Contacts of the helix formed by residues 467 - 477 (chain B) in PDB entry 2JDQ
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 PRO 467 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A ARG* 4.5 19.7 - - - +
333A VAL* 6.2 0.2 - - - -
336A ASN* 4.0 27.5 + - + +
454B GLY* 3.7 13.9 - - - +
457B GLU* 4.3 20.0 - - + -
465B ILE 3.5 8.5 - - - +
466B ASN* 1.3 83.6 - - - +
468B TYR* 1.3 87.5 + - + +
469B CYS 3.5 0.2 + - - -
470B ALA* 3.9 6.8 + - - +
471B LEU* 3.8 17.7 + - + +
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Residues in contact with TYR 468 (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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299A ARG* 6.3 1.3 - - - -
413B ALA 4.7 1.2 + - - -
416B ILE* 4.0 14.2 - - + +
417B LYS* 3.6 30.9 + - - +
420B VAL* 3.7 35.4 - - + -
425B ILE* 4.2 3.8 - - + -
450B ILE* 3.3 36.1 - - + -
451B LEU* 4.2 10.3 - - + -
453B LEU* 4.3 2.7 - - + -
454B GLY* 3.5 31.0 - - - -
466B ASN* 2.9 8.3 + - - +
467B PRO* 1.3 93.0 - - + +
469B CYS* 1.3 59.3 + - - +
471B LEU* 3.6 10.2 + - + +
472B ILE* 2.9 33.4 + - + +
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Residues in contact with CYS 469 (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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451B LEU* 4.0 15.5 - - - -
465B ILE* 6.2 0.9 - - + -
466B ASN* 3.2 35.9 + - - +
468B TYR* 1.3 76.7 - - - +
470B ALA* 1.3 59.4 + - - +
472B ILE* 3.3 4.8 + - - +
473B GLU* 2.9 36.9 + - - +
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Residues in contact with ALA 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ILE* 4.0 14.8 - - + +
332A GLN* 4.9 6.1 - - + -
333A VAL* 3.9 22.9 - - + +
336A ASN* 4.3 19.3 - - - +
466B ASN 4.5 1.2 + - - -
467B PRO 3.9 3.3 + - - +
468B TYR 3.5 0.2 - - - -
469B CYS* 1.3 76.7 - - - +
471B LEU* 1.3 52.6 + - - +
473B GLU* 3.4 13.4 + - - +
474B GLU* 2.8 37.9 + - - +
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Residues in contact with LEU 471 (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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293A ILE* 3.4 38.6 - - + +
294A ASP* 4.9 0.9 - - - +
296A GLY* 6.1 2.2 - - - -
298A CYS* 6.3 0.2 - - + -
333A VAL* 3.9 17.0 - - + -
420B VAL* 3.7 30.3 - - + -
425B ILE* 3.8 19.0 - - + +
467B PRO* 3.8 16.8 + - + +
468B TYR* 3.7 13.5 - - + +
469B CYS 3.3 0.2 - - - -
470B ALA* 1.3 74.9 - - + +
472B ILE* 1.3 59.2 + - - +
474B GLU* 3.4 3.8 + - - +
475B ALA* 2.9 30.5 + - - +
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Residues in contact with ILE 472 (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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425B ILE* 3.9 24.0 - - + -
429B CYS* 4.1 11.9 - - - -
432B LEU* 6.5 0.2 - - + -
447B LEU* 3.8 26.7 - - + +
450B ILE* 5.3 1.3 - - + -
451B LEU* 3.7 40.2 - - + -
468B TYR* 2.9 20.7 + - + +
469B CYS* 3.8 4.7 - - - +
471B LEU* 1.3 75.0 - - - +
473B GLU* 1.3 57.0 + - - +
475B ALA* 3.2 0.9 + - - +
476B TYR* 2.9 32.5 + - + +
481B ILE* 4.2 19.3 - - + -
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Residues in contact with GLU 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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290A GLN* 4.9 0.3 + - - -
329A ILE* 4.1 23.0 - - + +
469B CYS* 2.9 18.3 + - - +
470B ALA* 3.4 18.5 + - - +
472B ILE* 1.3 73.8 - - - +
474B GLU* 1.3 67.0 + - - +
477B GLY* 3.0 26.0 + - - -
478B LEU* 3.8 28.6 + - + +
481B ILE* 4.1 31.0 - - + +
485B GLN* 5.5 1.0 - - - +
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Residues in contact with GLU 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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290A GLN* 2.6 54.1 + - + +
293A ILE* 4.2 21.2 - - + +
294A ASP* 3.9 10.7 - - - +
327A ASP* 4.5 3.3 - - - +
329A ILE* 3.2 27.9 - - + +
330A GLN* 3.2 39.2 + - + +
333A VAL* 4.2 7.4 - - + -
470B ALA 2.8 22.0 + - - +
471B LEU* 3.7 7.2 - - - +
472B ILE 3.4 0.2 - - - -
473B GLU* 1.3 73.3 - - - +
475B ALA* 1.3 60.7 + - - +
477B GLY 4.6 0.2 + - - -
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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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290A GLN* 5.2 1.3 + - - -
294A ASP* 3.6 11.9 - - - +
425B ILE* 3.9 4.5 - - + -
426B LYS* 2.9 50.9 + - - +
429B CYS* 3.7 25.3 - - - +
430B ASP* 4.6 1.0 - - - +
471B LEU 2.9 18.4 + - - +
472B ILE 3.8 0.2 - - - +
474B GLU* 1.3 77.5 - - - +
476B TYR* 1.3 59.7 + - - +
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Residues in contact with TYR 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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290A GLN* 6.1 0.2 - - - -
429B CYS* 3.9 29.2 - - + -
432B LEU* 3.9 40.8 + - + +
433B THR* 4.6 7.4 - - + -
472B ILE* 2.9 19.7 + - + +
475B ALA* 1.3 77.5 - - - +
477B GLY* 1.3 59.7 + - - +
480B LYS* 3.5 57.3 + - + +
481B ILE* 3.6 22.9 - - + -
484B LEU* 4.0 27.9 - - + +
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Residues in contact with GLY 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN* 5.4 4.5 - - - -
473B GLU* 3.0 17.8 + - - +
474B GLU 4.6 1.5 + - - -
475B ALA 3.8 0.4 - - - -
476B TYR* 1.3 80.3 - - - +
478B LEU* 1.3 64.8 + - - -
479B ASP 3.3 2.9 - - - -
480B LYS* 3.4 4.4 + - - -
481B ILE* 3.1 25.2 + - - +
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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