Contacts of the helix formed by residues 102 - 109 (chain D) in PDB entry 1O97
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 TYR 102 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ILE* 4.2 5.4 - - - -
142C HIS* 5.1 0.4 - - - +
6D ILE* 3.9 7.8 - - - +
70D PHE* 3.5 19.5 - + - -
72D PRO* 3.8 18.6 - - + +
75D PHE* 3.8 31.9 - + + -
76D GLU* 3.9 21.1 - - + +
79D VAL* 3.7 30.8 - - + +
93D LEU* 3.6 31.6 - - + +
94D PRO* 5.9 0.2 - - - +
98D ASP* 3.6 4.7 - - + -
99D SER* 3.1 23.3 + - - -
100D LEU 3.2 1.4 + - - -
101D GLY* 1.3 80.3 - - - +
103D ALA* 1.3 70.8 + - - +
104D SER 3.2 3.1 - - - -
105D SER* 2.9 16.4 + - - -
106D LEU* 2.9 19.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 3.6 26.7 - - + -
99D SER 2.8 22.6 + - - +
100D LEU* 4.7 1.0 + - - -
102D TYR* 1.3 80.6 - - - +
104D SER* 1.3 59.2 + - - +
106D LEU* 3.4 6.8 + - - +
107D ALA* 3.0 26.3 + - - +
114D PHE* 3.8 13.1 - - + -
116D THR* 5.7 0.2 - - + -
152D VAL* 5.2 0.7 - - + +
154D THR* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE* 3.9 6.0 - - - +
128C ALA 4.7 1.4 + - - -
129C SER* 2.8 39.9 + - - -
132C ILE* 3.4 18.7 - - - +
133C SER* 3.5 2.9 + - - -
100D LEU 5.2 1.9 + - - -
102D TYR 3.2 0.6 - - - -
103D ALA* 1.3 76.6 - - - +
105D SER* 1.4 54.4 + - - +
107D ALA* 3.7 2.7 - - - +
108D SER* 2.7 36.2 + - - -
114D PHE* 3.7 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ILE* 3.7 19.7 - - - +
136C SER* 3.2 30.5 + - - -
142C HIS* 4.3 11.1 - - - -
76D GLU* 2.6 28.4 + - - -
102D TYR* 2.9 11.1 + - - -
104D SER* 1.4 76.4 + - - +
106D LEU* 1.3 66.5 + - - +
108D SER 3.2 10.0 + - - -
109D LYS* 3.2 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLU* 3.7 38.0 + - + +
79D VAL* 3.7 25.4 - - + -
80D SER* 3.9 22.9 - - - +
83D ILE* 4.3 12.3 - - + -
91D VAL* 5.7 0.2 - - + -
93D LEU* 4.9 3.4 - - + -
102D TYR* 2.9 20.9 + - + +
103D ALA* 3.5 10.8 - - - +
105D SER* 1.3 79.0 - - - +
107D ALA* 1.3 60.7 + - - +
109D LYS* 3.8 2.8 + - - +
110D THR* 3.3 24.6 + - + +
112D TYR* 4.3 11.6 - - + -
152D VAL* 4.6 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE* 4.9 4.3 - - + -
226C MET* 3.1 21.0 - - + +
103D ALA 3.0 14.9 + - - +
104D SER 4.1 3.6 - - - +
105D SER 3.2 0.4 - - - -
106D LEU* 1.3 78.4 - - - +
108D SER* 1.3 61.8 + - - +
110D THR* 3.0 18.6 + - - -
112D TYR* 4.8 7.4 - - + +
113D GLY 5.3 1.1 - - - +
114D PHE* 3.6 43.1 - - + -
152D VAL* 5.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE* 3.7 14.2 - - - +
133C SER* 2.9 24.3 + - - -
136C SER* 3.5 20.6 - - - -
137C TYR* 3.6 35.3 + - - -
226C MET* 5.0 1.6 - - - +
104D SER 2.7 22.1 + - - -
105D SER 3.2 1.8 + - - -
107D ALA* 1.3 76.1 - - - +
109D LYS* 1.3 63.2 + - - +
110D THR 3.2 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C SER* 3.4 13.5 - - - +
137C TYR* 6.2 0.2 - - - -
76D GLU* 3.7 15.3 - - - +
105D SER 3.2 17.7 - - - +
106D LEU 4.2 1.6 - - - +
107D ALA 3.3 0.8 - - - -
108D SER* 1.3 75.8 - - - +
110D THR* 1.3 67.2 + - + +
----------------------------------------------------------
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