Contacts of the helix formed by residues 380 - 392 (chain C) in PDB entry 2ONL
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 380 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A PHE* 3.9 16.2 - - - -
161A ASP* 3.0 25.4 + - + -
163A GLU* 2.8 47.3 - - + +
379C SER* 1.3 75.5 - - - +
381C PRO* 1.3 70.6 - - + +
382C LEU* 3.0 19.6 + - - +
383C LEU* 2.8 30.0 + - - +
384C LEU* 3.0 18.3 + - - +
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Residues in contact with PRO 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 3.5 15.9 - - - +
163A GLU* 2.9 23.3 - - - +
380C ASN* 1.3 84.4 - - + +
382C LEU* 1.3 60.9 + - - +
384C LEU* 3.7 9.8 + - + +
385C LYS* 3.0 36.5 + - + +
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Residues in contact with LEU 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 3.1 20.5 + - - +
82A ASN* 4.0 8.5 - - - +
129A PHE* 4.1 11.4 - - + -
132A TYR* 4.9 1.6 - - + -
133A GLN* 4.0 30.1 - - + +
136A ARG* 3.2 27.1 - - - +
163A GLU* 5.3 1.1 - - + +
380C ASN* 2.9 13.6 + - - +
381C PRO* 1.3 75.1 - - - +
383C LEU* 1.3 66.7 + - - +
385C LYS* 2.9 28.5 + - - +
386C ARG* 3.0 52.5 + - - +
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Residues in contact with LEU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PHE* 3.3 45.1 - - + -
161A ASP 5.5 0.4 - - - +
311A TYR* 3.7 19.7 - - + -
375C ILE* 3.7 36.1 - - + +
378C ALA* 4.0 11.2 - - + +
379C SER* 5.0 0.7 - - - -
380C ASN* 2.8 27.9 + - - +
382C LEU* 1.3 75.1 - - - +
384C LEU* 1.3 62.5 + - - +
386C ARG* 3.2 4.8 + - + +
387C ARG* 2.8 55.9 + - - +
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C SER* 4.5 11.2 - - - -
380C ASN* 3.0 36.8 + - - +
381C PRO* 3.8 11.2 - - + +
383C LEU* 1.3 76.2 - - - +
385C LYS* 1.3 52.7 + - - +
387C ARG* 3.0 10.5 + - - +
388C LYS* 2.8 58.4 + - + +
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Residues in contact with LYS 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 3.9 7.3 + - - -
136A ARG* 4.6 0.2 - - - +
313A ASP* 5.8 0.2 - - - +
316A ASP* 3.1 26.6 + - - +
381C PRO* 3.0 24.3 + - + +
382C LEU* 2.9 40.6 + - - +
384C LEU* 1.3 78.8 - - - +
386C ARG* 1.3 65.8 + - - +
388C LYS* 3.2 21.8 + - - +
389C LYS* 3.2 23.9 + - - +
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Residues in contact with ARG 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE* 5.5 1.0 - - + -
132A TYR* 3.4 24.0 + - - -
136A ARG* 4.4 0.4 - - - -
310A GLN 4.2 8.7 - - - +
311A TYR* 3.1 51.6 + - + +
312A HIS 5.0 0.9 - - - -
313A ASP* 4.0 22.0 + - - +
316A ASP* 2.2 42.2 + - - +
382C LEU* 3.0 39.8 + - - +
383C LEU* 3.6 11.9 - - + +
385C LYS* 1.3 82.2 - - - +
387C ARG* 1.3 59.1 + - - +
389C LYS* 3.8 9.6 + - - +
390C ALA* 3.0 27.8 + - - +
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Residues in contact with ARG 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C ILE* 3.9 14.8 + - - +
376C GLU* 3.7 18.6 + - - +
378C ALA 3.6 20.0 + - - -
379C SER* 5.0 5.9 + - - +
383C LEU* 2.8 45.5 + - - +
384C LEU* 3.4 7.4 - - - +
386C ARG* 1.3 77.4 - - - +
388C LYS* 1.3 65.7 + - - +
390C ALA* 3.1 20.1 + - + +
391C ARG* 3.2 5.4 + - - -
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Residues in contact with LYS 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C LEU* 2.8 44.9 + - + +
385C LYS* 3.5 23.6 - - - +
387C ARG* 1.3 77.0 - - - +
389C LYS* 1.3 58.7 + - - +
391C ARG* 2.9 18.5 + - - -
392C ALA 3.2 8.8 + - - -
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Residues in contact with LYS 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A HIS 4.7 11.3 + - - +
313A ASP* 4.3 25.6 - - + +
314A PRO* 6.5 0.4 - - - -
385C LYS 3.2 11.7 + - - +
386C ARG* 4.3 8.1 - - - +
388C LYS* 1.3 78.8 - - - +
390C ALA* 1.3 62.8 - - - +
391C ARG 3.0 0.4 + - - -
392C ALA* 2.8 34.9 - - - +
393C LEU* 4.6 0.5 - - - -
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Residues in contact with ALA 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLN 6.0 1.6 - - - +
386C ARG 3.0 20.8 + - - +
387C ARG* 3.1 17.3 - - + +
388C LYS 3.0 0.6 - - - -
389C LYS* 1.3 85.5 - - - +
391C ARG* 1.3 56.0 + - - +
392C ALA 4.7 0.2 - - - -
393C LEU* 4.0 11.0 - - - +
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Residues in contact with ARG 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C ARG 3.2 5.4 + - - -
388C LYS 2.9 8.6 + - - -
390C ALA* 1.3 78.6 - - - +
392C ALA* 1.3 57.9 + - - +
393C LEU 3.0 14.4 + - - +
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Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C LYS 3.2 11.2 + - - -
389C LYS* 2.8 26.1 + - - +
391C ARG* 1.3 70.7 - - - +
393C LEU* 1.3 57.2 + - - +
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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