Contacts of the helix formed by residues 413 - 432 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 5.1 1.3 - - - +
188L ALA* 3.2 40.0 + - - +
191L GLU* 3.6 19.9 - - + +
192L CYS* 3.5 20.3 - - - +
406L THR* 3.7 8.7 - - - +
407L LEU* 3.5 29.9 - - - +
412L GLY* 1.3 69.8 - - - -
414L ALA* 1.3 62.1 + - - +
415L PRO* 4.1 0.2 - - - +
416L GLY* 3.1 1.2 + - - -
417L ALA* 2.8 30.5 + - - +
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Residues in contact with ALA 414 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191L GLU* 3.1 26.7 + - - +
194L ARG* 3.8 28.7 - - + +
195L GLY* 3.6 5.9 - - - -
413L ASN* 1.3 77.4 - - - +
415L PRO* 1.3 71.0 - - + +
417L ALA* 3.2 3.6 + - - +
418L VAL* 3.0 27.7 + - - +
4S TRP* 4.0 16.2 - - + -
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Residues in contact with PRO 415 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409L HIS* 3.8 11.1 + - + +
411L TRP* 3.6 37.5 - - + +
412L GLY 3.5 12.1 - - - +
413L ASN 4.1 0.2 - - - +
414L ALA* 1.3 95.4 - - + +
416L GLY* 1.3 56.6 + - - +
418L VAL* 3.3 4.7 + - + +
419L ALA* 2.9 28.8 + - - +
454L GLU* 3.7 24.6 - - + +
2S GLN 3.9 14.8 - - - +
3S VAL* 5.5 0.4 - - - -
4S TRP* 4.8 10.3 - - + +
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Residues in contact with GLY 416 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405L GLY 4.5 1.3 - - - +
406L THR* 3.8 13.9 - - - -
409L HIS* 3.5 30.0 - - - -
412L GLY 3.0 12.2 + - - -
413L ASN 3.1 3.6 + - - -
415L PRO* 1.3 76.0 - - - +
417L ALA* 1.3 61.3 + - - +
419L ALA* 3.5 3.3 + - - +
420L ASN* 3.2 28.3 + - - +
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Residues in contact with ALA 417 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L CYS 3.2 28.0 - - - +
195L GLY* 3.4 13.9 - - - -
197L LEU* 3.6 24.9 - - + +
406L THR* 3.8 3.5 - - - +
413L ASN 2.8 11.7 + - - +
414L ALA 3.4 9.0 - - - +
416L GLY* 1.3 73.9 - - - +
418L VAL* 1.3 65.7 + - - +
420L ASN* 3.2 4.9 + - - +
421L ARG* 2.9 23.7 + - - +
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Residues in contact with VAL 418 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195L GLY* 3.3 18.6 - - - +
414L ALA 3.0 19.5 + - - +
415L PRO* 3.6 7.4 - - + +
417L ALA* 1.3 74.9 - - - +
419L ALA* 1.3 57.9 + - - +
421L ARG* 3.2 2.6 + - - -
422L VAL* 2.8 46.9 + - + +
452L SER* 4.8 0.9 - - - +
454L GLU* 3.9 20.2 - - + +
4S TRP* 3.5 53.8 - - + -
17S TYR* 4.8 4.3 - - + -
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Residues in contact with ALA 419 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384L VAL* 4.2 5.2 - - + -
409L HIS* 4.1 2.9 - - + -
415L PRO 2.9 16.3 + - - +
416L GLY 3.6 6.3 - - - +
417L ALA 3.3 0.2 - - - -
418L VAL* 1.3 76.9 - - - +
420L ASN* 1.3 56.9 + - - +
422L VAL* 4.0 1.1 - - - +
423L ALA* 3.0 31.5 + - - +
454L GLU* 3.6 21.3 - - - +
455L LEU* 3.6 24.3 - - + +
458L ALA* 3.9 16.2 - - + -
