Contacts of the helix formed by residues 413 - 432 (chain B) in PDB entry 1RBO
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 ASN 413 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ALA* 3.2 39.6 + - - +
191B GLU* 3.6 19.7 - - + +
192B CYS* 3.5 21.4 - - - +
406B THR* 3.7 9.3 - - - +
407B LEU* 3.5 30.7 - - - +
412B GLY* 1.3 69.3 - - - -
414B ALA* 1.3 62.3 + - - +
415B PRO* 4.1 0.2 - - - +
416B GLY* 3.1 1.3 + - - +
417B ALA* 2.8 30.7 + - - +
72S LEU* 5.1 1.2 - - - +
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Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU* 3.2 26.2 + - - +
194B ARG* 3.8 28.7 - - + +
195B GLY* 3.6 5.7 - - - -
413B ASN* 1.3 76.5 - - - +
415B PRO* 1.3 71.4 - - + +
417B ALA* 3.2 3.5 + - - +
418B VAL* 3.0 27.6 + - - +
4C TRP* 4.0 15.9 - - + -
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Residues in contact with PRO 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B HIS* 3.8 11.0 + - + +
411B TRP* 3.6 36.3 - - + +
412B GLY 3.5 11.7 - - - +
414B ALA* 1.3 95.9 - - + +
416B GLY* 1.3 56.2 + - - +
418B VAL* 3.3 4.5 + - + +
419B ALA* 2.9 28.8 + - - +
454B GLU* 3.7 23.7 - - + +
2C GLN 3.9 15.0 - - - +
3C VAL* 5.5 0.2 - - - -
4C TRP* 4.8 11.0 - - + +
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Residues in contact with GLY 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLY 4.5 1.8 - - - +
406B THR* 3.8 13.7 - - - -
409B HIS* 3.5 30.3 - - - -
412B GLY 3.0 11.8 + - - -
413B ASN 3.1 4.2 + - - -
415B PRO* 1.3 76.4 - - - +
417B ALA* 1.3 61.1 + - - +
419B ALA* 3.5 3.8 + - - +
420B ASN* 3.2 27.5 + - - +
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B CYS 3.2 27.4 - - - +
195B GLY* 3.4 14.6 - - - -
196B GLY* 4.9 0.2 - - - -
197B LEU* 3.6 24.7 - - + +
406B THR* 3.8 3.3 - - - +
413B ASN 2.8 11.9 + - - +
414B ALA 3.4 8.5 - - - +
416B GLY* 1.3 75.1 - - - +
418B VAL* 1.3 64.1 + - - +
420B ASN* 3.2 4.4 + - - +
421B ARG* 2.9 24.1 + - - +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLY* 3.3 17.3 - - - +
414B ALA 3.0 19.3 + - - +
415B PRO* 3.6 7.9 - - + +
417B ALA* 1.3 76.3 - - - +
419B ALA* 1.3 58.1 + - - +
421B ARG* 3.2 3.3 + - - +
422B VAL* 2.8 46.6 + - + +
452B SER* 4.8 1.1 - - - +
454B GLU* 3.9 19.7 - - + +
4C TRP* 3.5 54.3 - - + -
17C TYR* 4.8 3.8 - - + -
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 4.2 4.9 - - + -
409B HIS* 4.1 2.5 - - + -
415B PRO 2.9 16.1 + - - +
416B GLY 3.6 6.5 - - - +
417B ALA 3.3 0.2 - - - -
418B VAL* 1.3 77.1 - - - +
420B ASN* 1.3 57.2 + - - +
422B VAL* 4.0 1.1 - - - +
423B ALA* 3.0 31.4 + - - +
454B GLU* 3.6 20.6 - - - +
455B LEU* 3.6 24.3 - - + +
458B ALA* 3.9 17.3 - - + -
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Residues in contact with ASN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 4.0 4.4 - - + +
197B LEU* 4.4 12.5 - - + +
384B VAL* 3.4 25.0 - - - +
387B MET* 3.5 16.8 - - + +
402B PHE* 3.7 31.4 - - + +
405B GLY 3.3 13.5 + - - +
406B THR* 3.2 20.8 + - - -
