Contacts of the helix formed by residues 467 - 488 (chain B) in PDB entry 2JB2
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 TRP 467 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG* 3.4 23.1 - - + -
86B PRO* 4.1 7.0 - - + -
89B HIS* 3.6 28.5 - + + -
227B ASP* 3.3 49.8 + - + -
228B GLN* 3.5 17.0 - - - -
232B MET* 4.6 1.6 - - + -
459B ASP* 3.8 0.9 - - - +
464B ALA* 3.1 28.7 + - + +
465B ILE 3.5 14.2 + - - -
466B ALA* 1.3 76.7 - - - +
468B GLN* 1.3 65.5 + - - +
469B HIS 4.0 3.1 - - - +
470B GLY* 2.8 15.6 + - - -
471B ALA 3.5 2.1 + - - -
1489B FAD 3.2 39.0 + + - -
1490B PHE* 3.2 40.3 + + - -
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Residues in contact with GLN 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 4.8 1.1 - - + -
51B VAL* 3.8 12.0 - - + +
82B ALA* 3.8 8.8 - - - +
85B ILE* 4.1 2.3 - - - +
91B THR* 3.7 19.9 - - + +
239B MET* 3.4 29.0 - - - +
242B ILE* 3.7 9.7 - - - +
243B TYR* 2.7 47.0 + - - +
467B TRP* 1.3 71.0 - - - +
469B HIS* 1.3 64.0 + - - +
471B ALA* 3.0 7.8 + - - +
472B LEU* 2.9 27.6 + - + +
1489B FAD 2.9 47.1 + - - +
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Residues in contact with HIS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLU* 4.0 20.5 - - + +
193A PRO 2.9 29.8 + - - -
194A GLY* 4.2 1.1 - - - -
88B SER 4.5 0.8 + - - -
89B HIS* 3.5 39.0 + + + +
90B ILE* 3.0 44.4 + - + +
91B THR* 3.5 8.7 + - - -
464B ALA* 4.0 11.3 - - + +
467B TRP* 3.1 2.8 - - + +
468B GLN* 1.3 78.1 - - - +
470B GLY* 1.3 56.5 + - - +
473B THR* 2.8 53.7 + - + +
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Residues in contact with GLY 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ASP* 3.8 4.3 - - - -
462B SER* 3.2 32.2 - - - -
464B ALA* 3.6 12.2 + - - +
467B TRP 2.8 11.0 + - - -
469B HIS* 1.3 79.5 - - - +
471B ALA* 1.3 60.4 + - - +
473B THR* 3.3 4.7 + - - -
474B SER* 3.1 25.8 + - - -
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Residues in contact with ALA 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 4.0 5.8 - - + -
23B ALA* 3.7 18.7 - - + +
458B GLY 4.0 1.8 - - - -
459B ASP* 3.6 12.9 - - + +
467B TRP 3.5 3.0 + - - -
468B GLN 3.0 8.2 + - - +
470B GLY* 1.3 75.8 - - - +
472B LEU* 1.3 58.9 + - - +
474B SER* 3.4 2.9 + - - -
475B ALA* 3.0 28.6 + - - +
1489B FAD 3.4 41.5 - - - +
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Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 3.8 19.5 - - + +
26B CYS* 3.6 30.1 - - + -
90B ILE* 3.8 13.7 - - + -
91B THR* 3.8 40.4 - - + +
94B TYR* 4.0 18.8 - - + -
242B ILE* 6.2 1.1 - - + -
243B TYR* 4.4 5.2 - - - +
246B PHE* 4.3 15.7 - - + -
468B GLN* 2.9 23.6 + - + +
471B ALA* 1.3 72.8 - - - +
473B THR* 1.3 61.2 + - - +
475B ALA* 3.4 3.3 + - - +
476B ARG* 3.0 35.4 + - - +
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Residues in contact with THR 473 (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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194A GLY* 3.7 8.3 - - - -
195A ALA* 3.5 24.7 + - - +
198A ASN* 6.2 0.2 - - - -
90B ILE* 4.1 14.8 - - + -
469B HIS* 2.8 54.2 + - + +
470B GLY* 3.3 7.6 + - - -
472B LEU* 1.3 74.2 - - - +
474B SER* 1.3 60.6 + - - +
476B ARG* 3.3 8.5 + - - +
477B ASP* 3.0 34.0 + - - +
