Contacts of the helix formed by residues 18 - 32 (chain C) in PDB entry 2M6X
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 GLY 18 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 5.4 7.3 - - - +
15C GLY 5.3 0.2 - - - -
16C ASN 3.1 7.2 + - - -
17C HIS* 1.3 75.0 - - - +
19C PHE* 1.3 65.2 + - - +
20C PHE 3.8 0.4 - - - -
21C TRP* 4.3 8.4 - - - -
22C GLY* 3.6 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 3.7 20.9 - - + -
50A LEU* 3.9 24.2 - - + -
53A VAL* 3.8 34.4 - - + +
33B LYS* 6.1 1.8 - - - -
18C GLY* 1.3 70.3 - - - +
20C PHE* 1.3 123.1 + + + +
22C GLY* 3.2 10.7 + - - -
23C LEU* 3.4 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 5.3 14.4 - - + +
29B ALA* 3.4 28.8 - - + +
30B TRP* 4.2 42.6 - + + -
33B LYS* 5.9 9.0 - - - -
19C PHE* 1.3 111.2 - + + +
21C TRP* 1.3 63.4 + - - +
23C LEU* 3.3 20.3 + - + +
24C LEU 3.6 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 6.4 1.6 - - + -
21B TRP* 6.2 0.4 - - - -
25B VAL* 4.3 33.4 - - + +
29B ALA* 4.2 7.6 - - - +
16C ASN* 3.4 46.7 + - + +
17C HIS* 5.8 0.4 - - - -
18C GLY* 4.5 12.1 - - - +
19C PHE 3.2 1.0 - - - +
20C PHE* 1.3 79.7 - - - +
22C GLY* 1.3 73.8 + - - +
23C LEU 3.4 0.2 + - - -
24C LEU* 3.4 21.8 + - + +
25C VAL* 3.8 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 6.2 1.6 - - - -
56A LEU* 5.7 8.3 - - - -
18C GLY 3.6 8.6 + - - -
19C PHE 3.2 7.7 + - - -
21C TRP* 1.3 97.4 - - - +
23C LEU* 1.3 63.0 + - - +
24C LEU 3.3 0.3 + - - -
25C VAL* 3.4 11.6 + - - +
26C VAL* 3.5 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 5.8 3.8 - - + -
49A PRO* 3.6 25.8 - - + +
52A LEU* 4.6 9.4 - - + -
53A VAL* 3.7 25.6 - - + -
32B VAL* 5.7 2.2 - - + -
33B LYS* 5.8 6.1 - - - +
36B LEU* 5.3 9.2 - - + -
19C PHE* 3.4 43.5 + - + +
20C PHE* 3.6 12.3 - - + +
21C TRP 3.3 0.4 - - - -
22C GLY* 1.3 76.4 - - - +
24C LEU* 1.3 63.7 + - - +
25C VAL 3.4 0.2 + - - -
26C VAL* 3.4 7.6 + - + +
27C THR* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL 5.8 0.2 - - - +
28B LEU* 3.5 49.6 - - + +
29B ALA* 4.0 11.0 - - + +
32B VAL* 4.1 21.0 - - + +
20C PHE 3.6 6.9 + - - +
21C TRP* 3.4 17.0 + - + +
22C GLY 3.2 0.6 - - - -
23C LEU* 1.3 79.9 - - - +
25C VAL* 1.3 76.2 + - + +
27C THR* 3.5 2.8 + - - -
28C LEU* 3.1 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.9 44.0 - - + +
22C GLY 3.4 6.0 + - - +
23C LEU 3.3 0.8 - - - -
24C LEU* 1.3 89.6 - - + +
26C VAL* 1.3 64.1 + - + +
28C LEU* 3.9 4.5 - - - +
29C ALA* 3.3 21.0 + - - +
20D PHE* 4.4 15.5 - - + -
21D TRP* 3.4 39.0 - - + -
24D LEU* 4.9 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.5 26.5 - - + -
22C GLY 3.5 16.4 - - - +
23C LEU* 3.9 6.1 - - + +
24C LEU 3.3 0.4 - - - -
25C VAL* 1.3 76.2 - - + +
27C THR* 1.3 64.2 + - - +
29C ALA* 3.3 10.9 + - - +
30C TRP* 3.1 36.5 + - + +
19D PHE* 6.4 0.4 - - + -
20D PHE* 4.5 40.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 5.4 0.2 - - - -
32B VAL* 5.0 11.1 - - + +
35B ARG* 4.8 8.1 - - + +
36B LEU* 3.2 45.7 - - + +
23C LEU 3.0 17.4 + - - -
24C LEU* 3.8 6.7 - - - -
26C VAL* 1.3 78.5 - - - +
28C LEU* 1.3 65.5 + - + +
30C TRP* 3.3 31.5 + - + +
31C HIS* 3.1 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 6.1 0.4 - - + -
32B VAL* 5.0 4.3 - - + -
35B ARG* 3.7 32.5 - - - +
24C LEU* 3.1 49.6 + - + +
25C VAL* 3.9 5.4 - - - +
27C THR* 1.3 81.8 - - + +
29C ALA* 1.3 64.2 + - - +
31C HIS* 3.4 8.6 + - + +
32C VAL* 3.2 30.9 + - + +
24D LEU* 4.4 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL 3.3 11.7 + - - +
26C VAL 3.7 8.3 - - - +
27C THR 3.2 0.8 - - - -
28C LEU* 1.3 80.2 - - - +
30C TRP* 1.3 59.1 + - - +
32C VAL* 2.7 28.0 - - - +
33C LYS 4.3 0.2 + - - -
20D PHE* 3.0 42.0 - - + +
21D TRP* 4.9 0.7 - - - -
23D LEU* 3.9 13.9 - - + +
24D LEU* 4.0 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 3.4 36.3 - + - -
52A LEU* 5.8 0.9 - - + -
36B LEU* 3.9 19.3 - - + -
39B GLY* 2.6 39.0 + - - -
40B ALA* 4.0 8.3 - - - -
42B TYR* 3.8 26.5 - + + +
45B LEU* 5.7 4.6 - - + +
26C VAL* 3.1 36.9 + - + +
27C THR* 3.3 45.8 + - + +
29C ALA* 1.3 80.3 - - - +
31C HIS* 1.3 79.1 + - - +
33C LYS* 2.9 35.3 + - + +
19D PHE* 6.4 2.9 - - + -
20D PHE* 5.6 0.2 - - - +
23D LEU* 5.0 6.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
35B ARG* 4.7 29.4 + - + +
38B PRO* 5.5 5.8 - - + -
39B GLY* 3.8 21.9 - - - -
27C THR* 3.1 20.7 + - + +
28C LEU* 3.7 10.8 - - + +
29C ALA 3.3 0.2 - - - -
30C TRP* 1.3 84.5 - - + +
32C VAL* 1.3 60.3 + - + +
33C LYS* 2.7 32.5 + - - +
34C GLY* 3.6 3.8 + - - -
35C ARG* 4.7 7.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.2 14.8 + - + +
29C ALA* 2.7 31.9 - - - +
31C HIS* 1.3 77.2 - - + +
33C LYS* 1.3 66.1 + - - +
34C GLY 3.2 0.7 - - - -
35C ARG* 2.8 34.5 + - - +
36C LEU* 3.1 10.5 + - - +
23D LEU* 5.2 0.2 - - + -
24D LEU* 3.8 16.4 - - + -
27D THR* 3.4 25.4 - - + +
28D LEU* 5.2 4.5 - - + -
31D HIS* 3.7 22.1 - - + +
----------------------------------------------------------
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