Contacts of the helix formed by residues 43 - 53 (chain C) in PDB entry 2QMR
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 TYR 43 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASN* 4.5 18.2 - - + +
42C GLN* 1.3 91.7 - - + +
44C PRO* 1.4 64.3 - - + +
45C ASP* 3.2 3.4 - - - +
46C PHE* 3.4 35.5 - + + +
47C ASN* 3.6 21.2 + - - -
87C VAL* 5.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN 5.2 2.2 - - - +
40C LEU* 3.7 33.0 - - + -
41C ASN* 3.9 6.3 - - + +
42C GLN* 3.5 13.7 - - - +
43C TYR* 1.4 91.5 - - + +
45C ASP* 1.3 76.9 + - - +
47C ASN* 3.5 17.2 + - + +
48C ASN* 3.5 17.7 + - - +
51C ILE* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TYR* 3.2 1.1 - - - -
44C PRO* 1.3 92.0 - - - +
46C PHE* 1.3 65.8 + - - +
48C ASN* 2.9 22.6 + - - +
49C TYR* 3.0 21.3 - - - +
72C LEU* 3.7 13.7 - - + +
75C ASN* 3.3 25.5 + - - +
83C PHE* 2.9 36.9 - - + -
87C VAL* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TYR* 3.4 27.9 + + + +
45C ASP* 1.3 79.5 - - - +
47C ASN* 1.3 92.6 + - - +
48C ASN 3.6 0.2 + - - -
49C TYR* 3.6 14.6 + - - +
50C LEU* 4.6 7.5 + - + +
87C VAL* 3.7 26.4 - - + +
90C PHE* 3.9 40.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PRO* 5.6 1.0 - - - +
10C GLN* 3.4 34.8 - - + +
14C GLN* 6.4 0.9 - - + -
43C TYR* 3.6 28.9 + - - -
44C PRO* 3.5 10.1 + - - +
45C ASP 3.1 1.0 - - - -
46C PHE* 1.3 96.5 - - - +
48C ASN* 1.3 56.9 + - - +
49C TYR 3.1 5.2 - - - -
50C LEU* 2.9 39.8 + - + +
51C ILE* 3.2 21.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PRO* 3.5 9.0 + - - +
45C ASP* 2.9 24.3 + - - +
47C ASN* 1.3 74.9 - - - +
49C TYR* 1.3 51.2 + - - +
50C LEU 3.5 0.2 - - - -
51C ILE* 3.4 13.4 - - - +
52C PHE* 2.7 34.4 + - - +
68C SER* 2.9 28.8 + - - +
71C ILE 5.3 1.0 + - - -
72C LEU* 3.5 44.2 - - + +
75C ASN* 4.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASP* 3.0 27.3 - - + +
46C PHE* 3.6 11.2 - - - -
47C ASN 3.1 0.2 - - - -
48C ASN* 1.3 73.2 - - - +
50C LEU* 1.3 57.9 + - - +
51C ILE 2.9 5.6 - - - -
52C PHE* 3.5 7.9 - + - +
53C VAL* 2.7 48.7 + - + +
54C LEU* 2.8 14.6 + - - +
72C LEU* 3.3 38.3 - - + +
83C PHE* 5.5 0.2 - - - -
87C VAL* 5.3 4.1 - - + +
90C PHE* 4.1 26.2 - + + -
91C ILE* 2.8 55.7 - - + +
94C GLU* 4.6 5.2 - - + -
95C CYS* 5.1 1.8 - - - -
113C LEU* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LYS 5.5 0.7 - - - +
7C PRO* 3.7 33.2 - - + +
46C PHE* 4.6 6.1 + - + +
47C ASN* 2.9 29.8 + - + +
49C TYR* 1.3 77.6 - - - +
51C ILE* 1.3 57.9 + - + +
54C LEU* 3.7 31.4 - - + +
55C THR* 3.3 23.1 + - - +
90C PHE* 5.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLN 5.5 1.8 - - - +
11C GLY* 5.5 7.9 - - - -
14C GLN* 4.4 26.7 - - + +
15C ILE* 5.3 14.1 - - + +
18C LEU* 6.5 1.1 - - + -
44C PRO 5.7 0.2 - - - +
47C ASN* 3.2 23.8 + - + +
48C ASN* 3.4 25.4 - - - +
49C TYR 2.9 0.2 - - - -
50C LEU* 1.3 81.9 - - + +
52C PHE* 1.3 57.4 + - - +
55C THR* 3.2 21.7 - - + +
59C SER* 5.2 1.1 - - - +
64C THR* 5.2 12.3 - - + +
65C ARG* 3.3 16.0 - - + +
68C SER* 4.1 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASN 2.7 22.6 + - - +
49C TYR* 3.4 11.4 + + + -
51C ILE* 1.3 78.3 - - - +
53C VAL* 1.3 77.3 + - + +
55C THR 5.3 0.2 - - - -
65C ARG* 3.1 57.7 + - + +
66C SER* 3.8 16.4 - - - -
68C SER* 4.4 3.6 - - - +
69C GLY* 4.2 10.5 - - - +
72C LEU* 5.6 0.4 - - + -
95C CYS* 5.9 1.1 - - - -
106C ILE* 4.0 12.9 - - + +
109C THR* 3.6 25.6 - - + -
110C VAL* 3.6 37.7 - - + -
113C LEU* 4.5 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR* 2.7 34.5 + - + +
52C PHE* 1.3 100.3 - - + +
54C LEU* 1.3 62.9 + - + +
55C THR 3.6 1.2 - - - -
56C LYS* 5.1 1.6 + - - +
65C ARG* 4.0 12.4 + - - +
94C GLU* 3.3 29.2 - - + +
95C CYS* 5.3 2.7 - - - +
98C ASN* 3.1 51.9 - - + +
110C VAL* 5.6 2.9 - - + -
----------------------------------------------------------
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