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Residues in contact with ASN 420 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170L LEU* 4.0 4.2 - - + +
197L LEU* 4.4 12.7 - - + +
384L VAL* 3.3 25.2 - - - +
387L MET* 3.5 16.2 - - + +
402L PHE* 3.7 32.1 - - + +
405L GLY 3.3 13.2 + - - +
406L THR* 3.2 20.8 + - - -
416L GLY 3.2 13.7 + - - +
417L ALA* 3.2 8.4 + - - +
419L ALA* 1.3 77.7 - - - +
421L ARG* 1.3 56.5 + - - +
423L ALA 3.4 0.3 + - - -
424L LEU* 3.0 30.5 + - - +
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Residues in contact with ARG 421 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L ARG* 3.7 25.0 - - - +
170L LEU* 3.5 18.1 - - + +
195L GLY 4.4 1.8 - - - +
196L GLY* 3.0 33.7 + - - +
198L ASP* 4.5 1.0 + - - -
234L GLU* 2.9 40.4 + - - -
417L ALA 2.9 16.2 + - - +
418L VAL* 3.8 3.6 - - - +
420L ASN* 1.3 74.6 - - - +
422L VAL* 1.3 57.4 + - - +
424L LEU* 3.4 2.1 + - - +
425L GLU* 2.8 59.5 + - - +
13S GLU* 3.1 19.2 + - - +
17S TYR* 3.5 37.2 - - + -
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Residues in contact with VAL 422 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418L VAL* 2.8 39.0 + - + +
419L ALA* 4.0 2.9 - - - +
421L ARG* 1.3 70.1 - - - +
423L ALA* 1.3 59.3 + - - +
425L GLU* 3.3 4.6 + - - +
426L ALA* 2.8 30.0 + - - +
448L ALA* 4.4 1.8 - - + -
451L TRP* 3.5 30.3 - - + -
452L SER* 4.0 21.1 - - - +
455L LEU* 4.2 13.0 - - + -
17S TYR* 3.8 29.8 - - + +
18S LEU* 4.2 2.3 - - - +
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Residues in contact with ALA 423 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384L VAL* 4.3 6.5 - - + -
387L MET* 3.9 17.5 - - + -
419L ALA 3.0 19.7 + - - +
420L ASN 3.7 4.0 - - - +
421L ARG 3.4 0.2 - - - -
422L VAL* 1.3 77.8 - - - +
424L LEU* 1.3 62.9 + - - +
426L ALA* 3.4 4.8 + - - +
427L CYS* 3.1 28.6 + - - -
445L ILE* 4.1 18.9 - - + +
455L LEU* 4.0 18.2 - - + -
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Residues in contact with LEU 424 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L ARG* 4.2 13.7 - - + +
168L PRO* 3.4 50.7 - - + +
170L LEU* 3.6 28.0 - - + -
387L MET* 3.7 21.4 - - - +
391L THR* 3.8 20.4 - - - +
400L LEU* 4.3 2.5 - - + -
420L ASN 3.0 18.5 + - - +
421L ARG* 3.6 4.5 - - - +
423L ALA* 1.3 76.5 - - - +
425L GLU* 1.3 59.3 + - - +
427L CYS* 3.1 5.2 + - - +
428L VAL* 2.9 30.8 + - + +
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Residues in contact with GLU 425 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L ARG* 4.3 10.7 + - - -
421L ARG* 2.8 56.8 + - - +
422L VAL* 4.0 2.0 - - - +
424L LEU* 1.3 78.3 - - + +
426L ALA* 1.3 57.4 + - - +
428L VAL* 3.8 6.5 - - + +
429L GLN* 2.9 32.1 + - - +
13S GLU 3.5 1.2 - - - +
14S THR* 3.7 3.8 - - + -
15S LEU* 3.0 34.0 + - + +
17S TYR* 2.8 33.8 + - - +
18S LEU* 3.7 18.2 + - + +
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Residues in contact with ALA 426 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422L VAL 2.8 20.9 + - - +
423L ALA* 3.6 6.7 - - - +
425L GLU* 1.3 72.7 - - - +
