Contacts of the helix formed by residues 418 - 432 (chain A) in PDB entry 3UON
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 PRO 418 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PRO 5.0 4.3 - - - +
416A CYS 3.1 13.0 - - - +
417A ILE* 1.3 89.6 - - + +
419A ASN* 1.3 64.8 - - - +
420A THR* 3.4 7.9 - - - +
421A VAL* 3.3 35.5 + - + +
422A TRP* 3.0 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 5.5 0.2 + - - -
418A PRO* 1.3 69.4 - - - +
420A THR* 1.3 65.8 + - - +
421A VAL 3.0 1.8 - - - -
422A TRP* 3.0 16.1 + - - +
423A THR* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A PRO* 3.4 6.8 - - - +
419A ASN* 1.3 78.4 - - - +
421A VAL* 1.3 60.5 + - + +
423A THR* 3.5 9.4 + - - -
424A ILE* 3.0 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A MET* 3.4 25.9 - - + +
417A ILE* 3.7 14.4 - - + -
418A PRO* 3.3 36.1 - - + +
419A ASN 3.0 0.8 - - - -
420A THR* 1.3 77.6 - - + +
422A TRP* 1.3 65.5 + - - +
424A ILE* 3.0 15.4 + - + +
425A GLY 2.9 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 4.5 0.4 - - - +
403A TYR* 3.9 29.2 - + - -
406A MET* 3.4 51.8 - - + +
407A VAL* 4.1 14.1 - - + -
410A ASN* 3.8 30.3 + - + -
414A ALA 5.3 0.2 + - - -
417A ILE* 3.3 29.1 + - + +
418A PRO 3.0 24.4 + - - -
419A ASN* 3.0 15.3 + - - +
421A VAL* 1.3 78.2 - - - +
423A THR* 1.3 57.6 + - - +
425A GLY* 3.2 2.3 + - - -
426A TYR* 2.9 41.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 3.3 22.2 + - + +
84A THR* 4.8 11.4 - - + +
419A ASN* 2.9 24.0 + - - -
420A THR* 3.6 12.7 - - - -
421A VAL 3.1 0.2 - - - -
422A TRP* 1.3 75.1 - - - +
424A ILE* 1.3 63.3 + - + +
426A TYR* 3.2 2.3 + - - +
427A TRP* 3.0 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A THR* 3.0 27.8 - - + +
421A VAL* 3.0 15.8 + - + +
423A THR* 1.3 75.6 - - + +
425A GLY* 1.3 66.3 + - - +
427A TRP* 3.2 7.5 + - - +
428A LEU* 3.0 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PRO* 5.0 1.3 - - - -
403A TYR* 3.9 15.6 - - - +
406A MET* 3.7 21.3 - - - -
421A VAL 2.9 10.9 + - - -
422A TRP 3.2 4.0 + - - -
424A ILE* 1.3 77.8 - - - +
426A TYR* 1.3 59.9 + - - +
428A LEU* 3.4 10.2 + - - +
429A CYS* 3.2 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 3.7 39.3 - + + +
99A TRP* 5.7 2.7 - + - -
100A LEU* 6.0 1.6 - - - +
103A ASP* 4.7 1.8 - - - -
104A TYR* 4.3 6.8 + + - -
403A TYR* 3.4 37.4 + + - -
422A TRP* 2.9 29.2 + + + +
423A THR 3.5 8.1 - - - +
424A ILE 3.2 0.2 - - - -
425A GLY* 1.3 75.8 - - - +
427A TRP* 1.3 57.2 + - - +
429A CYS* 3.4 4.9 + - - +
430A TYR* 3.0 62.4 + + + -
1162A QNB 3.9 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 4.1 15.3 - - + -
33A LEU* 3.8 28.0 - - + -
77A MET* 3.8 35.7 - - + -
80A TYR* 3.4 29.8 - + - -
81A THR* 3.0 31.2 - - + -
84A THR* 5.1 2.7 + - - -
423A THR* 3.0 41.7 + - + +
424A ILE* 3.9 6.3 - - - +
426A TYR* 1.3 74.4 - - - +
428A LEU* 1.3 60.9 + - + +
430A TYR* 3.6 13.0 - + + +
431A ILE* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE 5.0 2.5 - - - +
399A THR* 3.5 28.4 - - + +
402A PRO* 3.6 34.3 - - + -
424A ILE* 3.0 34.6 + - + +
425A GLY* 3.6 6.1 - - - +
427A TRP* 1.3 75.1 - - + +
429A CYS* 1.3 65.8 + - - +
430A TYR 3.1 0.3 + - - -
431A ILE* 3.2 35.4 - - + +
432A ASN 3.2 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A THR 3.6 13.0 + - - -
400A TRP* 4.0 32.7 + - + +
403A TYR* 3.6 24.0 - - - -
425A GLY 3.2 15.3 + - - -
426A TYR 3.6 7.6 - - - +
428A LEU* 1.3 79.4 - - - +
430A TYR* 1.3 65.7 + - - +
432A ASN* 3.5 12.0 - - - +
433A SER* 4.3 5.2 + - - -
1162A QNB 3.8 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.9 17.3 - - + +
76A SER* 3.7 25.7 + - - -
77A MET* 3.6 29.6 - - + +
80A TYR* 3.8 36.1 - + + +
99A TRP* 4.1 5.4 - - - -
103A ASP* 3.1 20.0 + - - -
426A TYR* 3.0 43.0 + + - +
427A TRP* 3.6 23.1 - + + +
428A LEU 3.1 0.4 - - - -
429A CYS* 1.3 75.6 - - - +
431A ILE* 1.3 58.5 + - - +
432A ASN 3.0 4.0 - - - -
433A SER* 2.8 31.2 + - - -
1162A QNB 3.9 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.6 34.8 - - + -
77A MET* 3.9 0.9 - - + -
399A THR* 4.9 6.5 - - + -
427A TRP* 2.8 26.7 + - + +
428A LEU* 3.2 35.4 - - + +
430A TYR* 1.3 71.1 - - - +
432A ASN* 1.3 54.4 + - - +
433A SER 2.9 1.1 - - - -
434A THR* 2.6 40.2 + - - +
435A ILE* 3.0 20.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASP* 5.5 0.7 - - - +
392A ILE 4.9 0.4 + - - -
395A ALA* 3.0 46.3 + - - +
396A PHE* 3.3 9.7 - - - +
399A THR* 3.2 22.9 - - - +
400A TRP* 3.6 14.6 + - - +
428A LEU 3.2 5.3 + - - -
429A CYS 3.5 14.5 - - - +
430A TYR 3.0 0.6 + - - -
431A ILE* 1.3 77.6 - - - +
433A SER* 1.3 59.2 + - - +
434A THR 3.1 0.6 + - - -
435A ILE* 3.7 9.2 - - - +
436A ASN* 2.9 40.2 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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