Contacts of the helix formed by residues 417 - 427 (chain A) in PDB entry 1UN0
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 ARG 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A THR* 3.9 28.8 + - + +
374A GLU* 5.2 5.7 - - - +
377A GLN* 2.7 59.3 + - - +
413A GLY 2.8 7.8 + - - +
414A GLY* 3.3 18.1 - - - -
416A GLN* 1.3 77.6 - - - +
418A PRO* 1.3 63.2 - - + +
419A ASP* 3.2 27.6 + - + +
420A ILE* 3.3 30.3 + - + +
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Residues in contact with PRO 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A GLY* 3.5 13.2 - - - +
415A LEU 4.9 2.5 - - - +
416A GLN* 3.8 7.0 - - - +
417A ARG* 1.3 83.5 - - + +
419A ASP* 1.3 68.9 + - - +
420A ILE 3.1 2.5 - - - -
421A ILE* 3.5 4.0 + - - +
422A ARG* 3.2 41.1 + - - +
458A MET* 3.7 30.4 - - + +
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Residues in contact with ASP 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A GLN* 5.5 2.0 - - - +
417A ARG* 3.2 24.3 - - + +
418A PRO* 1.3 82.4 - - - +
420A ILE* 1.3 63.0 + - + +
422A ARG* 3.4 22.0 + - - +
423A TYR* 3.0 24.9 + - - +
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A THR* 4.5 10.3 - - + +
376A ILE* 4.0 22.7 - - + -
377A GLN* 4.2 7.2 - - - +
380A ILE* 3.7 30.1 - - + -
410A ALA* 3.4 24.0 - - + +
413A GLY* 4.0 12.1 - - - +
414A GLY* 4.6 2.9 - - - +
417A ARG* 3.5 42.8 - - + +
418A PRO 3.1 0.4 - - - -
419A ASP* 1.3 74.0 - - - +
421A ILE* 1.3 66.9 + - - +
423A TYR* 3.1 5.7 + - - +
424A LEU* 2.9 35.3 + - + +
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Residues in contact with ILE 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A SER* 3.4 43.3 - - - +
414A GLY* 3.5 20.6 - - - -
418A PRO 3.5 2.0 + - - +
420A ILE* 1.3 75.9 - - - +
422A ARG* 1.3 64.2 + - - +
424A LEU* 3.2 7.7 + - + +
425A VAL* 3.0 36.5 + - + +
454A ASN 4.2 11.7 - - - +
455A ILE* 4.0 20.0 - - + -
458A MET* 3.8 39.7 - - + -
473A ASN* 4.4 1.8 - - - +
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Residues in contact with ARG 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A PRO* 3.2 38.5 + - - +
419A ASP* 3.5 24.4 + - - +
421A ILE* 1.3 80.3 - - - +
423A TYR* 1.3 57.4 + - - +
425A VAL* 3.7 6.5 - - - +
426A SER* 3.0 29.3 + - - -
458A MET* 3.6 22.1 - - - +
462A ASP* 3.1 28.1 + - - -
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Residues in contact with TYR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ILE* 3.9 37.4 + - + -
383A ASN* 5.0 5.0 + - - -
385A ILE* 3.6 25.6 - - + +
386A PRO* 3.5 27.0 - - - +
419A ASP 3.0 17.3 + - - +
420A ILE* 3.5 4.9 - - - +
422A ARG* 1.3 75.3 - - - +
424A LEU* 1.3 67.3 + - + +
426A SER* 2.8 22.0 + - - -
427A GLN* 2.9 46.0 + - + +
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ILE* 5.2 1.6 - - + -
385A ILE* 3.8 39.9 - - + -
407A ILE* 4.0 29.8 - - + +
410A ALA* 4.3 7.0 - - + -
411A SER* 4.0 25.8 - - - +
420A ILE* 2.9 30.3 + - + +
421A ILE* 3.5 11.9 - - + +
423A TYR* 1.3 78.9 - - + +
425A VAL* 1.3 64.2 + - + +
427A GLN* 3.2 14.8 + - - +
428A GLY 3.5 4.9 + - - -
429A CYS* 3.2 27.8 + - + +
455A ILE* 5.6 3.1 - - + -
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Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A ILE* 3.0 31.1 + - + +
422A ARG* 3.7 7.4 - - - +
423A TYR 3.3 0.2 - - - -
424A LEU* 1.3 75.1 - - - +
426A SER* 1.3 60.7 + - - +
428A GLY* 2.9 21.8 + - - -
429A CYS* 4.0 6.3 + - - -
430A ILE* 3.8 19.5 + - + +
455A ILE* 4.0 18.2 - - + -
473A ASN* 3.6 27.1 - - - +
476A PHE* 3.9 18.2 - - + -
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Residues in contact with SER 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A ARG 3.0 13.4 + - - -
423A TYR* 2.8 22.2 + - - -
425A VAL* 1.3 82.3 - - - +
427A GLN* 1.3 68.1 + - - +
428A GLY* 3.1 1.7 + - - -
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Residues in contact with GLN 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A ILE* 4.1 15.0 - - + -
386A PRO* 3.3 25.0 - - + +
389A VAL* 3.8 17.6 - - + +
423A TYR* 2.9 61.6 + - + +
424A LEU 3.6 6.5 - - - +
425A VAL 3.2 0.4 - - - -
426A SER* 1.3 84.9 + - - +
428A GLY* 1.3 58.0 - - - +
429A CYS 3.7 0.4 - - - -
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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