Contacts of the helix formed by residues 116 - 129 (chain D) in PDB entry 1B06
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 PHE 116 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D GLY 3.9 18.6 - - - -
100D LYS* 3.5 37.8 - - + +
101D PRO* 3.4 26.9 - - + -
109D ILE* 4.1 10.5 - - + +
110D ASP* 3.9 4.9 + - - -
115D SER* 1.3 74.3 - - - +
117D ASP* 1.3 63.7 + - - +
119D PHE* 3.4 17.1 + + - +
120D LYS* 2.9 65.1 + - + +
192D TRP* 4.5 3.1 - + - -
197D TRP* 3.5 29.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D SER* 3.2 10.3 + - - +
116D PHE* 1.3 80.5 - - - +
118D ARG* 1.3 64.4 + - - +
120D LYS* 3.4 20.3 + - - +
121D GLN* 3.1 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D TYR* 3.2 25.1 - - + +
115D SER* 3.4 11.3 + - - +
117D ASP* 1.3 75.3 - - - +
119D PHE* 1.3 68.5 - - - +
121D GLN* 2.9 39.8 + - - +
122D VAL* 2.8 43.9 + - - +
125D GLU* 5.0 8.9 + - - -
4F ILE* 6.0 1.3 - - + -
55F LEU* 3.1 21.2 + - - +
56F ILE* 2.9 34.8 + - - +
57F LYS 5.0 0.2 - - - -
58F GLY* 4.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ILE* 3.6 25.8 - - + -
113D TYR* 3.9 42.7 - + + +
115D SER 3.2 11.9 + - - +
116D PHE* 3.6 23.1 - + - +
118D ARG* 1.3 78.6 - - - +
120D LYS* 1.3 56.7 + - - +
122D VAL* 3.2 0.9 + - - +
123D PHE* 2.8 59.0 + + - +
138D LEU* 3.9 39.9 - - + -
147D LEU* 5.9 0.2 - - + -
149D ILE* 4.5 2.7 - - + -
167D LEU* 4.2 9.9 - - + -
192D TRP* 4.1 19.1 - + - -
197D TRP* 4.3 11.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PHE* 2.9 51.1 + - + +
117D ASP* 3.5 18.8 + - - +
119D PHE* 1.3 79.3 - - - +
121D GLN* 1.3 57.9 + - + +
124D SER* 3.0 34.5 + - - +
192D TRP* 3.6 51.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASP* 3.1 23.8 + - - +
118D ARG* 2.9 43.0 + - - +
120D LYS* 1.3 78.3 - - + +
122D VAL* 1.3 57.1 + - - +
124D SER* 3.5 4.8 + - - -
125D GLU* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D TYR* 4.4 13.2 - - + -
118D ARG* 2.8 55.1 + - - +
119D PHE 3.8 3.1 - - - +
121D GLN* 1.3 69.6 - - - +
123D PHE* 1.3 65.5 + - - +
125D GLU* 3.4 9.3 + - + +
126D SER* 2.8 34.7 + - - +
149D ILE* 3.9 17.3 - - + -
52F LEU* 5.1 7.2 - - + -
55F LEU* 4.6 13.2 - - + -
56F ILE* 4.3 20.4 - - + -
67F LEU* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D PHE* 2.8 40.1 + + + +
120D LYS 4.0 3.4 - - - +
122D VAL* 1.3 73.7 - - - +
124D SER* 1.3 58.7 + - - +
126D SER* 3.3 3.8 + - - -
127D ALA* 2.9 27.7 + - + +
136D THR* 3.4 33.8 - - + +
137D VAL 4.2 17.3 - - - -
138D LEU* 4.2 4.5 - - + -
149D ILE* 4.0 20.8 - - + +
167D LEU* 4.0 20.0 - - + -
169D VAL* 3.4 31.6 - - + -
188D LEU* 6.1 0.2 - - + -
191D TRP* 3.8 10.1 - + - -
192D TRP* 3.6 25.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LYS* 3.0 21.1 + - - +
121D GLN* 3.8 5.6 - - - -
122D VAL 3.3 0.2 - - - -
123D PHE* 1.3 76.9 - - - +
125D GLU* 1.3 58.4 + - - +
127D ALA* 3.2 6.9 + - - +
128D ASN* 2.9 43.2 + - - +
188D LEU* 5.3 6.2 - - - +
189D ASN* 5.0 6.2 + - - -
192D TRP* 3.2 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ARG* 5.0 8.0 + - - -
121D GLN 3.0 17.9 + - - +
122D VAL* 3.7 9.1 - - + +
123D PHE 3.3 0.2 - - - -
124D SER* 1.3 76.5 - - - +
126D SER* 1.3 63.7 + - - +
128D ASN* 3.4 7.0 + - - +
129D SER* 3.2 21.7 + - - -
55F LEU* 4.7 9.4 - - - +
62F GLN* 3.8 19.0 + - - +
65F TYR* 2.6 40.4 + - - -
67F LEU* 3.9 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D VAL* 2.8 28.3 + - - +
123D PHE 3.5 4.9 - - - -
125D GLU* 1.3 76.0 - - - +
127D ALA* 1.3 64.4 + - - +
129D SER* 2.8 20.9 + - - -
136D THR* 4.8 1.1 - - - -
149D ILE* 3.8 27.1 - - - +
151D THR* 3.2 16.3 - - - +
67F LEU* 3.6 20.2 - - - +
71F LEU* 4.0 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D PHE* 2.9 21.3 + - + +
124D SER* 3.2 7.8 + - - +
126D SER* 1.3 75.6 - - - +
128D ASN* 1.3 60.1 + - - +
129D SER 3.4 0.5 + - - -
130D LEU* 3.5 9.7 + - - +
136D THR* 3.1 28.2 + - + +
169D VAL* 5.3 0.2 - - + -
171D GLU* 2.6 29.9 - - - +
184D ARG* 3.7 0.7 + - - -
188D LEU* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D SER* 2.9 33.6 + - - +
125D GLU* 3.8 7.9 - - - +
126D SER 3.2 0.2 - - - -
127D ALA* 1.3 76.7 - - - +
129D SER* 1.3 58.8 + - - +
130D LEU 3.3 0.6 - - - +
184D ARG* 3.5 18.8 + - - +
185D GLY* 3.8 18.6 + - - -
188D LEU* 3.6 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D GLU* 3.2 12.2 + - - -
126D SER* 2.8 20.9 + - - -
128D ASN* 1.3 78.0 - - - +
130D LEU* 1.3 64.2 + - - +
131D PRO* 3.2 6.9 - - - +
151D THR* 4.2 0.5 - - - +
67F LEU* 4.3 15.7 - - - +
68F GLN* 2.8 36.7 + - - +
71F LEU* 4.3 1.4 - - - +
----------------------------------------------------------
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