Contacts of the helix formed by residues 44 - 54 (chain C) in PDB entry 4O9U
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 VAL 44 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ILE 3.1 17.5 + - - +
42C HIS* 4.2 8.7 - - - +
43C GLY* 1.3 73.1 - - - +
45C VAL* 1.3 56.6 + - - +
46C VAL* 3.0 11.7 + - - -
47C VAL* 3.2 19.6 + - + +
11D VAL* 5.3 0.7 - - + -
15D PHE* 3.3 35.2 - - + -
38D GLY 4.8 1.6 - - - +
39D MET* 3.8 16.4 - - + -
42D ALA* 4.8 9.4 - - + -
218D VAL* 4.8 5.2 - - + -
229D ALA* 4.9 5.2 - - + +
230D LEU* 3.4 29.9 - - + +
233D ALA* 4.2 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C HIS 3.4 19.5 + - - +
43C GLY 2.8 2.8 - - - +
44C VAL* 1.3 75.8 - - - +
46C VAL* 1.3 63.4 + - - +
47C VAL 3.5 0.2 - - - -
48C GLY 4.0 1.7 + - - -
49C ALA* 3.4 20.4 + - - +
72C GLY* 3.8 10.8 - - - -
75C ASN* 4.1 3.1 - - - +
92D GLY* 3.8 21.1 - - - +
95D ALA* 3.7 43.2 - - + +
96D ALA* 3.8 2.5 - - - +
99D ILE* 4.0 11.9 - - + +
218D VAL* 4.0 18.8 - - + -
230D LEU* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLY 2.8 21.3 - - - +
44C VAL* 4.6 1.1 - - - -
45C VAL* 1.3 76.9 - - - +
47C VAL* 1.3 55.8 + - - +
49C ALA* 2.9 7.5 + - - +
50C MET* 2.6 43.7 + - - +
69C VAL* 3.8 16.4 - - + +
72C GLY* 3.4 19.7 - - - +
73C ALA* 3.5 16.8 - - + +
76C ALA* 3.8 10.5 - - + -
39D MET* 5.2 0.7 - - - -
43D VAL* 5.1 10.1 - - + -
62D LEU* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 3.2 17.4 + - + +
46C VAL* 1.3 78.1 - - - +
48C GLY* 1.3 56.5 + - - +
50C MET* 3.3 10.0 + - - +
51C VAL* 2.9 34.4 + - + +
8D TYR* 3.5 16.8 - - + +
39D MET* 6.4 0.4 - - - -
42D ALA* 3.7 39.9 - - + +
43D VAL* 4.2 12.1 - - + +
46D THR* 3.4 22.1 + - + +
227D ASN* 4.4 15.0 - - - +
229D ALA* 5.9 0.9 - - + -
230D LEU* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL 4.1 3.2 + - - -
45C VAL 4.0 2.4 + - - -
46C VAL 3.2 0.4 - - - -
47C VAL* 1.3 77.7 - - - +
49C ALA* 1.3 60.6 + - - +
50C MET 3.2 0.7 - - - -
51C VAL* 3.4 7.6 + - - +
52C VAL* 3.0 31.9 + - - +
99D ILE* 4.2 22.1 - - - +
225D VAL* 6.1 4.0 - - - -
227D ASN* 5.0 4.3 - - - -
230D LEU* 4.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL 3.4 16.1 + - - +
46C VAL 2.9 8.4 + - - +
48C GLY* 1.3 76.1 - - - +
50C MET* 1.3 56.5 + - - +
52C VAL* 3.6 11.1 - - - +
53C LEU* 3.2 27.4 + - - +
65C GLY* 4.0 2.9 - - - +
68C GLY* 3.5 35.0 - - - +
69C VAL* 3.3 10.9 - - + +
95D ALA 4.8 2.7 - - - +
98D THR* 4.7 6.3 - - - +
99D ILE* 4.2 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 2.6 55.0 + - + +
47C VAL* 3.4 12.1 - - - +
49C ALA* 1.3 73.6 - - - +
51C VAL* 1.3 58.9 + - - +
52C VAL 3.3 0.2 - - - -
53C LEU* 3.4 2.0 + - - +
54C GLY* 3.0 25.8 + - - -
69C VAL* 4.1 7.4 - - + -
43D VAL* 3.8 29.4 - - + +
46D THR* 3.3 23.6 - - - +
47D PHE* 4.5 9.0 - - + -
52D MET* 3.9 11.9 - - + +
58D ILE* 3.8 27.6 - - + +
62D LEU* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 2.9 28.7 + - + +
48C GLY* 3.7 8.1 - - - +
50C MET* 1.3 76.3 - - - +
52C VAL* 1.3 58.9 + - + +
54C GLY 3.5 3.5 + - - -
55C HIS* 2.8 35.3 - - + -
46D THR* 4.6 6.5 - - - +
49D TRP* 3.5 64.2 - - + +
52D MET* 4.7 7.2 - - - -
225D VAL* 6.5 1.6 - - + -
227D ASN* 4.6 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLY 3.0 19.9 + - - +
49C ALA* 3.6 14.4 - - - +
51C VAL* 1.3 78.2 - - + +
53C LEU* 1.3 64.6 + - - +
55C HIS* 3.3 14.6 + - - +
56C ALA* 3.7 11.3 + - - +
65C GLY* 4.9 6.5 - - - -
98D THR* 5.2 2.2 - - - +
99D ILE* 4.9 18.2 - - + +
102D VAL* 3.9 32.0 - - + +
103D GLU* 3.4 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA 3.2 18.6 + - - +
50C MET 3.8 4.3 - - - +
51C VAL 3.3 0.4 - - - -
52C VAL* 1.3 74.8 - - - +
54C GLY* 1.3 57.8 + - - +
55C HIS 3.0 8.7 + - - -
56C ALA* 3.6 11.8 + - + +
62C LYS* 3.4 34.3 - - + +
65C GLY* 3.9 13.5 - - - +
66C PHE* 3.8 16.8 - - + +
69C VAL* 3.8 20.4 - - + -
54D ASN* 3.8 19.0 + - + +
57D LEU* 4.3 10.1 - - + +
58D ILE* 3.7 37.7 - - + +
61D ALA* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C MET 3.0 13.2 + - - -
51C VAL 3.9 1.8 - - - -
52C VAL 3.4 0.4 - - - -
53C LEU* 1.3 74.6 - - - +
55C HIS* 1.3 70.4 + - - +
56C ALA 3.8 0.7 - - - -
51D GLY 4.2 2.9 - - - +
52D MET* 3.9 10.7 - - - -
53D GLY* 3.4 38.2 + - - -
54D ASN* 4.6 3.5 + - - -
58D ILE* 3.8 8.9 - - - +
----------------------------------------------------------
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