Contacts of the helix formed by residues 111 - 119 (chain A) 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 CYS 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 4.1 3.4 - - + -
54A LEU* 4.0 16.2 - - - -
57A MSE 4.0 22.4 - - + -
58A PHE* 4.0 10.3 - - + -
106A THR 3.8 1.0 + - - -
107A LYS 3.5 21.3 - - - +
108A ILE 3.1 20.2 + - - +
109A SER 3.6 0.4 - - - -
110A ARG* 1.3 77.8 - - - +
112A PRO* 1.3 73.3 - - + +
113A HIS* 4.0 0.9 - - - -
114A LEU* 3.0 32.5 + - - +
115A LEU* 3.0 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 4.7 9.4 - - + -
57A MSE 5.7 2.5 - - + -
110A ARG 3.6 4.0 - - - +
111A CYS* 1.3 85.6 - - + +
113A HIS* 1.3 52.7 + - - +
115A LEU* 3.7 12.0 - - + +
116A ASP* 2.8 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.2 56.6 + + - -
53A THR* 3.5 24.1 - - + +
54A LEU* 4.1 11.7 - - + -
57A MSE 3.7 39.6 - - + +
111A CYS* 3.0 2.6 + - - +
112A PRO* 1.3 78.0 - - - +
114A LEU* 1.3 63.4 + - - +
116A ASP* 3.6 4.9 - - - +
117A PHE* 3.0 25.6 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.1 15.5 - - + -
50A PHE* 3.6 26.0 - - + -
54A LEU* 5.1 3.1 - - + -
101A LEU* 3.9 31.2 - - + -
102A MSE 4.1 13.2 - - + -
108A ILE 3.9 11.2 - - - +
109A SER* 3.6 27.8 - - - +
111A CYS* 3.0 18.5 + - - +
113A HIS* 1.3 80.9 - - - +
115A LEU* 1.3 68.1 + - + +
117A PHE* 3.2 10.0 + - - +
118A PHE* 3.2 34.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 5.3 3.8 - - - +
4A THR* 3.3 27.1 - - + +
5A PHE* 3.8 5.2 - - + -
6A ILE* 3.7 41.1 - - + +
32A TRP* 3.7 8.1 - - + -
110A ARG* 3.6 29.8 - - - +
111A CYS 3.0 15.0 + - - +
112A PRO* 3.7 13.9 - - + +
114A LEU* 1.3 82.9 - - + +
116A ASP* 1.3 61.4 + - - +
118A PHE* 3.4 1.0 + - - +
119A LYS* 3.2 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 5.0 0.2 + - - -
112A PRO 2.8 21.4 + - - +
113A HIS* 3.6 6.5 - - - +
115A LEU* 1.3 71.8 - - - +
117A PHE* 1.3 67.5 + - - +
118A PHE 3.3 0.5 + - - -
119A LYS* 3.3 33.5 + - - +
121A ARG* 6.0 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 2.9 64.4 + - + -
46A GLU* 3.5 37.2 - - + -
47A ILE* 3.8 21.5 - - + -
50A PHE* 3.7 32.1 - + + -
113A HIS* 3.0 20.9 + + + +
114A LEU 3.2 4.7 + - - +
116A ASP* 1.3 78.0 + - - +
118A PHE* 1.3 87.9 + + - +
121A ARG* 4.2 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.7 19.5 - - + -
9A ILE* 3.8 40.6 - - + -
28A PHE* 4.3 20.2 - + + -
30A VAL* 3.9 23.4 - - + +
32A TRP* 4.0 7.8 + - - -
40A VAL* 3.5 25.2 - - + +
42A ARG* 4.1 3.8 - - + +
47A ILE* 6.2 2.0 - - + -
50A PHE* 4.4 10.8 - + - -
97A TYR* 6.2 0.7 - + - -
98A CYS* 5.3 4.3 - - - -
101A LEU* 4.5 10.5 - - + -
114A LEU* 3.2 33.3 + - + +
115A LEU 3.8 1.6 - - - +
116A ASP 3.2 0.4 - - - -
117A PHE* 1.3 104.0 - + - +
119A LYS* 1.3 61.2 + - - +
120A VAL 3.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 4.8 11.7 - - - +
32A TRP* 3.5 27.8 - - + -
40A VAL* 4.1 0.4 - - - -
42A ARG* 2.7 27.0 + - - -
115A LEU* 3.2 32.6 + - - +
116A ASP* 3.3 28.5 + - - +
117A PHE 4.1 0.3 - - - +
118A PHE* 1.3 77.7 - - - +
120A VAL* 1.3 66.5 + - - +
121A ARG* 4.1 2.8 - - - +
----------------------------------------------------------
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