Contacts of the helix formed by residues 413 - 432 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LEU* 5.2 1.0 - - - +
188H ALA* 3.2 39.8 + - - +
191H GLU* 3.6 19.7 - - + +
192H CYS* 3.5 21.2 - - - +
406H THR* 3.7 8.8 - - - +
407H LEU* 3.5 31.2 - - - +
412H GLY* 1.3 70.4 - - - -
414H ALA* 1.3 62.0 + - - +
415H PRO* 4.1 0.2 - - - +
416H GLY* 3.1 1.0 + - - -
417H ALA* 2.8 31.0 + - - +
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Residues in contact with ALA 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H GLU* 3.1 26.4 + - - +
194H ARG* 3.8 29.6 - - + +
195H GLY* 3.6 5.6 - - - -
413H ASN* 1.3 77.3 - - - +
415H PRO* 1.3 71.1 - - + +
417H ALA* 3.2 4.0 + - - +
418H VAL* 3.0 27.4 + - - +
4I TRP* 4.0 16.2 - - + -
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Residues in contact with PRO 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409H HIS* 3.8 11.1 + - + +
411H TRP* 3.6 36.1 - - + +
412H GLY 3.5 12.1 - - - +
414H ALA* 1.3 95.9 - - + +
416H GLY* 1.3 55.5 + - - +
418H VAL* 3.3 5.2 + - + +
419H ALA* 2.9 29.6 + - - +
454H GLU* 3.7 24.0 - - + +
2I GLN 3.9 15.7 - - - +
4I TRP* 4.8 10.8 - - + +
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Residues in contact with GLY 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405H GLY 4.5 1.5 - - - +
406H THR* 3.8 13.5 - - - -
409H HIS* 3.5 30.4 - - - -
412H GLY 3.0 12.0 + - - -
413H ASN 3.1 4.0 + - - -
415H PRO* 1.3 77.3 - - - +
417H ALA* 1.3 61.3 + - - +
419H ALA* 3.5 4.2 + - - +
420H ASN* 3.2 27.9 + - - +
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Residues in contact with ALA 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192H CYS 3.2 27.6 - - - +
195H GLY* 3.4 13.6 - - - -
197H LEU* 3.6 25.3 - - + +
406H THR* 3.8 3.5 - - + +
413H ASN 2.8 11.5 + - - +
414H ALA 3.4 8.5 - - - +
416H GLY* 1.3 74.5 - - - +
418H VAL* 1.3 65.8 + - - +
420H ASN* 3.2 4.2 + - - +
421H ARG* 2.9 23.9 + - - +
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Residues in contact with VAL 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H GLY* 3.3 17.9 - - - +
414H ALA 3.0 19.9 + - - +
415H PRO* 3.3 7.8 + - + +
417H ALA* 1.3 76.8 - - - +
419H ALA* 1.3 57.7 + - - +
421H ARG* 3.2 2.9 + - - -
422H VAL* 2.8 47.0 + - + +
452H SER* 4.8 0.7 - - - +
454H GLU* 3.9 20.9 - - + +
4I TRP* 3.5 54.3 - - + -
17I TYR* 4.8 3.1 - - + -
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Residues in contact with ALA 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H VAL* 4.2 4.9 - - + -
409H HIS* 4.1 2.7 - - + -
415H PRO 2.9 16.5 + - - +
416H GLY 3.6 6.1 - - - +
417H ALA 3.3 0.2 - - - -
418H VAL* 1.3 76.0 - - - +
420H ASN* 1.3 57.3 + - - +
422H VAL* 4.0 1.2 - - - +
423H ALA* 3.0 30.5 + - - +
454H GLU* 3.6 20.4 - - - +
455H LEU* 3.6 25.2 - - + +
458H ALA* 3.9 17.0 - - + -
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Residues in contact with ASN 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H LEU* 4.0 3.9 - - + +