427L CYS* 1.3 58.0 + - - +
429L GLN* 3.5 7.3 + - - +
430L ALA* 3.0 29.6 + - - +
444L ILE* 3.8 16.6 - - + +
445L ILE* 5.5 1.1 - - + -
448L ALA* 4.0 25.4 - - + -
451L TRP* 5.3 0.2 - - + -
18S LEU* 3.8 12.9 - - + +
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Residues in contact with CYS 427 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387L MET* 4.0 6.5 - - - -
388L PRO* 3.7 43.1 - - - -
391L THR* 4.0 18.2 - - - +
423L ALA 3.1 17.1 + - - -
424L LEU* 3.1 9.2 + - - +
426L ALA* 1.3 74.6 - - - +
428L VAL* 1.3 62.4 + - - +
430L ALA* 3.4 0.4 + - - -
431L ARG* 2.9 31.5 + - - +
437L LEU* 3.7 16.2 - - + +
444L ILE* 4.3 8.7 - - - -
445L ILE* 4.2 7.2 - - - -
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Residues in contact with VAL 428 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L GLY 3.7 17.7 - - - +
167L ARG* 3.9 22.0 - - + -
168L PRO* 4.1 13.9 - - + -
391L THR* 4.7 4.7 - - + -
396L ASP* 4.7 0.2 - - - +
424L LEU* 2.9 23.4 + - + +
425L GLU* 3.8 7.6 - - - +
427L CYS* 1.3 75.3 - - - +
429L GLN* 1.3 59.4 + - - +
431L ARG* 3.6 19.0 - - - +
432L ASN* 2.9 50.3 + - - +
14S THR* 4.6 5.8 - - + -
15S LEU* 4.5 13.0 - - + -
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Residues in contact with GLN 429 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425L GLU 2.9 18.1 + - - +
426L ALA* 3.8 5.5 - - - +
428L VAL* 1.3 77.6 - - - +
430L ALA* 1.3 61.9 + - - +
432L ASN* 3.3 3.2 + - - +
433L GLU* 2.9 46.0 + - - +
15S LEU* 4.3 6.7 - - + +
18S LEU* 3.6 25.0 - - + +
19S PRO* 5.6 0.8 + - - +
21S LEU* 3.4 30.5 - - - +
25S GLN* 3.8 20.6 + - - +
29S GLN* 3.9 17.8 + - - +
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Residues in contact with ALA 430 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426L ALA 3.0 18.7 + - - +
427L CYS 3.8 3.4 - - - +
429L GLN* 1.3 75.5 - - - +
431L ARG* 1.3 63.3 + - - +
433L GLU* 3.1 14.4 + - - -
434L GLY 3.2 0.2 + - - -
435L ARG* 3.0 41.8 + - + +
437L LEU* 4.6 0.2 - - + -
444L ILE* 3.5 38.8 - - + -
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Residues in contact with ARG 431 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L GLY 4.1 1.8 + - - -
391L THR* 4.0 17.8 + - - +
395L GLY* 4.6 4.4 - - - -
396L ASP* 2.8 47.2 + - - +
427L CYS 2.9 19.2 + - - +
428L VAL* 3.6 20.5 - - - +
430L ALA* 1.3 75.7 - - - +
432L ASN* 1.3 85.3 + - - +
434L GLY* 2.9 21.7 + - - -
435L ARG 3.9 12.6 - - - +
437L LEU* 4.1 24.3 - - + +
32S TYR* 3.6 17.3 + - + -
113S ILE* 6.2 0.2 - - - +
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Residues in contact with ASN 432 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L GLY 5.3 0.7 - - - +
428L VAL* 2.9 31.3 + - - +
429L GLN 3.7 3.4 - - - +
431L ARG* 1.3 111.0 + - - +
433L GLU* 1.3 60.6 + - - +
434L GLY* 3.1 1.1 + - - -
15S LEU* 5.5 0.2 - - - +
28S ARG 4.2 4.5 - - - +
29S GLN* 3.0 33.7 + - - +
32S TYR* 3.2 55.7 - - + +
113S 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