Contacts of the helix formed by residues 123 - 133 (chain D) in PDB entry 3WBR
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 THR 123 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 5.6 3.2 + - - +
122A ASN* 4.9 8.3 - - + -
123A THR* 3.6 30.5 - - + +
91D GLN* 5.1 5.4 + - - +
121D ILE* 3.7 6.3 - - - +
122D ASN* 1.3 86.6 - - + +
124D ARG* 1.3 63.8 + - - +
125D GLU* 3.6 16.6 + - - +
126D GLU* 3.1 23.7 + - - +
127D GLN* 3.0 18.5 + - - +
165E VAL* 3.7 11.7 - - - -
167E PHE* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER* 4.2 25.9 + - - +
123D THR* 1.3 74.1 - - - +
125D GLU* 1.3 67.3 + - - +
127D GLN* 3.2 4.3 + - + +
128D ASP* 2.8 65.6 + - - +
165E VAL* 3.9 6.2 - - + +
167E PHE* 3.6 33.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
91A GLN* 3.4 51.6 - - + +
92A SER* 2.7 38.0 + - - -
90D PHE* 3.8 14.7 - - + -
91D GLN* 5.2 0.4 - - - +
123D THR* 3.2 16.7 - - - +
124D ARG* 1.3 82.9 + - - +
126D GLU* 1.3 57.9 + - - +
128D ASP* 3.3 10.3 + - - +
129D PHE* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE* 3.8 17.0 - - + -
91D GLN* 5.5 1.1 - - - +
95D TYR* 2.5 32.7 + - + +
120D VAL 3.2 9.1 - - - +
121D ILE* 4.1 3.1 - - + -
122D ASN* 2.8 31.4 + - - +
123D THR* 3.1 20.7 + - - +
125D GLU* 1.3 74.9 - - - +
127D GLN* 1.3 60.4 + - - +
129D PHE* 3.3 1.0 + - - +
130D ILE* 2.9 46.8 + - + +
207D LYS* 2.7 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ILE* 3.4 21.0 - - + +
123D THR 3.0 7.3 + - - +
124D ARG 3.2 8.9 + - - +
126D GLU* 1.3 76.6 - - - +
128D ASP* 1.3 65.7 + - - +
130D ILE* 3.7 4.9 - - - +
131D ILE* 3.2 38.7 + - + +
183D ILE* 3.6 22.2 - - - +
191D TRP* 4.7 5.1 + - - +
192D GLY* 4.6 8.1 - - - +
193D TRP* 3.1 21.1 + - - +
167E PHE* 3.5 56.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ARG* 2.8 55.9 + - - +
125D GLU* 3.5 13.2 - - - +
126D GLU 3.2 0.2 - - - -
127D GLN* 1.3 78.5 - - - +
129D PHE* 1.3 64.0 - - - +
131D ILE* 3.0 33.9 - - + +
132D GLN* 3.4 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D THR* 3.5 31.4 - - + -
89D SER 3.6 21.3 - - - -
90D PHE* 3.5 38.4 - + + -
95D TYR* 3.4 34.3 - + + -
125D GLU 2.8 20.4 + - - +
126D GLU 3.8 2.7 - - - +
128D ASP* 1.3 69.5 - - - +
130D ILE* 1.3 74.7 + - + +
132D GLN* 3.4 22.0 + - - +
133D ASN* 2.9 44.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D TYR* 4.2 20.0 - - + -
97D ILE* 5.5 1.1 - - + -
119D VAL* 3.8 18.2 - - + -
121D ILE* 3.8 33.7 - - + -
126D GLU* 2.9 32.7 + - + +
127D GLN* 3.7 5.6 - - - +
129D PHE* 1.3 83.0 - - + +
131D ILE* 1.3 56.4 + - - +
133D ASN* 3.0 23.5 + - - +
134D LEU* 3.2 20.5 - - + +
183D ILE* 4.8 8.3 - - + -
205D ILE* 3.9 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D GLN* 3.2 18.3 + - + +
128D ASP* 3.0 39.9 - - + +
130D ILE* 1.3 73.6 - - - +
132D GLN* 1.3 62.6 + - + +
134D LEU* 3.0 31.3 + - + +
183D ILE* 4.0 24.0 - - + -
191D TRP* 3.9 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D ASP* 3.4 26.5 + - - +
129D PHE* 3.7 20.0 - - - +
130D ILE 3.3 0.4 - - - -
131D ILE* 1.3 81.0 - - + +
133D ASN* 1.3 63.0 + - - +
134D LEU 3.7 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D THR* 3.1 29.1 + - - +
95D TYR* 6.0 1.3 - - + -
97D ILE* 3.7 33.7 - - + +
129D PHE* 2.9 50.6 + - + -
130D ILE* 3.0 11.9 + - - +
132D GLN* 1.3 81.4 - - - +
134D LEU* 1.3 59.0 + - - +
135D LYS* 5.2 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