Contacts of the helix formed by residues 350 - 366 (chain A) in PDB entry 3UO9
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 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A VAL* 1.3 80.5 - - - +
351A ASN* 1.3 65.0 + - - +
352A ALA* 3.5 11.0 + - - +
353A GLU* 3.1 33.5 + - - +
354A LYS* 3.0 19.9 + - - +
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Residues in contact with ASN 351 (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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350A ASN* 1.3 74.7 - - - +
352A ALA* 1.3 58.3 + - - +
354A LYS* 3.2 23.4 + - - +
355A PHE* 2.9 32.1 + - - +
409A GLY* 3.0 34.2 + - - +
410A ILE* 5.4 0.3 - - - +
412A ASP* 3.9 14.8 - - - +
413A PHE* 3.8 18.1 - - + +
416A GLN* 4.2 14.4 - - - +
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Residues in contact with ALA 352 (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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350A ASN* 3.3 12.0 + - - +
351A ASN* 1.3 76.4 - - - +
353A GLU* 1.3 57.7 + - - +
355A PHE* 3.5 7.4 + - - +
356A ASP* 2.9 37.8 + - - +
416A GLN* 5.9 0.2 - - - -
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Residues in contact with GLU 353 (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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346A LYS* 5.5 0.4 - - + -
349A VAL* 3.7 32.4 - - + +
350A ASN* 3.1 25.9 + - - +
352A ALA* 1.3 77.0 - - - +
354A LYS* 1.4 58.2 + - - +
356A ASP* 3.8 7.9 - - + +
357A TYR* 3.0 29.3 + - - +
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Residues in contact with LYS 354 (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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342A THR 5.3 0.8 + - - -
343A SER 5.4 2.6 + - - -
345A ILE 3.3 23.9 + - - +
346A LYS* 3.4 23.8 + - + +
347A GLN* 4.8 6.9 - - - +
348A GLY 5.0 1.6 - - - +
349A VAL* 3.5 23.7 + - + -
350A ASN 3.0 13.9 + - - +
351A ASN* 3.6 26.7 + - - +
353A GLU* 1.4 71.2 - - - +
355A PHE* 1.3 65.7 + - - +
357A TYR* 3.3 7.7 + - - +
358A VAL* 3.0 26.7 + - - +
410A ILE* 4.0 21.4 - - - +
413A PHE* 3.6 27.1 - - + -
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Residues in contact with PHE 355 (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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351A ASN 2.9 20.4 + - - +
352A ALA* 3.5 7.4 - - - +
354A LYS* 1.3 72.4 - - - +
356A ASP* 1.3 66.1 + - - +
358A VAL* 3.2 4.2 + - - +
359A MET* 2.9 62.5 + - + +
373A PHE* 3.4 32.3 - + + -
413A PHE* 3.7 15.6 - + + -
416A GLN* 3.6 51.4 - - + +
417A LEU* 4.6 3.1 - - + -
420A ILE* 4.0 12.3 - - + -
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Residues in contact with ASP 356 (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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352A ALA* 2.9 27.4 + - - +
353A GLU* 3.8 7.6 + - - +
354A LYS 3.3 0.2 - - - -
355A PHE* 1.3 83.6 - - - +
357A TYR* 1.3 62.4 + - - +
359A MET* 3.3 6.7 + - - +
360A GLN* 3.0 25.8 + - - +
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Residues in contact with TYR 357 (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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295A ILE* 4.2 6.5 - - + -
299A ASP* 2.9 37.6 + - - -
345A ILE* 4.2 11.7 - - + -
346A LYS* 3.7 54.0 + - + -
353A GLU 3.0 17.8 + - - +
354A LYS 3.4 4.7 - - - +
356A ASP* 1.3 77.7 - - - +
358A VAL* 1.3 62.7 + - - +
360A GLN* 3.5 26.5 + - - +
361A PHE* 3.4 44.2 + + - +
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Residues in contact with VAL 358 (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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288A VAL* 5.9 1.6 - - + -
292A LYS* 5.7 4.5 - - + -
295A ILE* 4.1 20.0 - - + -
345A ILE* 4.2 24.9 - - + -
354A LYS 3.0 13.9 + - - +
355A PHE 3.7 6.3 - - - +
357A TYR* 1.3 74.4 - - + +
359A MET* 1.3 60.6 + - - +
361A PHE* 3.2 7.4 + - - +
362A LEU* 3.0 41.4 + - + +
413A PHE* 3.9 17.7 - - + -
417A LEU* 3.7 24.9 - - + -
420A ILE* 4.8 1.8 - - + -