416B GLY 3.2 13.4 + - - +
417B ALA* 3.2 7.7 + - - +
419B ALA* 1.3 78.4 - - - +
421B ARG* 1.3 57.6 + - - +
423B ALA 3.4 0.5 + - - -
424B LEU* 3.0 29.3 + - - +
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Residues in contact with ARG 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ARG* 3.7 24.4 - - - +
170B LEU* 3.5 18.3 - - + +
195B GLY 4.4 2.2 - - - +
196B GLY* 3.0 34.0 + - - +
198B ASP* 4.5 0.8 + - - -
234B GLU* 2.9 41.8 + - - -
417B ALA 2.9 17.4 + - - +
418B VAL* 3.8 2.9 - - - +
420B ASN* 1.3 75.8 - - - +
422B VAL* 1.3 59.0 + - - +
424B LEU* 3.4 2.1 + - - +
425B GLU* 2.8 59.8 + - - +
13C GLU* 3.1 18.8 + - - +
17C TYR* 3.5 37.3 - - + -
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B VAL* 2.8 38.3 + - + +
419B ALA* 4.0 2.9 - - - +
421B ARG* 1.3 69.1 - - - +
423B ALA* 1.3 59.8 + - - +
425B GLU* 3.3 5.1 + - - +
426B ALA* 2.8 29.5 + - - +
448B ALA* 4.4 2.0 - - + -
451B TRP* 3.5 30.7 - - + -
452B SER* 4.0 21.8 - - - +
455B LEU* 4.1 13.0 - - + -
17C TYR* 3.8 30.1 - - + +
18C LEU* 4.2 1.9 - - - +
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Residues in contact with ALA 423 (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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384B VAL* 4.3 7.0 - - + -
387B MET* 3.9 17.0 - - + -
419B ALA 3.0 19.8 + - - +
420B ASN 3.7 3.4 - - - +
422B VAL* 1.3 77.8 - - - +
424B LEU* 1.3 62.9 + - - +
426B ALA* 3.4 4.9 + - - +
427B CYS* 3.1 28.4 + - - -
445B ILE* 4.1 19.1 - - + +
455B LEU* 4.0 17.9 - - + +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ARG* 4.2 13.9 - - + +
168B PRO* 3.4 51.8 - - + +
170B LEU* 3.6 29.2 - - + -
387B MET* 3.7 20.3 - - - +
391B THR* 3.8 20.0 - - - +
400B LEU* 4.3 2.7 - - + -
420B ASN 3.0 17.4 + - - +
421B ARG* 3.6 5.2 - - - +
423B ALA* 1.3 77.1 - - - +
425B GLU* 1.3 59.3 + - - +
427B CYS* 3.1 5.7 + - - +
428B VAL* 2.9 30.6 + - + +
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Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ARG* 4.3 11.2 + - - -
421B ARG* 2.8 56.8 + - - +
422B VAL* 4.0 2.2 - - - +
424B LEU* 1.3 77.3 - - + +
426B ALA* 1.3 56.9 + - - +
428B VAL* 3.8 7.2 - - + +
429B GLN* 2.9 32.2 + - - +
13C GLU 3.5 0.9 - - - +
14C THR* 3.7 2.8 - - + -
15C LEU* 3.0 34.8 + - + +
16C SER 3.8 0.2 + - - -
17C TYR* 2.8 33.3 + - - +
18C LEU* 3.7 17.3 + - + +
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Residues in contact with ALA 426 (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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422B VAL 2.8 21.9 + - - +
423B ALA* 3.6 6.7 - - - +
425B GLU* 1.3 71.3 - - - +
427B CYS* 1.3 58.2 + - - +
429B GLN* 3.5 7.3 + - - +
430B ALA* 3.0 28.9 + - - +
444B ILE* 3.8 16.3 - - + +
445B ILE* 5.5 1.8 - - + -
448B ALA* 4.0 24.7 - - + -
451B TRP* 5.3 0.4 - - + -
18C LEU* 3.8 12.4 - - + +
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Residues in contact with CYS 427 (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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387B MET* 4.0 6.5 - - - -
