Contacts of the helix formed by residues 54 - 62 (chain A) in PDB entry 4DUB
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 SER 54 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 2.7 43.0 + - - +
52A LEU* 5.1 0.4 - - - +
53A SER* 1.3 80.6 - - - +
55A GLN* 1.3 64.5 + - - +
56A ARG* 3.7 5.7 + - - -
57A LEU* 3.3 17.5 + - - +
58A ILE* 3.0 22.0 + - - +
360A LEU* 3.9 2.7 - - - -
363A ASP* 3.5 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 1.3 71.4 - - - +
56A ARG* 1.3 70.5 + - - +
58A ILE* 4.4 1.3 - - - -
59A LYS* 2.9 54.6 + - - +
360A LEU* 3.6 19.1 - - + +
363A ASP* 2.8 17.6 + - - +
366A ILE* 3.5 30.9 - - + +
386A PRO* 4.0 12.7 - - - +
387A GLN* 2.8 24.8 + - - +
388A HIS 4.0 2.2 - - - +
389A ALA* 3.7 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 2.7 38.8 + - - +
54A SER* 3.2 6.6 + - - +
55A GLN* 1.3 88.8 + - - +
57A LEU* 1.3 74.0 + - + +
59A LYS* 3.6 23.4 - - - +
60A GLU* 4.0 10.5 + - - +
342A GLY* 3.6 25.5 + - - -
344A GLU* 2.8 25.4 + - - -
345A TYR* 4.6 1.4 - - - -
363A ASP* 4.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 3.7 35.2 - - + +
39A ILE* 3.8 32.3 - - + -
52A LEU* 4.2 17.8 - - + +
54A SER* 3.3 13.7 + - - +
56A ARG* 1.3 96.6 - - - +
58A ILE* 1.3 61.4 + - - +
59A LYS 3.2 1.6 - - - -
60A GLU* 3.0 24.3 + - - +
61A ALA* 3.0 13.0 + - - +
341A LEU* 4.2 10.5 - - + +
342A GLY* 3.7 28.0 - - - +
345A TYR* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.5 43.3 - - + +
53A SER* 3.8 9.2 - - - +
54A SER 3.0 21.4 + - - +
55A GLN 4.1 1.8 - - - +
57A LEU* 1.3 78.2 - - - +
59A LYS* 1.3 61.9 + - - +
61A ALA* 3.2 5.2 + - - +
62A CYS* 3.0 38.2 + - - -
355A VAL* 3.8 31.0 - - + -
360A LEU* 3.8 33.2 - - + -
388A HIS 4.2 9.9 - - - +
391A LYS* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 2.9 51.0 + - - +
56A ARG* 3.6 21.2 - - - +
58A ILE* 1.3 78.2 - - - +
60A GLU* 1.3 61.6 + - + +
62A CYS* 3.4 9.7 + - - +
63A ASP* 3.7 8.5 + - - +
387A GLN* 3.5 34.5 - - + +
388A HIS* 4.0 16.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 4.5 8.7 + - - +
57A LEU* 3.0 14.1 + - - +
59A LYS* 1.3 76.3 - - + +
61A ALA* 1.3 68.8 + - - +
62A CYS 3.0 1.8 - - - -
63A ASP* 3.1 22.7 + - - +
66A ARG* 2.9 36.3 + - - +
67A PHE* 3.3 10.4 - - - -
340A VAL 3.7 1.7 - - - +
341A LEU* 3.7 11.3 - - + -
342A GLY* 3.0 40.6 + - - -
343A GLY 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.7 29.2 - - + -
57A LEU 3.0 6.6 + - - +
58A ILE* 3.2 9.4 + - - +
60A GLU* 1.3 78.2 - - - +
62A CYS* 1.3 59.7 + - - +
63A ASP 3.2 1.9 + - - +
67A PHE* 3.4 32.6 - - - +
333A LEU* 3.5 30.3 - - + +
341A LEU* 4.5 0.8 - - - +
353A LEU* 4.0 5.6 - - + -
355A VAL* 4.7 4.7 - - + -
395A ASN* 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.0 29.6 + - - +
59A LYS 3.7 7.2 - - - +
60A GLU 3.0 0.6 - - - -
61A ALA* 1.3 76.2 - - - +
63A ASP* 1.3 58.9 + - - +
64A GLU* 3.2 8.5 + - - +
331A PHE* 4.8 7.4 - - - -
333A LEU* 5.4 1.3 - - - -
355A VAL* 5.8 0.2 - - - -
388A HIS* 3.9 18.7 + - + -
391A LYS* 3.7 25.6 - - - -
395A ASN* 3.1 50.9 + - - +
----------------------------------------------------------
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