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Residues in contact with SER 474 (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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195A ALA* 3.4 16.1 - - - +
456B PHE 4.7 0.2 + - - -
457B ALA* 3.4 9.0 - - - +
458B GLY 3.0 35.5 + - - -
461B LEU* 4.3 9.3 + - - +
470B GLY 3.1 20.1 + - - -
471B ALA 3.6 4.3 - - - -
472B LEU 3.3 0.2 - - - -
473B THR* 1.3 74.2 + - - +
475B ALA* 1.3 62.2 + - - +
477B ASP* 3.2 5.2 + - - +
478B VAL* 3.0 28.4 + - - +
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Residues in contact with ALA 475 (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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23B ALA* 3.3 15.5 - - - +
26B CYS* 3.9 11.7 - - + -
27B SER* 3.3 31.8 + - - +
30B GLU* 6.4 0.2 - - - -
457B ALA* 4.5 7.1 - - - +
471B ALA 3.0 13.7 + - - +
472B LEU 3.5 8.3 - - - +
474B SER* 1.3 76.1 - - - +
476B ARG* 1.3 56.7 + - - +
478B VAL* 3.2 3.0 + - - +
479B VAL* 2.9 34.8 + - - +
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Residues in contact with ARG 476 (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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5B LEU* 3.8 50.3 - - + +
26B CYS* 4.2 4.7 - - - -
30B GLU* 3.8 10.2 + - + -
90B ILE* 3.5 32.1 - - - +
94B TYR* 3.0 36.9 + - - +
472B LEU 3.0 22.4 + - - +
473B THR* 3.3 8.4 + - - +
475B ALA* 1.3 75.8 - - - +
477B ASP* 1.3 63.5 + - - +
479B VAL* 4.6 0.4 - - - -
480B THR* 2.8 30.3 + - - -
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Residues in contact with ASP 477 (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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195A ALA* 3.5 33.4 + - + +
196A GLY* 5.2 0.2 - - - -
198A ASN* 5.2 5.8 + - - +
473B THR* 3.0 18.4 + - - +
474B SER* 3.7 5.4 - - - +
476B ARG* 1.3 79.4 - - - +
478B VAL* 1.3 57.9 + - + +
480B THR* 3.2 8.0 + - - -
481B HIS* 2.9 48.3 + - + -
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE* 3.9 27.4 - - + -
448B LEU 6.2 0.4 - - - +
455B TYR* 3.7 33.2 - - + -
456B PHE 3.5 23.1 - - - +
457B ALA* 4.0 8.7 - - + -
474B SER* 3.0 21.5 + - - +
475B ALA* 3.8 3.1 - - - +
477B ASP* 1.3 73.4 - - + +
479B VAL* 1.3 65.8 + - - +
481B HIS* 3.2 12.5 + - - +
482B ILE* 2.9 24.0 + - + +
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Residues in contact with VAL 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.9 16.4 - - + -
6B ILE* 3.7 26.0 - - + -
27B SER* 3.7 36.3 - - - +
30B GLU* 4.3 9.2 - - + -
31B LEU* 3.7 24.0 - - + +
290B ILE* 4.4 2.5 - - + -
475B ALA 2.9 19.9 + - - +
476B ARG 3.9 3.6 - - - +
478B VAL* 1.3 76.5 - - - +
480B THR* 1.3 64.0 + - - +
482B ILE* 3.3 7.6 + - - +
483B HIS* 3.0 22.2 + - - +
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Residues in contact with THR 480 (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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5B LEU* 3.7 20.9 + - - +
6B ILE* 4.2 16.3 - - + +
476B ARG 2.8 18.4 + - - -
477B ASP* 3.2 12.7 + - - -
479B VAL* 1.3 76.5 - - - +
481B HIS* 1.3 62.2 + - + +
483B HIS* 3.2 3.3 + - - +
484B GLU* 3.0 50.5 + - + +
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Residues in contact with HIS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B LEU 5.2 8.4 + - - -