197H LEU* 4.4 12.5 - - + +
384H VAL* 3.3 25.0 - - - +
387H MET* 3.5 17.7 - - + +
402H PHE* 3.7 31.1 - - + +
405H GLY 3.3 13.1 + - - +
406H THR* 3.2 21.0 + - - -
416H GLY 3.2 13.6 + - - +
417H ALA* 3.2 8.5 + - - +
419H ALA* 1.3 78.7 - - - +
421H ARG* 1.3 57.0 + - - +
423H ALA 3.4 0.3 + - - -
424H LEU* 3.0 29.8 + - - +
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Residues in contact with ARG 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H ARG* 3.7 25.8 - - - +
170H LEU* 3.5 18.7 - - + +
195H GLY 4.4 2.0 - - - +
196H GLY* 3.0 32.5 + - - +
198H ASP* 4.5 1.0 + - - -
234H GLU* 2.9 40.8 + - - -
417H ALA 2.9 16.7 + - - +
418H VAL* 3.8 3.6 - - - +
420H ASN* 1.3 75.7 - - - +
422H VAL* 1.3 58.3 + - - +
424H LEU* 3.4 2.4 + - - +
425H GLU* 2.8 60.0 + - - +
13I GLU* 3.1 18.8 + - - +
17I TYR* 3.5 36.2 - - + -
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Residues in contact with VAL 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418H VAL* 2.8 38.5 + - + +
419H ALA* 4.0 2.9 - - - +
421H ARG* 1.3 69.9 - - - +
423H ALA* 1.3 60.5 - - - +
425H GLU* 3.3 5.0 + - - +
426H ALA* 2.8 29.8 + - - +
448H ALA* 4.4 2.2 - - + -
451H TRP* 3.5 29.2 - - + -
452H SER* 4.0 21.3 - - - +
455H LEU* 4.2 13.2 - - + -
17I TYR* 3.8 29.4 - - + +
18I LEU* 4.2 2.2 - - - +
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Residues in contact with ALA 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H VAL* 4.3 6.7 - - + -
387H MET* 3.9 16.4 - - + -
419H ALA 3.0 20.2 + - - +
420H ASN 3.7 3.8 - - - +
422H VAL* 1.3 77.4 - - - +
424H LEU* 1.3 62.4 + - - +
426H ALA* 3.4 5.2 + - - +
427H CYS* 3.1 28.4 + - - -
445H ILE* 4.1 19.0 - - + +
455H LEU* 4.0 17.9 - - + -
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Residues in contact with LEU 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H ARG* 4.2 13.9 - - + +
168H PRO* 3.4 50.7 - - + +
170H LEU* 3.6 27.8 - - + -
387H MET* 3.7 20.3 - - - +
391H THR* 3.8 21.3 - - - +
400H LEU* 4.3 2.5 - - + -
420H ASN 3.0 17.6 + - - +
421H ARG* 3.6 4.9 - - - +
423H ALA* 1.3 76.6 - - - +
425H GLU* 1.3 58.6 + - - +
427H CYS* 3.1 5.5 + - - +
428H VAL* 2.9 30.6 + - + +
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Residues in contact with GLU 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H ARG* 4.3 10.8 + - - -
421H ARG* 2.8 58.3 + - - +
422H VAL* 4.0 2.2 - - - +
424H LEU* 1.3 77.8 - - + +
426H ALA* 1.3 56.2 + - - +
428H VAL* 3.8 7.0 - - + +
429H GLN* 2.9 32.1 + - - +
13I GLU 3.5 1.0 - - - +
14I THR* 3.7 3.8 - - + -
15I LEU* 3.0 35.7 + - + +
17I TYR* 2.8 33.8 + - - +
18I LEU* 3.7 17.6 + - + +
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Residues in contact with ALA 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422H VAL 2.8 21.7 + - - +
423H ALA* 3.6 7.4 - - - +
424H LEU 3.2 0.2 - - - -
425H GLU* 1.3 71.7 - - - +
427H CYS* 1.3 58.8 + - - +
429H GLN* 3.8 6.2 - - - +
