Contacts of the helix formed by residues 443 - 455 (chain A) in PDB entry 3U0Z
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 443 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 1.3 76.0 - - - +
444A ASP* 1.3 62.8 + - - +
445A PRO* 3.5 21.4 - - + +
446A LEU* 2.9 37.0 + - - +
447A ARG* 3.2 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASN* 1.3 73.3 - - - +
445A PRO* 1.3 76.9 - - + +
447A ARG* 2.4 34.1 + - - +
448A GLU* 2.8 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASN* 3.5 19.7 - - + +
444A ASP* 1.3 94.5 - - + +
446A LEU* 1.3 59.1 + - + +
448A GLU* 3.1 10.2 + - + +
449A GLU* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 4.3 30.7 - - + -
443A ASN* 2.9 30.3 + - - +
445A PRO* 1.3 75.8 - - + +
447A ARG* 1.3 67.1 + - - +
449A GLU* 3.4 19.2 + - - +
450A ILE* 3.1 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 3.2 48.4 + - + +
440A SER* 4.4 8.0 + - - +
442A LEU* 2.4 31.6 + - + +
443A ASN* 3.2 22.2 + - - +
444A ASP* 2.4 41.3 + - - +
446A LEU* 1.3 78.5 - - - +
448A GLU* 1.3 58.2 + - + +
450A ILE* 3.6 7.5 + - - +
451A VAL* 3.1 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP* 2.8 39.7 + - + +
445A PRO* 3.6 6.8 - - - +
447A ARG* 1.3 75.4 - - + +
449A GLU* 1.3 66.9 + - - +
450A ILE 3.2 1.1 - - - -
451A VAL* 4.1 3.0 - - - +
452A ASN* 2.9 33.5 + - - +
471A ASN* 5.5 4.2 + - - -
474A THR* 3.6 30.7 - - + +
478A SER* 5.3 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PRO* 2.9 25.3 + - - +
446A LEU* 3.7 22.1 - - + +
448A GLU* 1.3 74.4 - - - +
450A ILE* 1.3 60.5 + - + +
452A ASN* 3.4 5.1 + - - +
453A PHE* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 4.5 20.9 - - + -
442A LEU* 4.0 25.4 - - + -
446A LEU* 3.1 22.9 + - + +
447A ARG* 3.8 4.3 - - - +
449A GLU* 1.3 74.9 - - + +
451A VAL* 1.3 72.7 + - + +
453A PHE* 2.8 17.4 + - - +
454A ASN* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 4.6 20.9 - - + -
447A ARG* 3.1 23.3 + - + +
448A GLU* 4.3 3.6 - - - +
450A ILE* 1.3 80.6 - - + +
452A ASN* 1.3 62.1 + - - +
454A ASN* 3.4 6.2 + - - +
455A CYS* 3.0 36.4 + - - +
474A THR* 6.4 1.1 - - + -
477A LEU* 3.6 42.1 - - + +
478A SER* 4.5 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A GLU* 2.9 28.4 + - - +
449A GLU* 3.6 6.5 - - - +
451A VAL* 1.3 78.1 - - - +
453A PHE* 1.3 61.6 + - - +
455A CYS 3.8 1.0 - - - -
456A ARG* 3.2 24.2 + - - +
459A VAL* 5.2 2.8 - - - +
470A PRO 5.1 0.7 - - - +
473A VAL* 4.4 8.3 - - - +
474A THR* 3.2 34.2 + - - +
477A LEU* 3.7 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLU 3.0 13.0 + - - +
450A ILE* 2.8 12.2 + - - +
452A ASN* 1.3 77.7 - - - +
454A ASN* 1.3 75.2 + - - +
456A ARG* 2.7 74.2 + - - +
466B ALA 4.8 4.3 - - - -
468B ALA 5.9 2.5 - - - -
470B PRO* 4.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ILE* 2.9 35.2 + - - +
451A VAL* 4.0 7.0 - - - +
453A PHE* 1.3 91.0 - - - +
455A CYS* 1.3 64.2 + - - +
456A ARG* 3.3 1.1 + - - -
457A LYS 5.0 1.4 + - - -
505A GLN* 5.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A VAL* 3.0 25.6 + - - +
452A ASN 3.8 2.5 - - - -
454A ASN* 1.3 81.7 - - - +
456A ARG* 1.3 63.8 + - - +
457A LYS 3.3 2.5 - - - -
458A LEU* 3.0 17.7 + - + +
459A VAL* 3.0 23.0 + - - +
477A LEU* 3.9 31.6 - - + -
480A LEU* 5.3 7.0 - - - -
551A TYR* 4.9 23.6 - - - -
----------------------------------------------------------
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