455B TYR* 4.2 20.8 + - + +
477B ASP* 2.9 37.9 + - + +
478B VAL* 3.2 13.0 + - + +
480B THR* 1.3 80.2 - - + +
482B ILE* 1.3 63.4 + - - +
484B GLU* 3.3 20.0 + - - +
485B ARG* 3.0 23.9 + - - +
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Residues in contact with ILE 482 (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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15B VAL* 4.6 9.0 - - + -
31B LEU* 4.6 4.9 - - + -
36B TYR* 4.2 20.6 - - + -
288B TYR* 4.0 34.8 - - + -
290B ILE* 3.7 37.0 - - + -
455B TYR* 3.6 33.9 - - + -
478B VAL* 2.9 17.1 + - + +
479B VAL* 3.7 9.0 - - - +
481B HIS* 1.3 74.8 - - - +
483B HIS* 1.3 57.5 + - - +
485B ARG* 3.2 8.0 + - - +
486B VAL* 2.9 27.4 + - - +
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Residues in contact with HIS 483 (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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6B ILE* 3.6 33.4 - - + +
7B GLY* 3.2 33.8 + - - -
8B LYS 4.1 2.5 + - - -
9B VAL* 3.8 25.1 - - + -
10B LYS* 6.3 0.2 - - + -
36B TYR* 2.7 33.3 + + + +
479B VAL 3.0 16.6 + - - +
480B THR 3.2 5.1 + - - +
482B ILE* 1.3 77.5 - - - +
484B GLU* 1.3 60.8 + - + +
486B VAL* 3.3 3.6 + - - +
487B ALA* 3.0 30.7 + - + +
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Residues in contact with GLU 484 (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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480B THR* 3.0 34.8 + - + +
481B HIS* 3.8 19.7 - - - +
483B HIS* 1.3 77.1 - - + +
485B ARG* 1.3 64.4 + - - +
487B ALA* 3.3 8.9 + - - +
488B GLN* 3.1 36.7 + - - +
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Residues in contact with ARG 485 (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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288B TYR* 3.7 27.9 + - - +
450B PRO* 4.2 5.9 - - - +
452B ASP* 2.6 47.5 + - - +
453B LYS* 3.9 7.7 - - - +
455B TYR* 2.9 32.3 + - - +
481B HIS 3.0 12.9 + - - +
482B ILE 3.4 9.6 - - - +
484B GLU* 1.3 74.9 - - - +
486B VAL* 1.3 65.6 + - - +
488B GLN* 3.0 35.5 + - - +
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Residues in contact with VAL 486 (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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9B VAL* 3.7 22.7 - - + -
10B LYS 4.9 0.9 - - - +
13B HIS* 3.5 35.2 + - + +
36B TYR* 3.9 17.3 - - + +
288B TYR* 3.7 33.0 - - + +
482B ILE 2.9 19.5 + - - +
483B HIS* 3.7 5.8 - - + +
485B ARG* 1.3 75.8 - - - +
487B ALA* 1.3 62.9 + - - +
488B GLN 3.3 4.9 + - - -
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Residues in contact with ALA 487 (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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483B HIS* 3.0 16.6 + - + +
484B GLU* 3.5 13.2 - - - +
485B ARG 3.2 0.2 - - - -
486B VAL* 1.3 79.4 - - - +
488B GLN* 1.3 59.2 + - - +
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Residues in contact with GLN 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B GLU* 3.1 28.3 + - - +
485B ARG* 3.0 29.3 + - - +
486B VAL 4.3 3.8 - - - -
487B ALA* 1.3 81.4 - - + +
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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