430H ALA* 3.0 29.6 + - - +
444H ILE* 3.8 15.3 - - + +
445H ILE* 5.5 1.6 - - + -
448H ALA* 4.0 25.1 - - + -
451H TRP* 5.3 0.4 - - + -
18I LEU* 3.8 12.3 - - + +
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Residues in contact with CYS 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387H MET* 4.0 5.8 - - - -
388H PRO* 3.7 44.2 - - - -
391H THR* 4.0 17.9 - - - +
423H ALA 3.1 17.1 + - - -
424H LEU 3.1 9.5 + - - +
426H ALA* 1.3 75.0 - - - +
428H VAL* 1.3 60.2 + - - +
430H ALA* 3.8 0.2 - - - +
431H ARG* 2.9 31.7 + - - +
437H LEU* 3.7 16.4 - - + +
444H ILE* 4.3 8.1 - - - -
445H ILE* 4.2 7.9 - - - -
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Residues in contact with VAL 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H GLY 3.7 17.7 - - - +
167H ARG* 3.9 21.8 - - + -
168H PRO* 4.1 13.9 - - + -
391H THR* 4.7 4.7 - - + -
396H ASP* 4.7 0.2 - - - +
424H LEU* 2.9 24.3 + - + +
425H GLU* 3.8 7.9 - - + +
427H CYS* 1.3 75.0 - - - +
429H GLN* 1.3 59.2 + - - +
431H ARG* 3.6 19.2 - - - +
432H ASN* 2.9 50.2 + - - +
14I THR* 4.6 5.6 - - + -
15I LEU* 4.5 12.3 - - + -
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Residues in contact with GLN 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425H GLU 2.9 17.2 + - - +
426H ALA* 3.8 5.3 - - - +
428H VAL* 1.3 78.9 - - - +
430H ALA* 1.3 62.0 + - - +
432H ASN* 3.3 2.9 + - - +
433H GLU* 2.9 45.5 + - - +
15I LEU* 4.3 6.5 - - + +
18I LEU* 3.6 25.5 - - + +
19I PRO* 5.6 1.1 + - - +
21I LEU* 3.4 30.7 - - - +
25I GLN* 3.8 20.8 + - - +
29I GLN* 3.9 17.7 + - - +
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Residues in contact with ALA 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426H ALA 3.0 17.9 + - - +
427H CYS 3.8 3.1 - - - +
429H GLN* 1.3 76.4 + - - +
431H ARG* 1.3 63.5 + - - +
433H GLU* 3.1 14.1 + - - -
434H GLY 3.2 0.2 + - - -
435H ARG* 3.0 41.6 + - + +
444H ILE* 3.5 38.1 - - + -
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Residues in contact with ARG 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H GLY 4.1 2.0 + - - -
391H THR* 4.0 18.2 + - - +
395H GLY* 4.6 4.6 - - - -
396H ASP* 2.8 47.8 + - - +
427H CYS 2.9 18.1 + - - +
428H VAL* 3.6 21.4 + - - +
430H ALA* 1.3 75.3 - - - +
432H ASN* 1.3 86.0 + - - +
434H GLY* 2.9 21.7 + - - -
435H ARG 3.9 12.8 + - - +
437H LEU* 4.1 23.4 - - + +
32I TYR* 3.6 17.5 + - + -
113I ILE* 6.2 0.4 - - - +
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Residues in contact with ASN 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H GLY 5.3 0.5 - - - +
428H VAL* 2.9 31.5 + - - +
429H GLN 3.7 4.0 - - - +
431H ARG* 1.3 109.7 + - - +
433H GLU* 1.3 61.6 + - - +
434H GLY 3.3 0.7 + - - -
15I LEU* 5.5 0.2 - - - +
28I ARG 4.2 4.1 - - - +
29I GLN* 3.0 33.4 + - - +
32I TYR* 3.2 55.5 - - + +
113I ILE* 4.8 3.1 - - - +
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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