388B PRO* 3.7 42.8 - - - -
391B THR* 4.0 18.2 - - - +
423B ALA 3.1 17.2 + - - -
424B LEU* 3.1 9.4 + - - +
426B ALA* 1.3 74.7 - - - +
428B VAL* 1.3 60.7 + - - +
431B ARG* 2.9 31.4 + - - +
437B LEU* 3.7 16.4 - - + +
444B ILE* 4.3 8.5 - - - -
445B ILE* 4.2 7.2 - - - -
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Residues in contact with VAL 428 (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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166B GLY 3.7 17.5 - - - +
167B ARG* 3.9 21.5 - - + -
168B PRO* 4.1 14.4 - - + -
391B THR* 4.7 4.5 - - + -
396B ASP* 4.7 0.2 - - - +
424B LEU* 2.9 24.3 + - + +
425B GLU* 3.8 7.9 - - - +
427B CYS* 1.3 75.3 - - - +
429B GLN* 1.3 59.8 + - - +
431B ARG* 3.6 18.5 - - - +
432B ASN* 2.9 50.7 + - - +
14C THR* 4.6 5.4 - - + -
15C LEU* 4.5 13.5 - - + -
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Residues in contact with GLN 429 (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 GLU 2.9 17.8 + - - +
426B ALA* 3.8 5.5 - - - +
428B VAL* 1.3 77.6 - - - +
430B ALA* 1.3 63.5 + - - +
432B ASN* 3.3 3.2 + - - +
433B GLU* 2.9 44.4 + - - +
15C LEU* 4.3 7.2 - - + +
18C LEU* 3.6 25.7 - - + +
19C PRO* 5.6 1.1 + - - +
21C LEU* 3.4 30.7 - - - +
25C GLN* 3.8 21.3 + - - +
29C GLN* 3.9 17.2 + - - +
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Residues in contact with ALA 430 (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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426B ALA 3.0 19.2 + - - +
427B CYS 3.8 3.4 - - - +
428B VAL 3.3 0.2 - - - -
429B GLN* 1.3 75.7 + - - +
431B ARG* 1.3 63.3 + - - +
433B GLU* 3.1 14.2 + - - -
434B GLY 3.2 0.2 + - - -
435B ARG* 3.0 41.7 + - + +
437B LEU* 4.6 0.2 - - + -
444B ILE* 3.5 37.9 - - + -
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Residues in contact with ARG 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY 4.1 2.0 + - - -
391B THR* 4.0 18.8 + - - +
395B GLY* 4.6 4.4 - - - -
396B ASP* 2.8 47.0 + - - +
427B CYS 2.9 17.7 + - - +
428B VAL* 3.6 20.7 + - - +
430B ALA* 1.3 76.1 - - - +
432B ASN* 1.3 86.2 + - - +
434B GLY* 2.9 21.7 + - - -
435B ARG 3.9 13.4 + - - +
437B LEU* 4.1 22.8 - - + +
32C TYR* 3.6 18.2 + - + -
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Residues in contact with ASN 432 (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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166B GLY 5.3 0.9 - - - +
428B VAL* 2.9 29.8 + - - +
429B GLN 3.3 4.0 + - - +
431B ARG* 1.3 110.2 + - - +
433B GLU* 1.3 60.3 + - - +
434B GLY* 3.1 1.5 + - - -
28C ARG 4.2 4.5 - - - +
29C GLN* 3.0 33.6 + - - +
32C TYR* 3.2 56.2 - - + +
113C ILE* 4.8 2.8 - - - +
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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
------------------------------------------------------------
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