Contacts of the helix formed by residues 49 - 64 (chain O) in PDB entry 2I2R
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 49 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASN* 4.7 4.3 - - + -
38B GLN* 6.1 6.3 - - + -
212F PHE* 6.6 0.2 - - + -
214F ASN* 3.9 30.3 - - - +
216F MET* 5.2 10.3 - - + -
43O GLU* 3.5 9.2 - - - +
47O ASN 5.6 1.1 - - - +
48O PHE* 1.3 76.5 - - - +
50O LYS* 1.3 67.5 + - - +
51O ARG* 3.9 9.1 + - - +
52O GLU* 3.1 34.1 + - - +
53O LEU* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 5.6 8.6 - - - +
38B GLN* 6.6 0.2 - - + -
77L GLU* 5.5 8.7 + - - +
39O LEU* 3.9 35.9 - - + +
40O GLU* 3.1 39.6 + - - +
43O GLU* 3.1 37.4 + - + +
49O THR* 1.3 73.3 - - - +
51O ARG* 1.3 64.1 + - - +
53O LEU* 3.4 3.3 + - - +
54O GLN* 3.0 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASP* 5.7 4.2 + - - -
51F ARG* 4.4 38.7 - - - +
38K GLN* 5.1 10.5 - - - +
77L GLU* 5.2 9.5 - - - +
78L ASP* 4.7 20.0 + - - -
49O THR* 3.9 10.0 + - - +
50O LYS* 1.3 81.2 - - - +
52O GLU* 1.3 65.0 + - + +
54O GLN* 3.3 19.0 + - - +
55O VAL* 3.4 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O ASN 4.1 0.2 - - - +
48O PHE* 3.3 25.1 - - + -
49O THR* 3.1 36.7 + - - +
51O ARG* 1.3 79.5 - - + +
53O LEU* 1.3 67.2 + - - +
55O VAL* 3.0 11.1 + - - +
56O LEU* 2.9 28.0 + - + +
120O ARG* 2.9 31.5 + - - -
214O ASN* 5.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73L PHE* 4.3 2.8 - - + -
39O LEU* 3.8 13.9 - - + -
42O LEU* 3.7 34.3 - - + +
43O GLU* 3.6 31.2 - - + +
46O THR* 4.6 1.8 - - - +
48O PHE* 3.7 29.4 - - + +
49O THR 2.9 20.2 + - - +
50O LYS 3.7 4.3 - - - +
52O GLU* 1.3 76.7 - - - +
54O GLN* 1.3 57.8 + - - +
56O LEU* 3.6 6.3 - - - +
57O TYR* 2.8 29.6 + - - +
108O PHE* 4.2 5.0 - - + -
112O VAL* 4.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L GLU 3.0 26.3 + - - -
73L PHE* 3.6 29.9 + - + +
75L PHE* 3.1 24.3 + - - +
39O LEU* 4.4 12.0 - - + +
50O LYS* 3.0 20.8 + - - +
51O ARG* 3.4 14.6 - - - +
52O GLU 3.1 0.2 - - - -
53O LEU* 1.3 73.0 - - - +
55O VAL* 1.3 62.1 + - + +
57O TYR* 3.2 2.1 + - - +
58O ARG* 2.8 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K GLY* 5.9 1.1 - - - -
38K GLN* 6.0 2.7 - - - +
51O ARG* 3.6 19.3 - - + +
52O GLU* 3.0 10.4 + - - +
54O GLN* 1.3 75.0 - - + +
56O LEU* 1.3 61.1 + - + +
58O ARG* 3.2 30.7 + - - +
59O GLY* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K ALA* 3.8 29.6 - - + +
48O PHE* 3.6 44.4 - - + -
52O GLU* 2.9 22.4 + - + +
53O LEU* 3.6 8.7 - - - +
55O VAL* 1.3 78.2 - - + +
57O TYR* 1.3 56.9 + - - +
59O GLY* 3.0 4.3 + - - -
60O PHE* 2.8 27.7 + - - +
108O PHE* 4.0 3.3 - - + -
111O PHE* 4.6 6.4 - - + -
112O VAL* 4.5 15.5 - - + -
115O LEU* 4.1 22.9 - - + -
119O LEU* 5.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L GLU* 2.3 37.5 + - + +
73L PHE* 3.6 46.0 - + + -
74L PHE* 3.9 13.7 - + - -