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Residues in contact with MET 359 (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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355A PHE* 2.9 51.3 + - + +
356A ASP* 3.3 8.7 + - - +
358A VAL* 1.3 72.1 - - - +
360A GLN* 1.3 58.8 + - - +
362A LEU* 3.4 4.5 + - - +
363A ASN* 2.9 39.9 + - - +
371A VAL* 4.0 26.7 - - + +
372A GLY* 3.6 27.6 - - - +
373A PHE* 4.5 2.9 - - + -
420A ILE* 3.7 28.9 - - + -
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Residues in contact with GLN 360 (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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356A ASP 3.0 13.0 + - - +
357A TYR* 3.5 31.2 - - + +
358A VAL 3.3 0.2 - - - -
359A MET* 1.3 76.1 - - - +
361A PHE* 1.3 63.6 + - + +
363A ASN* 3.4 13.8 + - - +
364A LYS* 3.1 48.8 + - + +
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Residues in contact with PHE 361 (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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295A ILE* 3.7 28.7 - - + -
298A ASN* 3.5 25.8 - - + -
299A ASP* 4.0 5.8 - - - -
357A TYR* 3.4 45.5 + + - +
358A VAL 3.3 9.6 - - - +
360A GLN* 1.3 82.3 - - + +
362A LEU* 1.3 58.7 + - - +
364A LYS* 3.2 15.4 + - + +
365A MET* 3.0 44.9 + - + +
447A VAL* 3.4 28.9 - - + -
448A LEU* 3.8 13.0 - - + -
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Residues in contact with LEU 362 (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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284A LEU* 4.7 4.3 - - + -
288A VAL* 4.6 9.9 - - + -
291A LEU* 4.0 33.7 - - + -
295A ILE* 4.5 7.4 - - + -
358A VAL* 3.0 25.8 + - + +
359A MET* 3.6 6.5 - - - +
361A PHE* 1.3 76.0 - - - +
363A ASN* 1.3 60.8 + - - +
365A MET* 3.1 19.0 + - + +
366A ALA* 3.0 25.1 + - - +
371A VAL* 4.0 13.5 - - + -
420A ILE* 3.7 42.8 - - + -
430A MET* 3.7 11.4 - - + +
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Residues in contact with ASN 363 (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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359A MET* 2.9 25.4 + - - +
360A GLN* 3.5 16.1 - - - +
361A PHE 3.3 0.2 - - - -
362A LEU* 1.3 75.1 - - - +
364A LYS* 1.3 59.5 + - + +
366A ALA 3.4 1.4 + - - -
367A GLY 3.3 3.5 + - - -
368A ASN* 2.8 47.3 + - - +
369A GLU 4.7 1.9 - - - +
371A VAL* 3.4 30.7 + - - +
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Residues in contact with LYS 364 (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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360A GLN* 3.1 37.3 + - + +
361A PHE* 3.2 15.6 + - - +
363A ASN* 1.3 76.6 - - + +
365A MET* 1.3 61.8 + - - +
367A GLY* 3.1 11.7 + - - -
368A ASN* 4.7 8.7 - - - +
440A CYS* 3.7 15.8 - - - +
443A THR* 5.0 0.3 + - - -
445A GLU* 3.3 41.3 + - - +
446A ARG 4.9 4.5 - - - -
447A VAL* 3.8 22.6 - - + +
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Residues in contact with MET 365 (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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291A LEU* 4.1 30.3 - - - +
295A ILE* 3.8 22.4 - - + -
361A PHE* 3.0 39.0 + - + +
362A LEU* 3.1 19.7 + - + +
364A LYS* 1.3 75.0 - - - +
366A ALA* 1.3 56.5 + - - +
367A GLY 3.2 3.2 + - - -
429A VAL* 3.2 13.0 - - - +
430A MET* 4.0 18.2 - - + +
433A THR* 2.8 34.7 + - + +
434A LEU* 5.7 0.9 - - - -
440A CYS* 3.8 0.5 - - - -
447A VAL* 3.6 15.7 - - + -
448A LEU* 4.0 24.5 - - + -
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Residues in contact with ALA 366 (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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362A LEU 3.0 14.9 + - - +
363A ASN 4.0 3.4 - - - +
364A LYS 3.2 0.4 - - - -
365A MET* 1.3 75.7 - - - +
367A GLY* 1.3 64.4 + - - +
368A ASN 3.1 0.4 - - - -
369A GLU* 3.1 35.7 + - - +
371A VAL* 4.0 2.9 - - + -
426A SER* 3.7 19.1 - - - +
429A VAL* 3.5 17.5 - - - +
430A MET* 3.8 17.7 - - + -
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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