Contacts of the helix formed by residues 49 - 60 (chain D) in PDB entry 1UDY
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 49 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR* 3.5 28.5 - - + -
47D GLU 3.3 4.0 - - - +
48D TYR* 1.3 88.5 - - + +
50D VAL* 1.3 64.6 + - - +
51D PRO* 3.3 3.6 - - - -
52D LEU* 3.0 27.9 + - + -
53D LEU* 3.0 30.1 + - + +
94D VAL* 4.4 12.8 - - + -
97D ALA* 5.0 3.4 - - + -
219D CYS* 3.5 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 3.0 32.9 + - + +
49D PRO* 1.3 70.1 - - - +
51D PRO* 1.3 73.9 - - + +
53D LEU* 3.0 9.3 + - + +
54D LYS* 2.8 46.7 + - + +
172D LYS* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR* 3.6 20.2 - - + +
48D TYR 4.6 2.0 - - - +
49D PRO* 3.4 4.0 - - + -
50D VAL* 1.3 97.2 - - + +
52D LEU* 1.3 60.3 + - + +
54D LYS* 3.7 7.3 + - + +
55D ARG* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 3.6 20.5 - - + -
34D GLU* 3.9 26.9 - - + +
35D ILE* 4.4 9.9 - - + -
38D VAL* 3.8 23.8 - - + -
39D ALA* 6.3 0.2 - - - -
42D TYR* 4.0 18.6 - - + +
49D PRO* 3.0 12.5 + - + +
51D PRO* 1.3 77.9 - - + +
53D LEU* 1.3 61.8 + - - +
55D ARG* 3.5 4.5 - - + +
56D ALA* 2.9 28.9 + - - +
94D VAL* 4.0 35.7 - - + -
98D ILE* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 3.3 46.0 - - + +
49D PRO* 3.0 25.2 + - + +
50D VAL* 3.6 7.4 - - + +
52D LEU* 1.3 75.5 - - - +
54D LYS* 1.3 66.9 + - + +
56D ALA* 3.1 4.9 + - - +
57D TRP* 2.9 25.0 + - - +
62D MET* 4.0 5.4 - - + +
94D VAL* 4.4 5.6 - - + +
97D ALA* 4.0 13.9 - - + -
98D ILE* 3.6 30.5 - - + -
128D PRO* 5.6 1.1 - - - -
130D MET* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D VAL* 2.8 39.2 + - + +
51D PRO* 4.0 6.5 - - + +
53D LEU* 1.3 76.2 - - + +
55D ARG* 1.3 63.7 + - - +
57D TRP* 3.4 10.9 + - - +
58D GLU* 3.1 34.0 + - - +
128D PRO* 3.5 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 3.6 12.3 - - + -
34D GLU* 2.7 53.2 + - - +
51D PRO 3.1 18.8 + - - +
52D LEU* 3.5 8.1 - - + +
53D LEU 3.1 0.4 - - - -
54D LYS* 1.3 75.7 - - - +
56D ALA* 1.3 63.0 + - - +
58D GLU* 3.0 21.8 + - - +
59D LEU* 2.9 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 4.0 16.8 - - + -
52D LEU 2.9 18.6 + - - +
53D LEU* 3.1 5.4 + - - +
55D ARG* 1.3 75.4 - - - +
57D TRP* 1.3 63.3 + - - +
59D LEU* 3.1 12.2 + - - +
61D LEU* 3.1 33.3 + - + +
62D MET* 4.4 6.5 - - - -
98D ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LEU 2.9 15.3 + - - +
54D LYS* 3.5 8.1 - - - +
56D ALA* 1.3 76.4 - - - +
58D GLU* 1.3 78.6 + - + +
60D GLY* 3.3 11.3 + - - -
62D MET* 3.6 24.5 - - + +
63D ASN* 3.6 24.6 - - - +
124D MET 3.0 18.8 + - - -
125D THR* 3.3 25.1 + - - +
126D GLU 3.7 10.8 - - - -
127D GLU 3.6 13.2 - - - -
128D PRO* 3.5 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS* 3.1 25.4 + - - +
55D ARG* 3.0 27.4 + - - +
57D TRP* 1.3 94.1 - - + +
59D LEU* 1.3 64.2 + - + +
60D GLY* 3.1 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D THR* 4.3 20.1 - - + +
30D PHE* 3.6 42.8 - - + -
34D GLU* 4.6 1.6 - - - +
55D ARG* 2.9 62.9 + - - +
56D ALA 3.1 6.9 + - - +
58D GLU* 1.3 78.6 - - + +
60D GLY* 1.3 61.7 + - - +
61D LEU* 3.5 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 5.7 4.5 - - - -
56D ALA 3.2 2.6 + - - -
57D TRP 3.3 8.9 + - - -
58D GLU 3.1 7.0 + - - -
59D LEU* 1.3 78.3 - - - +
61D LEU* 1.3 59.9 + - - +
62D MET 3.2 13.2 + - - +
64D THR* 4.0 10.7 + - - -
73D LEU* 4.9 18.8 - - - +
75D LEU* 5.5 1.0 - - - +
83D ILE* 4.8 3.1 - - - +
----------------------------------------------------------
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