Contacts of the helix formed by residues 38 - 50 (chain C) in PDB entry 3IKH
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 38 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASN* 3.6 11.9 - - - -
10C THR* 3.3 14.0 + - - -
37C GLY* 1.3 73.0 - - - -
39C LYS* 1.3 59.4 + - - -
40C GLY 3.2 2.9 - - - -
41C ALA 3.9 1.1 - - - -
42C ASN* 2.8 39.5 + - - -
501C GOL 3.1 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASN* 3.1 5.9 + - - +
38C GLY* 1.3 71.1 - - - +
40C GLY* 1.3 63.9 + - - +
42C ASN* 4.1 0.2 - - - +
43C GLN* 3.2 30.3 + - - +
136C GLN* 3.7 13.5 - - + -
138C ASN* 3.8 17.7 - - - +
161C ASN* 3.0 28.9 - - - +
163C SER* 3.4 36.2 + - - +
164C PRO* 4.4 5.8 - - + -
231C GLY 5.3 0.8 - - - -
232C ASP* 2.8 36.2 + - - +
501C GOL 4.1 19.3 - - - +
900C ATP 3.9 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.7 10.2 - - - +
7C GLY* 4.3 1.8 - - - -
8C ASN* 3.2 20.3 + - - -
38C GLY 3.2 0.8 - - - -
39C LYS* 1.3 82.4 - - - +
41C ALA* 1.3 61.4 + - - +
43C GLN 3.9 0.2 - - - -
44C ALA* 3.0 24.8 + - - +
56C LEU* 3.9 7.2 - - - -
136C GLN* 3.2 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASN 2.9 8.3 + - - +
9C ILE* 3.5 39.9 - - + -
36C ILE* 5.4 1.1 - - + -
37C GLY 3.5 13.9 - - - +
38C GLY 3.3 0.6 + - - -
40C GLY* 1.3 75.7 - - - +
42C ASN* 1.3 59.3 + - - +
44C ALA* 4.5 0.2 - - - -
45C ILE* 2.8 45.3 + - + +
56C LEU* 3.7 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE 4.4 0.5 - - - +
37C GLY* 3.3 19.8 - - - -
38C GLY 2.8 24.2 + - - +
39C LYS 4.1 0.2 - - - +
41C ALA* 1.3 71.9 - - - +
43C GLN* 1.3 64.7 + - - +
45C ILE* 4.0 3.2 - - - +
46C ILE* 3.1 32.5 + - - +
229C GLY* 4.6 1.2 - - - -
232C ASP* 3.0 35.0 + - + +
270C THR* 3.4 12.0 - - - +
271C LEU* 5.4 0.5 - - - +
274C PHE* 3.5 26.3 - - + -
501C GOL 3.1 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 5.2 0.2 - - + -
39C LYS 3.2 17.3 + - - +
40C GLY 4.1 1.6 - - - +
41C ALA 3.3 0.2 - - - -
42C ASN* 1.3 74.1 - - - +
44C ALA* 1.3 67.4 + - - +
47C LEU* 3.0 30.5 + - - +
134C LEU* 3.4 24.7 - - + +
136C GLN* 3.0 27.0 - - - +
161C ASN* 3.1 20.1 + - - -
232C ASP* 2.9 41.1 - - + +
235C LEU* 3.6 26.1 - - + +
236C ALA* 3.7 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.9 19.4 - - + +
40C GLY 3.0 18.6 + - - +
41C ALA 3.9 1.6 - - - +
43C GLN* 1.3 77.4 - - - +
45C ILE* 1.3 63.3 + - - +
47C LEU* 3.3 3.1 + - - +
48C SER* 3.0 24.8 + - - -
54C THR* 3.9 10.7 - - - +
56C LEU* 3.8 15.9 - - + -
78C LEU* 3.6 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 5.2 4.3 - - + -
41C ALA* 2.8 34.0 + - + +
42C ASN* 4.0 6.3 - - - +
44C ALA* 1.3 74.9 - - - +
46C ILE* 1.3 62.0 + - + +
48C SER* 2.7 23.0 + - - -
49C ARG* 2.9 26.1 + - - +
73C ILE* 3.6 25.4 - - + -
76C GLU* 3.8 28.7 - - + +
78C LEU* 3.9 16.8 - - + -
271C LEU* 3.8 33.9 - - + -
274C PHE* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ASN 3.1 17.9 + - - +
45C ILE* 1.3 74.0 - - + +
47C LEU* 1.3 67.7 + - - +
49C ARG* 3.1 10.1 + - - +
50C CYS* 3.1 22.3 + - - -
232C ASP 4.3 1.8 - - - +
233C THR* 3.3 42.0 - - + +
236C ALA* 3.5 20.4 - - + -
237C VAL* 3.8 23.8 - - + +
274C PHE* 3.8 35.4 - - + -
275C PRO* 5.1 2.0 - - + +
280C LEU* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C VAL* 3.7 28.9 - - + -
5C VAL* 4.4 4.9 - - + -
43C GLN 3.0 23.5 + - - +
44C ALA* 3.6 2.5 - - - +
46C ILE* 1.3 75.5 - - - +
48C SER* 1.3 64.0 + - - +
50C CYS* 3.0 18.0 + - - +
52C ILE* 3.2 30.7 + - + +
54C THR* 3.6 11.4 - - + +
134C LEU* 3.9 20.9 - - + -
236C ALA* 3.3 30.3 - - + +
239C LEU* 4.1 15.7 - - + -
240C ALA* 4.0 15.7 - - + +
243C LEU* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ALA 3.0 13.1 + - - -
45C ILE* 2.7 24.6 + - - +
47C LEU* 1.3 77.0 - - - +
49C ARG* 1.3 57.2 + - - +
51C GLY* 3.0 19.9 + - - -
52C ILE 3.5 15.8 + - - +
54C THR* 3.7 5.5 + - - -
76C GLU* 4.8 0.2 - - - +
77C PRO* 3.5 44.0 - - - +
78C LEU* 3.7 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 2.9 26.3 + - - +
46C ILE* 3.1 5.8 + - - +
48C SER* 1.3 78.2 + - - +
50C CYS* 1.3 58.4 + - - +
51C GLY 3.1 1.4 + - - -
76C GLU* 2.8 42.6 + - - +
77C PRO* 4.3 4.5 - - + -
271C LEU* 3.6 24.6 + - - +
274C PHE* 3.5 23.6 + - - +
275C PRO 3.0 28.2 + - - -
276C GLY* 3.9 6.1 - - - -
277C SER* 3.4 46.6 + - - +
280C LEU* 3.5 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.1 17.7 + - - -
47C LEU 3.0 11.7 + - - +
49C ARG* 1.3 76.0 - - - +
51C GLY* 1.3 59.8 + - - +
52C ILE* 4.5 0.7 - - + -
237C VAL* 4.2 13.2 - - - -
240C ALA* 3.5 32.5 - - + -
244C LEU* 3.8 19.9 - - - +
280C LEU* 3.7 24.9 - - - -
281C ALA 6.0 0.4 - - - +
284C LEU* 4.1 21.5 - - + +
----------------------------------------------------------
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