Contacts of the helix formed by residues 17 - 27 (chain C) in PDB entry 2M3X
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 ASP 17 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PRO* 3.3 20.5 - - - +
16C PRO* 1.3 74.8 - - + +
18C PHE* 1.3 65.7 + - - +
19C VAL 3.2 2.9 - - - -
20C ASP* 3.1 24.8 + - + +
21C VAL* 3.3 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 3.5 41.3 - - + -
15C PRO* 3.1 32.6 + - + +
17C ASP* 1.3 81.3 + - - +
19C VAL* 1.3 68.1 + - + +
21C VAL* 3.1 18.5 + - + +
22C ILE* 3.2 46.7 + - + +
39C ILE* 4.9 0.9 - - + -
41C ILE* 3.9 37.9 - - + -
46C VAL* 5.1 0.7 - - + -
48C PHE* 3.7 32.3 - + - -
68C LEU* 5.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO 4.5 9.2 - - - +
17C ASP 3.2 0.6 - - - -
18C PHE* 1.3 79.6 - - + +
20C ASP* 1.3 69.4 + - - +
22C ILE* 3.3 8.2 + - - +
23C ARG* 3.2 21.3 + - + +
66C ILE* 4.4 34.5 - - + +
68C LEU* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO 4.1 5.0 - - - +
17C ASP* 3.1 23.2 + - + +
19C VAL* 1.3 81.2 - - - +
21C VAL* 1.3 63.7 + - + +
23C ARG* 3.3 23.4 + - - +
24C ILE* 3.2 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASP* 3.4 26.5 - - + +
18C PHE* 3.1 10.9 + - + +
20C ASP* 1.3 77.9 - - + +
22C ILE* 1.3 66.7 + - + +
24C ILE* 3.2 22.7 + - + +
25C LYS* 3.2 38.2 + - - +
41C ILE* 6.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 4.7 14.8 - - + -
18C PHE* 3.2 41.9 + - + +
19C VAL* 3.3 8.0 + - - +
21C VAL* 1.3 79.5 - - + +
23C ARG* 1.3 62.2 + - - +
25C LYS* 3.1 12.6 + - + +
26C LEU* 3.0 49.4 + - + +
39C ILE* 3.3 36.3 - - + -
48C PHE* 5.4 0.7 - - + -
66C ILE* 5.0 7.0 - - + -
68C LEU* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C VAL* 3.2 8.7 + - + +
20C ASP* 3.6 24.3 + - - +
22C ILE* 1.3 78.1 - - - +
24C ILE* 1.3 69.2 + - - +
26C LEU* 3.2 4.7 + - - +
27C GLN* 3.2 26.5 + - + +
60C VAL* 4.6 4.9 - - + +
61C GLU 4.9 6.5 - - - +
62C ASP* 3.5 44.9 + - - +
64C THR 4.5 8.4 + - - -
66C ILE* 3.7 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASP* 3.2 23.1 - - + +
21C VAL* 3.2 14.5 + - + +
23C ARG* 1.3 82.1 - - + +
25C LYS* 1.3 66.2 + - + +
27C GLN* 3.3 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 3.2 34.7 + - + +
22C ILE* 3.1 15.5 + - + +
24C ILE* 1.3 80.8 - - + +
26C LEU* 1.3 64.5 + - + +
27C GLN 4.1 1.9 - - - +
29C LYS* 3.0 25.3 + - - -
39C ILE* 5.4 17.0 - - + -
41C ILE* 6.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 5.9 5.2 - - + -
6C LEU* 5.0 10.8 - - + -
22C ILE* 3.0 44.9 + - + +
23C ARG* 4.0 2.7 - - - +
25C LYS* 1.3 78.8 - - + +
27C GLN* 1.3 70.1 + - - +
29C LYS* 3.1 32.3 + - + +
31C VAL* 4.9 13.5 - - + -
37C ILE* 4.1 29.2 - - + -
60C VAL* 3.8 24.5 - - + +
66C ILE* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ARG* 3.2 12.6 + - + +
24C ILE* 3.3 37.9 + - - +
25C LYS 4.1 4.5 - - - +
26C LEU* 1.3 78.2 - - - +
28C GLY* 1.3 59.3 + - - +
29C LYS* 3.6 4.7 + - - -
60C VAL* 3.4 22.6 - - + +
61C GLU* 4.7 9.2 - - - -
62C ASP* 3.5 29.0 + - - +
----------------------------------------------------------
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