53O LEU 2.8 21.1 + - - +
54O GLN 3.6 4.3 - - - +
56O LEU* 1.3 71.7 - - - +
58O ARG* 1.3 53.9 + - + +
60O PHE* 3.2 6.1 + + - +
61O LYS* 2.7 61.3 + - + +
67O GLY* 5.5 4.7 - - - -
108O PHE* 3.3 47.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K TRP* 3.5 53.8 - - - +
73L PHE 4.1 13.6 + - - +
74L PHE* 4.1 33.8 - - + +
83L PHE* 5.4 3.6 - - - -
54O GLN* 2.8 25.5 + - - +
55O VAL* 3.7 34.6 + - - +
57O TYR* 1.3 73.1 - - + +
59O GLY* 1.3 61.7 + - - +
61O LYS* 4.1 5.3 - - - +
62O ASN* 2.7 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K GLY* 4.1 31.5 - - - +
7K ALA* 5.9 1.6 - - - -
8K TRP* 4.8 1.6 - - - -
55O VAL 2.9 14.1 + - - -
56O LEU* 3.3 5.4 - - - -
58O ARG* 1.3 75.9 - - - +
60O PHE* 1.3 61.2 + - - +
62O ASN* 3.2 13.6 + - - +
63O GLU* 3.3 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K TRP* 4.1 17.0 - + - +
56O LEU 2.8 11.8 + - - +
57O TYR* 3.5 12.8 - + - +
59O GLY* 1.3 67.8 - - - +
61O LYS* 1.3 62.7 + - + +
62O ASN 2.8 10.9 + - - -
63O GLU* 2.9 12.7 + - - +
64O CYS* 3.1 18.3 + - - +
67O GLY* 3.6 30.1 - - - -
69O VAL* 3.5 33.2 - - + -
106O VAL* 5.1 1.1 - - + -
107O LYS 4.4 2.2 - - - -
108O PHE* 3.4 48.2 - + + -
111O PHE* 3.8 45.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L LEU* 4.2 2.7 - - + +
70L GLU* 2.8 24.1 + - - +
74L PHE* 4.4 7.9 - - + -
119L ALA 4.0 1.6 + - - -
120L PHE* 2.4 64.6 + - + +
122L GLY* 5.7 0.4 - - - -
57O TYR* 2.7 50.8 + - + +
58O ARG* 4.2 5.8 - - - +
60O PHE* 1.3 76.1 - - + +
62O ASN* 1.3 57.9 + - - +
64O CYS 3.3 14.1 - - - +
65O PRO* 3.0 35.3 + - - +
67O GLY* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 62 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L PHE* 6.2 1.6 - - - -
86L ARG* 4.4 19.2 + - - +
120L PHE* 4.5 10.1 - - - -
58O ARG* 2.7 29.1 + - - +
59O GLY* 3.2 5.5 + - - +
60O PHE 2.9 1.0 - - - -
61O LYS* 1.3 81.4 - - - +
63O GLU* 1.3 71.6 + - - +
64O CYS* 3.3 3.6 + - - -
65O PRO* 4.5 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K ALA 5.8 1.4 + - - -
4K GLY* 4.9 5.2 + - - +
5K VAL* 4.7 17.7 + - - +
8K TRP* 3.3 46.2 - - + +
60K ARG* 5.9 0.7 + - - -
59O GLY 3.3 8.8 + - - +
60O PHE 2.9 4.4 + - - +
62O ASN* 1.3 84.3 - - - +
64O CYS* 1.3 61.9 + - - +
65O PRO* 4.6 0.8 - - - +
73O THR* 5.2 1.7 - - - +
76O GLN* 5.5 2.6 + - - -
77O ILE* 4.0 32.6 - - + +
80O GLN* 4.0 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 64 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K TRP* 6.0 0.9 - - - -
60O PHE* 3.1 20.6 + - - +
61O LYS* 3.3 13.8 - - - +
63O GLU* 1.3 79.0 - - - +
65O PRO* 1.3 70.4 - - + +
66O SER* 3.9 15.7 - - - -
67O GLY* 3.6 16.8 + - - -
68O VAL 4.2 5.2 - - - -
69O VAL* 3.5 32.8 - - - -
73O THR* 4.5 17.9 - - + -
77O ILE* 5.1 1.3 - - + -
----------------------------------------------------------
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