3 - - - +
391B LEU* 1.3 58.5 + - - +
393B GLU 3.4 0.2 + - - -
394B TYR* 2.9 31.5 + - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 4.3 5.4 - - + -
348B ILE* 4.4 6.3 - - + +
351B MET* 3.4 36.1 - - + +
352B MET* 3.9 14.8 - - + +
355B MET* 3.1 37.5 - - + +
361B VAL* 3.5 26.5 - - + -
363B VAL* 3.6 18.2 - - + -
387B ILE* 3.0 26.6 + - + +
388B TYR* 3.1 7.8 + - + +
390B ALA* 1.3 76.7 - - + +
392B LEU* 1.3 61.6 + - - +
394B TYR* 3.4 4.4 + - - +
395B TYR* 3.1 16.6 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 4.1 18.5 - - + +
121B GLU* 3.9 32.3 - - + +
124B ILE* 4.3 24.0 - - + -
388B TYR 2.8 16.3 + - - +
389B GLN* 3.2 9.8 + - + +
391B LEU* 1.3 70.7 - - - +
393B GLU* 1.3 67.1 + - - +
395B TYR* 2.9 6.4 + - + +
396B LEU* 2.9 54.5 + - + +
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Residues in contact with GLU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 5.8 0.9 - - - -
310B PRO* 4.1 27.2 - - + +
311B ILE* 4.5 10.7 - - - +
314B LEU* 3.9 13.9 - - + -
389B GLN 2.9 17.5 + - - +
390B ALA 3.5 4.9 - - - +
392B LEU* 1.3 76.2 - - - +
394B TYR* 1.3 58.1 + - - +
396B LEU* 5.0 0.7 - - - -
397B TYR* 3.1 40.3 + - + +
398B GLY 3.3 4.7 + - - -
660B GLN* 3.8 15.0 + - - +
663B LYS* 2.2 36.2 + - - +
667B LEU* 5.7 1.5 - - - +
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Residues in contact with TYR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B LEU* 3.9 20.6 - - + -
352B MET* 3.4 54.7 - - + +
355B MET* 4.1 20.2 - - + -
356B HIS* 2.9 40.1 + + - -
390B ALA 2.9 17.9 + - - +
391B LEU* 3.7 4.9 - - - +
392B LEU 3.1 0.4 - - - -
393B GLU* 1.3 74.9 - - - +
395B TYR* 1.3 57.5 + - - +
398B GLY* 3.0 33.1 - - - +
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 3.7 56.3 + - + +
118B GLU* 4.4 6.2 + - - -
120B LEU* 5.0 3.6 - - + -
121B GLU* 6.2 1.1 - - + -
355B MET* 4.2 15.5 - - + -
391B LEU 3.1 11.8 + - - +
392B LEU* 2.9 15.8 + - + +
394B TYR* 1.3 80.6 - - - +
396B LEU* 1.3 95.8 + - + +
397B TYR 3.3 1.0 + - - -
398B GLY* 3.9 3.1 + - - -
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLU* 4.9 11.7 - - + -
392B LEU* 2.9 45.3 + - + +
395B TYR* 1.3 98.6 - - + +
397B TYR* 1.3 94.7 + - + +
432B LYS* 4.9 7.4 - - - +
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Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLU* 3.1 22.8 + - - +
395B TYR 4.2 0.9 - - - -
396B LEU* 1.3 106.5 - - + +
398B GLY* 1.3 71.5 - - - +
399B ASP 3.0 4.6 + - - +
400B THR* 3.6 18.6 - - - +
432B LYS* 4.4 27.5 + - + -
435B ASN* 5.3 2.4 + - - +
436B VAL* 5.3 8.7 + - - +
659B PHE* 3.5 31.4 - + + -
660B GLN* 3.4 20.4 - - - +
663B LYS* 2.9 37.1 - - - -
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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