Contacts of the helix formed by residues 10 - 19 (chain C) in PDB entry 1C03
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 ASN 10 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.3 28.6 + - - +
9C ILE* 1.3 70.1 - - - +
11C TRP* 1.3 63.1 + - - +
12C THR* 3.3 33.2 + - - +
13C ILE* 3.3 9.3 + - + +
14C LEU* 3.2 19.8 + - - +
74C GLY* 2.6 26.2 + - - +
76C GLN* 3.7 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU* 5.6 5.4 - - - -
9C ILE* 3.4 37.3 + - + +
10C ASN* 1.3 72.1 - - - +
12C THR* 1.3 61.5 + - + +
14C LEU* 3.4 28.7 - - + +
15C ASN* 2.8 61.5 + - - +
18C ILE* 3.7 22.7 - - + -
158C GLU* 4.9 3.2 + - - -
159C LEU* 5.3 1.3 - - + -
162C TYR* 3.6 52.5 + + + -
163C TYR* 5.7 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 4.5 8.7 + - - +
13A ILE* 4.8 0.9 - - - +
16A GLU* 3.6 22.3 + - - +
10C ASN* 3.2 17.7 + - - +
11C TRP* 1.3 79.2 - - + +
13C ILE* 1.3 60.4 + - - +
15C ASN* 4.7 3.5 - - - +
16C GLU* 2.8 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 4.8 0.2 - - - +
13A ILE* 4.0 28.2 - - + +
16A GLU* 3.4 42.2 - - + +
17A ILE* 4.7 9.0 - - + -
10C ASN* 3.3 13.2 + - - +
11C TRP 3.2 0.2 - - - -
12C THR* 1.3 82.8 + - - +
14C LEU* 1.3 65.9 + - - +
15C ASN 3.3 0.4 - - - -
16C GLU* 3.2 15.2 + - - +
17C ILE* 3.5 12.5 + - + +
71C ALA 3.6 17.9 - - - +
72C ALA* 3.5 24.0 - - - +
74C GLY* 3.9 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 3.5 20.4 - - + -
10C ASN 3.2 14.4 + - - +
11C TRP* 3.4 36.1 - - + -
13C ILE* 1.3 78.7 - - - +
15C ASN* 1.3 61.5 + - - +
17C ILE* 3.1 16.8 + - + +
18C ILE* 2.9 44.6 + - + +
28C SER* 5.6 1.3 - - - -
32C ILE* 5.2 8.3 - - + -
73C LEU* 3.5 29.4 - - + +
159C LEU* 4.1 17.3 - - + -
163C TYR* 4.8 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TRP* 2.8 50.4 + - - +
12C THR* 4.7 5.2 - - - +
14C LEU* 1.3 76.4 - - - +
16C GLU* 1.3 60.8 + - - +
18C ILE* 3.4 11.3 + - - +
19C SER* 2.8 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 3.3 24.5 + - - +
12A THR* 3.6 20.0 + - - +
13A ILE* 3.5 25.1 - - + +
12C THR* 2.8 21.8 - - - +
13C ILE 3.2 4.8 + - - +
14C LEU 3.2 0.8 - - - -
15C ASN* 1.3 80.4 - - - +
17C ILE* 1.3 64.8 + - - +
19C SER* 3.9 16.8 - - - +
20C MET* 4.2 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.6 5.2 - - + -
68A GLY 5.4 0.4 - - - +
71A ALA* 4.1 33.9 - - + +
72A ALA* 4.6 5.6 - - + +
13C ILE 3.7 13.7 - - - +
14C LEU* 3.1 19.2 + - + +
16C GLU* 1.3 75.2 - - - +
18C ILE* 1.3 65.2 + - - +
19C SER 3.3 0.2 - - - -
20C MET* 3.3 10.8 + - - +
21C ASP 4.2 0.2 + - - -
27C PHE* 3.7 24.5 - - + -
28C SER* 4.2 14.8 - - - -
31C LEU* 3.8 30.1 - - + -
72C ALA 4.2 20.6 - - - +
73C LEU* 5.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TRP* 3.7 33.2 - - + -
14C LEU* 2.9 24.5 + - + +
15C ASN* 3.7 12.6 - - - +
17C ILE* 1.3 73.9 - - - +
19C SER* 1.3 55.5 + - - +
20C MET 2.9 2.2 - - - -
21C ASP* 2.7 48.2 + - + +
22C ASP* 4.9 1.4 - - - +
28C SER* 4.3 5.6 - - - +
162C TYR* 6.4 0.4 - - + -
163C TYR* 3.8 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASN* 2.8 23.2 + - - +
16C GLU* 3.9 15.6 - - - +
18C ILE* 1.3 75.8 - - - +
20C MET* 1.3 60.3 + - - +
21C ASP 3.2 0.3 + - - -
22C ASP* 3.0 34.1 - - - +
----------------------------------------------------------
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