Contacts of the helix formed by residues 26 - 37 (chain C) in PDB entry 6MUO
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 26 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 3.5 6.5 - - - +
24C GLN 3.7 0.6 - - - +
25C PHE* 1.3 86.5 - - + +
27C VAL* 1.3 65.7 + - - +
28C GLY 3.3 0.7 - - - +
29C ARG* 3.7 29.2 - - + +
30C VAL* 3.4 24.8 + - + +
52C ALA* 4.8 0.4 - - - +
37D TYR* 5.3 9.0 - - + -
40D TYR* 3.4 53.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG* 3.6 36.8 - - + +
18C SER* 3.0 32.6 + - - +
21C ALA* 5.3 2.0 - - + -
23C LEU* 4.3 10.1 - - + -
25C PHE 4.2 4.5 - - - +
26C PRO* 1.3 73.0 - - - +
28C GLY* 1.3 58.7 + - - +
30C VAL* 3.3 5.2 + - - +
31C HIS* 2.9 25.7 + - + +
48C PRO* 3.4 28.3 - - + +
49C VAL* 3.8 22.2 - - + -
52C ALA* 4.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG* 4.8 3.0 - - - +
26C PRO* 3.3 1.4 - - - +
27C VAL* 1.3 80.7 - - - +
29C ARG* 1.3 50.7 + - - +
31C HIS* 3.1 7.9 + - - +
32C ARG* 2.6 31.5 + - - +
-44I A 3.2 20.6 + - - +
-43I A 4.1 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PRO* 3.7 24.0 + - + +
27C VAL 3.4 0.8 - - - -
28C GLY* 1.3 71.7 - - - +
30C VAL* 1.3 64.1 + - + +
32C ARG* 3.9 5.6 - - - +
33C LEU* 3.2 33.1 + - + +
35D GLU* 3.1 42.3 + - - +
36D SER 2.8 28.5 + - - -
37D TYR* 4.0 21.9 - - + -
40D TYR* 3.4 22.4 + - - -
-45I A 5.9 0.4 + - - -
-44I A 3.3 14.6 + - - +
49J T 3.1 37.0 + - - -
50J A 3.5 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 5.9 2.5 - - + -
26C PRO* 3.4 19.0 + - + +
27C VAL 3.3 7.7 + - - +
28C GLY 3.2 0.2 - - - -
29C ARG* 1.3 79.5 - - + +
31C HIS* 1.3 56.5 + - - +
33C LEU* 3.3 5.9 + - - +
34C LEU* 3.0 31.3 + - + +
48C PRO* 3.8 23.6 - - + +
51C LEU* 4.0 27.1 - - + -
52C ALA* 5.0 10.3 - - + +
55C LEU* 5.0 12.1 - - + -
37D TYR* 4.6 14.6 - - + +
70D PHE* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG* 4.5 20.9 + - - +
27C VAL* 2.9 17.7 + - + +
28C GLY* 3.1 8.9 + - - +
30C VAL* 1.3 76.2 - - - +
32C ARG* 1.3 61.7 + - - +
34C LEU* 4.0 6.2 + - - +
35C ARG* 2.8 45.8 + - + -
43C VAL* 4.0 25.0 + - + +
44C GLY 4.3 6.7 + - - -
45C ALA* 5.5 4.0 - - - -
48C PRO* 3.7 26.9 - - + +
39J A 5.1 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLY 2.6 19.8 + - - +
29C ARG* 3.9 6.7 + - - +
30C VAL 3.2 0.4 - - - -
31C HIS* 1.3 75.9 - - - +
33C LEU* 1.3 76.9 + - - +
34C LEU 3.4 0.5 + - - -
35C ARG* 3.6 10.9 + - - +
36C LYS* 3.3 36.4 - - + +
35D GLU* 2.8 35.6 + - - -
-45I A 3.2 48.1 + - - -
-44I A 3.1 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ARG* 3.2 31.3 + - + +
30C VAL* 4.1 3.1 - - - +
32C ARG* 1.3 96.1 - - - +
34C LEU* 1.3 56.9 + - - +
35C ARG 3.1 0.7 - - - -
36C LYS* 3.1 23.1 + - + +
37C GLY* 3.5 10.4 + - - -
39C TYR* 4.7 4.2 - - - -
35D GLU* 5.1 3.4 - - - +
37D TYR* 4.4 19.3 - - + +
67D ASN* 5.5 3.4 - - - +
70D PHE* 4.4 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.0 20.6 + - + +
31C HIS* 4.0 5.4 + - - +
32C ARG 3.3 0.6 - - - -
33C LEU* 1.3 76.6 - - - +
35C ARG* 1.3 59.6 + - - +
39C TYR* 4.2 23.9 + - + +
40C ALA 5.0 0.9 + - - -
43C VAL* 3.7 36.6 - - + +
47C ALA* 5.8 4.3 - - + -
48C PRO* 5.2 6.1 - - + -
51C LEU* 3.8 29.6 - - + -
70D PHE* 4.2 13.5 - - + -
74D ALA* 4.2 17.0 - - + -
89D ILE* 4.6 23.3 - - + -
94D ILE* 5.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C HIS* 2.8 55.1 + - - +
32C ARG* 3.6 11.0 + - - +
33C LEU 3.1 0.4 - - - -
34C LEU* 1.3 79.1 - - - +
36C LYS* 1.3 67.0 + - + +
37C GLY 3.2 3.6 + - - -
38C ASN* 3.4 18.1 + - - +
40C ALA 5.1 5.3 - - - +
42C ARG* 6.1 1.3 - - - +
43C VAL* 3.7 21.7 - - + +
39J A 4.5 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 3.3 32.8 - - + +
33C LEU* 3.1 12.3 + - + +
35C ARG* 1.3 80.5 - - + +
37C GLY* 1.3 60.6 + - - +
38C ASN* 3.3 5.0 + - - -
82H HIS* 4.4 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU 3.5 7.8 + - - -
35C ARG 3.2 1.0 - - - -
36C LYS* 1.3 78.9 - - - +
38C ASN* 1.3 70.5 + - - +
39C TYR* 3.5 22.7 - - - -
82H HIS* 3.7 29.5 - - - -
----------------------------------------------------------
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