Contacts of the helix formed by residues 56 - 69 (chain C) in PDB entry 3EO1
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 THR 56 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA* 4.1 1.3 - - - +
55C ASP* 1.3 89.8 + - - +
57C THR* 1.3 66.1 + - - +
58C HIS* 3.0 9.7 - - - +
59C SER* 3.0 21.8 + - - -
60C THR* 2.8 25.7 + - - -
112C SER* 5.2 0.5 + - - -
80F PRO* 5.6 1.0 - - - +
83F LEU* 4.0 11.2 - - + +
103F ASN* 3.4 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 1.3 73.6 - - - +
58C HIS* 1.3 52.8 + - - +
60C THR* 2.9 8.9 + - - -
61C VAL* 2.7 41.3 + - + +
54E ILE* 3.4 41.2 + - + +
55E VAL* 4.1 12.6 - - + +
30F TRP* 5.0 0.4 - - + -
102F SER 3.5 13.0 + - - -
103F ASN* 3.7 9.3 + - - +
104F MET* 4.0 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 3.9 0.9 - - - +
57C THR* 1.3 80.4 - - - +
59C SER* 1.3 59.9 + - - +
60C THR 2.9 0.3 + - - -
61C VAL* 3.0 6.7 + - - +
62C LEU* 2.8 57.2 + - + +
112C SER 6.1 0.6 - - - -
39F TYR* 5.3 0.7 - - - -
41F ALA* 4.1 7.6 - - + +
42F ASN 2.5 30.7 + - - -
43F PHE* 4.5 4.0 - - + -
80F PRO* 4.7 9.9 - - + +
83F LEU* 3.6 20.4 - - + +
103F ASN 3.3 16.3 + - - +
104F MET* 3.2 27.3 - - - +
105F VAL* 4.3 0.9 - - - -
106F VAL* 3.1 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA* 4.2 4.5 - - - +
55C ASP* 3.5 16.9 - - - +
56C THR* 3.0 21.0 + - - -
58C HIS* 1.3 82.6 + - - +
60C THR* 1.3 60.2 + - - +
62C LEU* 4.1 3.6 - - - -
63C GLY* 3.4 15.2 + - - -
76C PRO* 4.0 14.2 - - - +
111C CYS* 3.2 22.0 - - - +
112C SER* 3.4 24.1 + - - -
80F PRO* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 4.8 3.0 - - + -
51C LEU* 3.8 21.9 + - + +
54C ALA* 3.1 17.8 - - + +
56C THR 2.8 15.6 + - - -
57C THR* 2.9 9.7 + - - -
58C HIS 2.9 0.4 - - - -
59C SER* 1.3 77.3 - - - +
61C VAL* 1.3 61.4 + - - +
63C GLY* 2.8 17.5 + - - -
64C LEU* 3.0 13.2 + - - +
54E ILE* 3.4 40.5 + - + +
74E GLU* 4.1 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C THR* 2.7 30.8 + - + +
58C HIS* 3.8 4.0 - - + +
60C THR* 1.3 72.0 - - - +
62C LEU* 1.3 62.3 + - + +
64C LEU* 3.5 6.7 + - - +
65C TYR* 3.0 21.7 + - - +
54E ILE* 4.1 17.0 - - + -
22F ILE* 3.7 21.5 - - + -
28F LEU* 3.3 33.7 - - + +
30F TRP* 4.5 12.8 - - + -
39F TYR* 3.8 18.4 - - - +
104F MET* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C HIS* 2.8 50.7 + - + +
59C SER* 4.4 4.7 - - - +
61C VAL* 1.3 74.7 - - + +
63C GLY* 1.3 57.6 + - - +
65C TYR* 4.1 6.1 - - + -
66C ASN* 3.0 29.1 + - - +
74C ALA* 2.9 46.0 - - + +
76C PRO* 4.2 10.5 - - + -
20F LEU* 4.1 11.2 - - + -
22F ILE* 4.1 22.7 - - + -
41F ALA* 4.9 0.4 - - + -
42F ASN 3.6 10.3 - - - +
43F PHE* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C CYS 5.3 3.4 - - - -
49C PRO 5.9 0.2 - - - -
50C TYR* 4.3 12.6 + - - -
51C LEU 5.6 1.3 - - - -
59C SER 3.4 10.9 + - - -
60C THR 2.8 11.0 + - - -
62C LEU* 1.3 78.7 - - - +
64C LEU* 1.3 58.5 + - - -
66C ASN* 3.9 2.5 - - - +
67C THR* 2.7 32.3 + - - -
76C PRO* 4.2 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 3.8 34.0 - - + +
60C THR 3.0 8.7 + - - +
61C VAL* 3.5 7.6 + - - +
63C GLY* 1.3 73.7 - - - +
65C TYR* 1.3 65.1 + - - +
67C THR* 3.1 8.0 - - + -
68C LEU* 3.0 43.7 - - + +
30E SER* 4.6 18.6 - - - -
31E SER* 5.7 0.7 - - - +
54E ILE* 6.2 0.9 - - + -
27F ASP 4.3 4.9 - - - +
28F LEU* 3.9 42.4 - - + +
30F TRP* 4.9 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL 3.0 18.6 + - - +
62C LEU* 3.5 15.5 - - + +
63C GLY 3.1 0.2 - - - -
64C LEU* 1.3 77.0 - - - +
66C ASN* 1.3 62.5 + - - +
68C LEU* 2.7 21.8 + - - -
69C ASN* 3.0 41.4 + - + +
72C ALA* 4.0 24.2 - - + +
74C ALA* 4.6 4.7 - - + -
20F LEU* 3.4 43.2 - - + +
21F TYR 4.8 6.8 + - - -
22F ILE* 4.5 12.1 - - + -
27F ASP* 4.2 34.8 - - + -
28F LEU* 4.9 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU 3.0 11.6 + - - +
63C GLY* 4.1 2.7 - - - +
65C TYR* 1.3 82.9 - - - +
67C THR* 1.3 62.5 + - - +
69C ASN 3.8 15.7 + - - -
70C PRO* 3.3 30.6 + - - +
73C SER* 4.4 1.0 - - - +
74C ALA* 3.5 38.9 - - - +
75C SER* 3.1 28.7 - - - +
76C PRO* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 3.6 31.9 + - + +
63C GLY 2.7 18.2 + - - -
64C LEU* 3.1 16.4 - - + -
65C TYR 2.8 1.2 + - - -
66C ASN* 1.3 81.4 - - - +
68C LEU* 1.3 67.1 + - + +
70C PRO* 3.8 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.0 35.7 - - + +
65C TYR* 2.7 5.4 + - - +
67C THR* 1.3 87.6 - - + +
69C ASN* 1.3 69.1 + - - +
70C PRO* 3.2 12.7 - - - +
26F GLN 5.4 5.2 - - - +
27F ASP* 4.5 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C TYR* 3.0 43.7 + - + +
66C ASN* 3.5 10.3 + - - -
68C LEU* 1.3 90.5 + - - +
70C PRO* 1.3 63.5 - - - +
71C GLU 3.1 3.8 - - - -
72C ALA* 3.0 32.0 + - + +
27F ASP* 5.1 5.0 + - - +
----------------------------------------------------------
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