Contacts of the helix formed by residues 96 - 108 (chain C) in PDB entry 1WNT
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 96 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 4.6 5.2 - - - -
90C GLN* 3.3 14.4 + - - +
94C GLU 3.4 15.7 - - - +
95C VAL* 1.3 78.9 - - - +
97C LYS* 1.3 65.0 + - - +
98C GLU* 2.8 38.3 + - - +
99C ALA* 3.1 14.9 + - - +
100C PHE* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 3.6 55.3 - - + +
65A GLU* 3.4 22.7 + - - +
109A ARG* 3.0 34.6 + - - +
96C THR* 1.3 71.2 - - - +
98C GLU* 1.3 52.5 + - + +
100C PHE* 3.1 4.3 + - - +
101C ASP* 2.6 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLN* 5.1 1.6 + - - -
96C THR* 2.8 37.2 + - - +
97C LYS* 1.3 74.2 - - + +
99C ALA* 1.3 62.4 - - - +
101C ASP* 2.9 20.2 + - - +
102C ARG* 2.9 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 3.7 30.0 - - + +
90C GLN* 2.8 35.2 - - - +
95C VAL* 5.3 0.9 - - + -
96C THR* 3.1 8.6 + - - +
98C GLU* 1.3 80.2 - - + +
100C PHE* 1.3 64.2 + - - +
103C SER* 2.7 30.5 + - - -
148C VAL* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 3.8 20.2 - + + -
105A GLU* 5.0 0.4 - - - -
108A LEU* 3.8 26.2 - - + -
109A ARG* 3.4 44.0 - - + -
112A ILE* 3.6 29.2 - - + -
95C VAL* 4.8 2.9 - - + -
96C THR 2.9 14.3 + - - +
97C LYS* 3.5 6.7 - - - +
99C ALA* 1.3 77.9 - - - +
101C ASP* 1.3 70.7 + - - +
104C PHE* 3.3 54.3 + + + +
148C VAL* 4.0 17.8 - - + +
151C SER* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 4.7 5.2 - - - +
109A ARG* 3.0 22.2 + - - -
97C LYS* 2.6 47.4 + - - +
98C GLU* 2.9 13.0 + - - +
100C PHE* 1.3 79.5 - - - +
102C ARG* 1.3 60.3 + - - +
104C PHE* 4.0 1.6 - - - +
105C GLU* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 4.6 14.3 - - - +
60C ASP* 2.7 42.1 + - - -
62C GLY* 3.5 6.7 - - - -
86C VAL* 4.4 17.3 - - + +
88C LEU* 4.0 20.4 - - + -
98C GLU 2.9 16.6 + - - +
99C ALA* 4.9 0.2 - - - -
101C ASP* 1.3 72.2 - - - +
103C SER* 1.3 56.3 - - - +
105C GLU* 2.8 39.9 + - - +
106C VAL* 3.0 38.9 + - + +
2245C NAP 3.9 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C VAL* 3.9 17.6 + - - +
88C LEU* 3.4 22.5 + - - +
99C ALA 2.7 21.6 + - - -
100C PHE 4.0 0.2 - - - -
102C ARG* 1.3 76.3 - - - +
104C PHE* 1.3 60.7 + - - +
107C ASN* 2.9 38.2 + - - +
148C VAL* 3.3 28.4 - - - +
149C TYR* 5.5 1.3 - - - +
152C THR* 4.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.6 17.0 - + + -
104A PHE* 3.6 40.4 - + + -
108A LEU* 3.9 6.3 - - + -
155A ALA* 4.3 1.1 - - + -
100C PHE* 3.3 43.4 + + + +
101C ASP 4.3 0.9 - - - +
102C ARG 3.0 1.0 - - - -
103C SER* 1.3 79.7 - - - +
105C GLU* 1.3 61.5 + - - +
108C LEU* 3.5 11.2 + - + +
109C ARG 3.1 22.2 + - - -
148C VAL* 3.3 21.3 - - + -
151C SER* 3.3 18.4 - - - -
152C THR* 3.0 52.0 - - + -
155C ALA* 4.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 4.9 1.1 - - - -
101A ASP* 5.2 3.3 - - - +
61C LEU 4.1 0.7 - - - +
62C GLY* 3.9 15.8 - - - +
101C ASP* 2.9 39.1 + - - +
102C ARG* 2.8 25.1 + - - +
104C PHE* 1.3 78.7 - - - +
106C VAL* 1.3 54.9 + - - +
109C ARG* 3.0 50.4 + - - +
110C ALA* 3.3 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 5.5 1.8 - - + -
62C GLY* 3.6 9.6 - - - +
84C ALA* 4.2 8.8 - - + +
85C ALA* 4.0 12.1 - - - +
86C VAL* 4.3 6.1 - - + +
102C ARG* 3.0 53.2 + - + +
103C SER 4.5 0.2 - - - +
105C GLU* 1.3 73.4 - - - +
107C ASN* 1.3 83.9 + - - +
108C LEU 3.1 2.2 + - - -
110C ALA* 3.4 22.6 - - - +
111C VAL* 4.4 0.7 + - - +
2245C NAP 3.4 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ALA 4.2 6.7 - - - +
85C ALA* 2.6 23.8 - - + +
86C VAL* 2.5 49.9 - - - +
103C SER* 2.9 27.2 + - - +
106C VAL* 1.3 78.6 - - - +
108C LEU* 1.3 59.0 + - - +
111C VAL* 3.1 21.7 - - - +
149C TYR* 3.8 8.3 - - - -
152C THR* 3.4 31.1 + - - +
153C LYS* 4.9 4.5 - - + +
156C LEU* 4.8 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.6 15.3 - - + -
104A PHE* 4.9 4.7 - - + -
151A SER* 5.2 3.8 - - - -
104C PHE* 3.5 20.9 + - + +
106C VAL 3.1 0.6 + - - -
107C ASN* 1.3 78.8 - - + +
109C ARG* 1.3 63.4 - - - +
110C ALA 3.2 2.2 - - - -
111C VAL* 3.0 23.1 - - - +
112C ILE* 3.1 29.3 + - + +
152C THR* 3.7 9.4 - - - +
155C ALA* 4.1 11.4 - - + -
156C LEU* 3.5 50.3 - - + +
159C LEU* 3.9 14.4 - - + -
----------------------------------------------------------
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