Contacts of the helix formed by residues 34 - 46 (chain C) 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 GLU 34 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 6.0 0.3 + - - -
30C PHE* 3.1 35.9 + - + +
33C GLU* 1.3 87.6 - - + +
35C ILE* 1.3 65.3 + - - +
36C ILE 3.5 0.7 - - - -
37C PRO* 3.5 7.1 - - - +
38C VAL* 3.6 20.1 - - - +
52C LEU* 3.8 11.9 - - + +
55C ARG* 2.9 58.3 + - - +
59C LEU* 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.1 44.8 + - + +
31C ALA* 3.6 17.3 - - + +
34C GLU* 1.3 74.7 - - - +
36C ILE* 1.3 60.5 + - - +
38C VAL* 3.4 3.3 + - - +
39C ALA* 3.0 26.6 + - + +
52C LEU* 4.4 12.6 - - + -
87C LEU* 4.4 22.2 - - + +
90C GLY* 4.0 3.1 - - - -
91C CYS* 3.9 33.2 - - + +
94C VAL* 4.2 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA 3.0 14.7 + - - +
32C ARG* 3.4 32.3 - - + +
35C ILE* 1.3 75.1 - - - +
37C PRO* 1.3 72.5 - - + +
38C VAL 3.3 0.3 + - - -
39C ALA* 3.8 12.9 + - - +
40C ALA* 4.9 1.9 + - - +
89C TYR* 3.9 28.5 - - + -
90C GLY* 3.8 15.7 - - - -
269C ARG* 4.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG 4.1 4.5 - - - +
33C GLU* 3.5 24.9 - - - +
34C GLU 3.5 14.1 - - - +
36C ILE* 1.3 97.1 - - + +
38C VAL* 1.3 63.5 + - + +
40C ALA* 5.0 4.7 + - - +
41C GLU* 5.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU 3.6 20.4 - - - +
35C ILE 3.6 4.5 - - - +
37C PRO* 1.3 84.2 - - + +
39C ALA* 1.3 66.4 + - - +
40C ALA 3.3 2.9 - - - -
41C GLU* 3.2 18.7 + - + +
42C TYR* 3.2 40.5 + - + -
52C LEU* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.0 17.6 + - - +
36C ILE* 4.2 7.2 - - - +
37C PRO 3.7 1.4 - - - -
38C VAL* 1.3 78.4 - - - +
40C ALA* 1.3 63.1 + - - +
42C TYR* 3.3 6.5 + - - +
43C ASP* 3.1 24.1 + - - +
90C GLY 4.1 8.1 - - - +
91C CYS* 3.9 29.6 - - + -
94C VAL* 6.1 2.2 - - - -
269C ARG* 5.9 0.4 - - - +
364C LYS* 4.1 12.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE 4.9 2.7 + - - +
37C PRO 5.0 3.6 + - - +
38C VAL 3.3 0.8 + - - -
39C ALA* 1.3 78.9 - - - +
41C GLU* 1.3 61.2 + - + +
43C ASP* 3.5 7.2 + - - +
44C ARG* 3.0 49.7 + - - +
364C LYS* 5.1 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PRO 5.7 2.0 - - - +
38C VAL* 3.2 14.1 + - + +
40C ALA* 1.3 76.6 - - + +
42C TYR* 1.3 63.6 + - + +
43C ASP 3.2 0.2 - - - -
44C ARG* 3.3 33.7 + - - +
45C THR* 3.0 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 3.2 50.9 + - + +
39C ALA* 3.9 8.1 - - - +
41C GLU* 1.3 76.4 - - + +
43C ASP* 1.3 60.5 + - - +
45C THR* 3.9 3.1 - - - -
46C GLY* 2.9 28.2 + - - -
47C GLU* 3.1 42.8 + - + -
48C TYR 4.1 4.5 - - - -
49C PRO* 3.5 24.5 - - + -
51C PRO* 3.4 31.5 - - + +
52C LEU* 4.2 13.8 - - + +
94C VAL* 5.7 1.8 - - + -
219C CYS* 3.6 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ALA 3.1 16.1 + - - +
40C ALA* 3.6 6.4 - - - +
41C GLU 3.2 0.2 - - - -
42C TYR* 1.3 78.1 - - - +
44C ARG* 1.3 62.8 + - - +
46C GLY 3.8 1.0 + - - -
217C GLN 5.1 0.2 + - - -
218C ARG* 2.6 74.7 + - - +
219C CYS* 4.8 2.7 - - - +
363C GLU* 4.7 0.7 - - - +
364C LYS* 3.7 28.3 - - + +
367C ARG* 2.9 31.4 + - - -
368C ASP* 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA* 3.0 32.0 + - - +
41C GLU* 3.3 31.3 + - - +
42C TYR 3.3 0.2 - - - -
43C ASP* 1.3 85.0 - - - +
45C THR* 1.3 64.0 + - + +
46C GLY 3.5 0.5 + - - -
218C ARG* 3.9 12.3 + - - +
358C THR* 3.5 29.3 + - - -
359C GLU* 4.1 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 3.0 30.0 + - + +
42C TYR* 3.9 4.5 - - - -
44C ARG* 1.3 78.2 - - + +
46C GLY* 1.3 58.2 + - - +
47C GLU* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR 2.9 13.9 + - - -
43C ASP 3.8 3.9 + - - -
44C ARG 3.3 4.8 + - - -
45C THR* 1.3 74.8 - - - +
47C GLU* 1.3 61.3 + - - +
48C TYR 3.7 0.7 + - - -
211C LYS* 3.3 31.8 + - - +
218C ARG* 3.7 21.9 - - - +
219C CYS* 4.1 0.2 - - - -
----------------------------------------------------------
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