Contacts of the helix formed by residues 104 - 115 (chain A) in PDB entry 1ORI
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 ILE 104 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 4.6 10.0 - - + +
42A PHE* 5.4 8.1 - - + -
45A HIS* 3.9 33.9 - - + +
80A GLY* 3.6 19.3 - - - +
81A THR* 4.3 11.9 - - + +
100A GLU* 3.6 24.2 - - + +
102A SER* 3.0 17.5 + - - +
103A SER* 1.3 79.6 + - - +
105A SER* 1.3 59.4 + - - +
107A TYR* 2.8 43.3 + - + +
108A ALA 3.0 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 3.6 33.2 - - - -
102A SER 3.6 3.8 + - - -
103A SER 3.0 0.6 - - - -
104A ILE* 1.3 82.8 - - - +
106A ASP* 1.3 66.0 + - - +
108A ALA* 3.1 11.3 + - - +
109A VAL* 3.0 29.8 + - - +
123A ILE* 4.0 14.5 - - - +
125A LYS* 3.5 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 3.5 14.0 - - - +
104A ILE 3.2 0.8 - - - -
105A SER* 1.3 79.8 + - - +
107A TYR* 1.3 68.6 + - + +
109A VAL* 3.4 15.0 - - - +
110A LYS* 3.2 25.1 - - - +
125A LYS* 3.2 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 4.1 13.9 - - - -
104A ILE* 2.8 30.8 + - + +
106A ASP* 1.3 82.2 - - + +
108A ALA* 1.3 68.4 + - - +
109A VAL 3.0 1.8 - - - -
110A LYS* 2.9 30.3 + - + +
111A ILE* 2.8 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 5.4 0.9 - - - +
80A GLY 3.5 23.3 + - - +
81A THR* 3.5 22.7 - - - +
82A GLY* 4.2 2.9 - - - +
100A GLU* 6.2 0.2 - - + -
104A ILE 3.0 5.9 + - - -
105A SER* 3.4 13.5 - - - +
107A TYR* 1.3 73.5 - - - +
109A VAL* 1.3 53.4 + - - +
111A ILE* 3.2 2.6 + - - +
112A VAL* 2.7 39.0 + - - +
123A ILE* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER* 3.0 18.3 + - - +
106A ASP* 3.4 13.5 - - - +
107A TYR 3.0 0.2 - - - -
108A ALA* 1.3 77.7 - - - +
110A LYS* 1.3 65.7 + - + +
112A VAL* 3.2 4.0 + - - +
113A LYS* 3.0 26.2 + - + +
123A ILE* 4.1 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASP* 3.2 19.5 - - - +
107A TYR* 2.9 32.7 + - + +
109A VAL* 1.3 78.3 - - + +
111A ILE* 1.3 57.6 + - + +
113A LYS* 4.0 6.1 - - - +
114A ALA* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 4.2 26.5 - - + +
86A MET* 3.5 29.4 - - + -
107A TYR* 2.8 26.9 + - + +
108A ALA* 3.6 5.6 - - - +
110A LYS* 1.3 77.4 - - + +
112A VAL* 1.3 65.9 + - + +
114A ALA* 3.5 3.0 + - - -
115A ASN* 2.7 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY* 5.1 5.8 - - - +
86A MET* 4.3 21.5 - - + -
108A ALA* 2.7 23.0 + - - +
109A VAL* 3.2 6.0 + - - +
111A ILE* 1.3 73.3 - - + +
113A LYS* 1.3 62.2 + - - +
115A ASN* 3.2 11.6 + - - +
116A LYS 3.4 0.2 + - - -
117A LEU* 3.3 22.0 + - + +
118A ASP* 3.5 28.7 - - + +
121A VAL* 3.7 37.2 - - + +
123A ILE* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 3.0 18.9 + - + +
110A LYS* 4.0 5.6 - - - +
112A VAL* 1.3 74.0 - - + +
114A ALA* 1.3 61.0 + - - +
115A ASN 2.8 10.8 + - - -
116A LYS* 2.8 18.4 + - - +
118A ASP* 3.8 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS 2.9 22.1 + - - +
111A ILE* 3.9 6.1 - - - +
112A VAL 3.5 0.2 - - - -
113A LYS* 1.3 78.3 - - + +
115A ASN* 1.3 62.2 + - - +
116A LYS* 3.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A MET* 4.3 19.0 - - - +
90A LYS* 5.7 3.1 + - - -
111A ILE* 2.7 40.7 + - - +
112A VAL 3.7 4.0 - - - +
113A LYS 2.8 1.6 + - - -
114A ALA* 1.3 83.1 - - - +
116A LYS* 1.3 73.8 + - - +
117A LEU* 3.5 12.6 - - + +
----------------------------------------------------------
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