Contacts of the helix formed by residues 46 - 54 (chain I) in PDB entry 6I3N
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 46 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LEU* 3.6 15.5 - - - +
39I VAL 3.3 23.3 - - - +
40I ARG* 3.4 21.5 + - - +
41I THR* 3.3 28.5 + - + +
44I ALA 3.5 1.4 + - - -
45I ALA* 1.3 78.6 - - - +
47I TRP* 1.3 67.1 + - + +
48I THR* 2.7 15.5 + - - +
49I ALA* 3.3 9.0 + - - +
50I LEU* 3.5 7.1 + - - +
96I LEU* 4.7 0.5 - - - +
98I ARG* 4.1 5.6 - - - +
31L ARG* 2.6 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LEU* 2.8 40.2 + - + +
38I ASN* 3.5 19.9 + - + +
40I ARG* 3.9 14.9 - - + +
46I ASP* 1.3 80.4 + - + +
48I THR* 1.3 69.3 + - + +
49I ALA 3.4 0.2 - - - -
50I LEU* 3.4 4.7 + - - +
51I ALA* 2.9 25.2 + - + +
61I ILE* 3.5 36.3 - - + -
64I LEU* 3.9 19.7 - - + -
65I GLU* 3.5 29.4 - - + -
70I PRO* 3.5 32.3 - - + +
71I THR* 3.6 17.0 - - + +
74I LEU* 3.6 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 48 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I ARG* 3.4 29.8 - - - +
46I ASP* 2.7 7.7 + - - +
47I TRP* 1.3 95.4 - - + +
49I ALA* 1.3 59.6 + - - +
51I ALA* 3.6 5.0 - - - +
52I GLU* 2.9 28.2 + - - +
61I ILE* 3.8 18.4 - - + +
65I GLU* 4.3 2.7 - - - +
27L MET* 4.1 19.6 - - + +
31L ARG* 2.6 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I ALA* 3.8 27.4 - - + -
46I ASP 3.3 10.1 + - - +
48I THR* 1.3 81.4 + - - +
50I LEU* 1.3 58.2 + - - +
52I GLU* 3.3 11.4 + - - +
53I GLU* 3.0 31.4 + - - +
96I LEU* 3.9 11.9 - - + -
27L MET* 5.8 0.2 - - - -
31L ARG* 4.2 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 6.5 0.4 - - + -
37I LEU* 4.5 14.4 - - + -
46I ASP 3.5 5.1 + - - +
47I TRP* 3.4 11.2 + - - +
48I THR 3.3 0.2 - - - -
49I ALA* 1.3 79.0 - - - +
51I ALA* 1.3 61.9 + - - +
53I GLU* 3.2 4.6 + - + +
54I MET* 3.1 48.6 + - + +
71I THR* 5.6 4.5 - - + -
74I LEU* 4.5 7.9 - - + -
75I LEU* 5.5 4.7 - - + -
89I LEU* 4.4 14.4 - - + -
92I LEU* 4.1 25.8 - - + -
93I LEU* 4.1 24.5 - - + -
96I LEU* 3.7 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I TRP* 2.9 24.1 + - + +
48I THR* 3.6 9.0 - - - +
49I ALA 3.3 0.2 - - - -
50I LEU* 1.3 76.3 - - - +
52I GLU* 1.3 61.5 + - - +
54I MET* 3.4 12.5 + - - +
56I PHE* 3.2 30.6 + - + +
61I ILE* 3.7 22.7 - - + -
74I LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I THR 2.9 16.8 + - - +
49I ALA* 3.6 8.9 - - - +
50I LEU 3.3 0.2 - - - -
51I ALA* 1.3 77.0 - - - +
53I GLU* 1.3 67.0 + - - +
55I ASP* 3.2 16.5 + - - +
56I PHE 4.4 4.8 + - - +
61I ILE* 4.0 10.7 - - + +
26L ASN* 2.6 41.0 + - + +
27L MET* 3.6 8.4 - - + +
28L ARG* 3.0 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ALA 3.0 18.4 + - - +
50I LEU* 3.2 12.5 + - + +
52I GLU* 1.3 80.2 - - + +
54I MET* 1.3 57.7 + - - +
55I ASP* 3.3 8.0 + - - +
88I ARG* 4.6 8.0 + - - -
92I LEU* 4.0 27.3 - - + +
95I LYS* 3.4 30.0 + - + +
96I LEU* 3.7 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I LEU* 3.1 36.0 + - + +
51I ALA* 3.9 0.2 - - - -
52I GLU 3.1 1.4 - - - -
53I GLU* 1.3 74.8 - - - +
55I ASP* 1.3 70.5 + - - +
56I PHE* 3.3 20.8 + - + -
74I LEU* 3.6 41.7 - - + +
75I LEU* 5.5 2.7 - - + -
78I TRP* 3.4 54.1 + - + +
81I ARG* 3.8 9.9 + - - -
88I ARG* 6.0 0.9 - - - +
89I LEU* 4.9 4.3 - - - -
92I LEU* 3.7 21.3 - - + -
----------------------------------------------------------
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