Contacts of the helix formed by residues 43 - 58 (chain C) in PDB entry 1O7K
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 ARG 43 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PRO* 3.9 18.4 - - - +
23C HIS* 3.1 61.6 + - + +
24C TYR 3.8 10.8 - - - +
25C VAL* 3.8 4.9 - - + +
42C ARG* 1.3 74.7 - - - +
44C PHE* 1.3 67.1 + - - +
45C THR* 4.3 2.9 - - - +
46C GLU* 3.0 42.9 + - + +
47C ILE* 3.0 11.4 + - - +
1124C SO4 3.3 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR 4.6 0.6 + - - -
26C TYR* 4.2 10.8 - - + -
42C ARG 4.0 0.6 + - - -
43C ARG* 1.3 73.4 - - - +
45C THR* 1.3 64.5 + - - +
47C ILE* 3.2 8.7 + - + +
48C TYR* 2.9 23.4 + - + +
75C LEU* 4.2 19.1 - - + -
76C PRO 3.5 25.8 - - - -
78C PRO* 3.9 31.2 - - + -
81C PHE* 3.7 14.1 - + - -
90C ARG* 3.6 41.3 - - + +
93C THR* 5.0 0.9 - - + -
94C LEU* 4.1 36.3 - - + -
1124C SO4 3.3 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 5.0 2.9 - - - -
44C PHE* 1.3 76.1 - - - +
46C GLU* 1.3 59.9 + - + +
48C TYR* 3.3 7.0 + - - +
49C GLU* 3.0 38.7 + - + +
78C PRO* 4.5 14.3 - - + +
1124C SO4 2.8 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR 4.5 0.2 - - - +
42C ARG* 3.7 4.5 - - - -
43C ARG* 3.0 47.4 + - + +
45C THR* 1.3 81.6 - - + +
47C ILE* 1.3 56.8 + - - +
49C GLU* 3.3 8.3 + - - +
50C PHE* 3.0 26.3 + - - +
117C PHE* 3.8 12.7 - - + -
121C ARG* 3.3 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 4.5 0.7 - - + -
28C PHE* 3.7 27.4 - - + -
42C ARG* 3.8 25.1 - - + +
43C ARG 3.0 14.6 + - - +
44C PHE* 3.5 13.9 - - + +
46C GLU* 1.3 72.7 - - - +
48C TYR* 1.3 61.0 + - - +
50C PHE* 3.2 9.1 + - + +
51C HIS* 2.9 26.5 + - - +
75C LEU* 4.1 13.2 - - + -
94C LEU* 3.9 33.9 - - + -
97C TYR* 4.8 10.8 - - + -
117C PHE* 3.8 15.5 - - + -
118C PHE* 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PHE* 2.9 20.7 + + + +
45C THR* 3.6 8.5 - - - +
47C ILE* 1.3 76.8 - - - +
49C GLU* 1.3 63.2 + - - +
51C HIS* 3.1 14.4 + + - +
52C LYS* 3.0 58.3 + - + +
75C LEU* 3.7 30.9 + - + -
76C PRO 3.9 10.5 - - - -
77C ALA* 3.5 31.3 + - + +
78C PRO* 3.8 23.8 - - + -
1125C SO4 4.3 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 3.0 26.3 + - + +
46C GLU* 3.6 10.5 - - - +
48C TYR* 1.3 78.2 - - + +
50C PHE* 1.3 64.1 + - - +
52C LYS* 3.5 26.9 + - - +
53C THR* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU 3.0 14.1 + - - +
47C ILE* 3.3 13.7 - - + +
49C GLU* 1.3 75.1 - - - +
51C HIS* 1.3 61.7 + - - +
54C LEU* 3.0 36.6 + - + +
97C TYR* 4.0 20.2 - + - -
101C LEU* 4.1 15.9 - - + -
113C HIS* 3.1 53.9 + + - -
114C LEU* 3.7 41.5 - - + -
117C PHE* 3.7 42.0 - + + -
118C PHE* 4.6 8.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE 2.9 13.3 + - - +
48C TYR* 3.1 17.9 + + - +
50C PHE* 1.3 76.1 - - - +
52C LYS* 1.3 70.0 + - + +
54C LEU* 3.4 5.4 + - - +
55C LYS* 3.1 42.7 + - + +
70C ARG* 4.1 1.6 - - - -
72C ILE* 4.3 7.1 - - + +
73C PRO 3.2 26.9 - - - -
75C LEU* 3.8 22.7 - - + +
97C TYR* 2.8 37.3 + + - +
1125C SO4 3.3 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TYR* 3.0 47.5 + - + +
49C GLU* 3.8 26.8 + - - +
51C HIS* 1.3 81.7 - - + +
53C THR* 1.3 62.2 + - - +
55C LYS* 3.3 13.9 + - + +
56C GLU* 3.2 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 3.1 20.1 + - - +
52C LYS* 1.3 74.6 - - - +
54C LEU* 1.3 65.7 + - - +
56C GLU* 3.2 13.4 + - + +
57C MSE 3.0 31.1 + - + +
113C HIS* 3.3 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PHE* 3.0 28.8 + - + +
51C HIS* 3.6 5.8 - - - +
52C LYS 3.3 0.2 - - - -
53C THR* 1.3 74.7 - - - +
55C LYS* 1.3 63.0 + - - +
57C MSE 3.3 3.8 + - - -
58C PHE* 3.1 43.6 + - + +
72C ILE* 4.3 21.8 - - + -
97C TYR* 4.5 6.7 - - - +
101C LEU* 4.0 26.7 - - + -
108C ILE* 4.2 15.7 - - + +
111C CYS* 3.9 28.5 - - - -
113C HIS* 3.8 16.4 + - + -
114C LEU* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C HIS* 3.1 37.8 + - + +
52C LYS* 3.4 15.7 - - - +
54C LEU* 1.3 77.7 - - - +
56C GLU* 1.3 59.2 + - + +
58C PHE 3.1 26.5 + - - +
59C PRO* 3.4 2.9 - - - +
62C ALA* 3.5 28.7 - - + +
70C ARG* 4.1 11.0 - - - +
72C ILE* 4.3 17.5 - - + -
1125C SO4 3.2 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LYS* 3.2 27.2 + - - +
53C THR* 3.2 16.4 + - - +
55C LYS* 1.3 76.8 - - + +
57C MSE 1.3 63.9 + - - +
59C PRO* 3.7 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C THR* 3.0 22.0 + - + +
54C LEU* 3.4 9.2 - - - +
56C GLU* 1.3 77.0 - - - +
58C PHE* 1.3 87.2 + - + +
59C PRO* 3.4 6.9 - - - +
111C CYS* 5.1 2.2 - - + -
112C PRO* 6.4 2.0 - - + -
113C HIS* 3.5 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.1 34.7 + - + +
55C LYS 3.2 4.0 - - - -
57C MSE 1.3 101.6 - - + +
59C PRO* 1.3 60.1 - - - +
60C ILE 3.2 3.0 + - - -
61C GLU* 3.3 21.7 + - - +
62C ALA* 2.8 27.5 + - - +
72C ILE* 4.2 10.1 - - + -
107C LYS* 3.7 39.5 - - + -
108C ILE* 3.7 25.6 - - + -
111C CYS* 3.9 27.1 - - + -
----------------------------------------------------------
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