Contacts of the helix formed by residues 114 - 132 (chain E) in PDB entry 6DWZ
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 GLY 114 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 3.0 26.0 - - - -
110E SER 3.7 5.5 + - - -
111E ALA* 3.1 6.4 + - - -
112E VAL 3.0 5.5 + - - -
113E SER* 1.3 76.0 - - - +
115E SER* 1.3 68.9 + - - +
117E PHE* 2.9 17.3 + - - +
118E ILE* 3.1 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 3.3 31.6 + - - +
105A ASP* 3.7 3.9 + - - -
113E SER 3.0 6.7 + - - -
114E GLY* 1.3 69.2 - - - -
116E GLY* 1.3 61.0 + - - +
117E PHE 2.7 0.9 + - - -
118E ILE* 2.6 37.0 + - - +
119E ASP* 3.3 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 4.7 1.6 - - - +
100A GLN* 4.5 1.5 - - - +
101A TRP* 3.7 17.7 + - - -
104A ARG* 3.0 35.2 - - - +
105A ASP* 3.2 9.9 + - - -
115E SER* 1.3 81.8 + - - +
117E PHE* 1.3 56.0 + - - +
118E ILE 3.3 0.2 - - - -
119E ASP* 4.0 2.6 - - - +
120E MET* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TRP* 3.1 22.2 - + - +
105A ASP* 3.0 18.7 + - - +
117A PHE* 4.6 0.2 - + - -
120A MET* 4.1 20.4 - - + -
124A PHE* 5.8 0.2 - + - -
141A LEU* 4.6 12.8 - - + -
98E CYS* 5.7 0.2 - - - -
101E TRP* 3.4 35.2 - + - -
111E ALA 3.5 6.1 - - - +
112E VAL* 3.0 41.1 - - + -
114E GLY 2.9 8.7 + - - +
115E SER 2.7 4.6 + - - -
116E GLY* 1.3 76.2 - - - +
118E ILE* 1.3 58.5 + - + -
120E MET* 3.2 25.4 - - + +
121E ILE* 3.2 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.3 21.5 - - + -
138A GLU* 5.6 8.7 - - + +
141A LEU* 3.8 28.5 - - + -
112E VAL 4.3 11.2 - - - +
113E SER* 4.3 9.6 - - - +
114E GLY 3.1 16.8 - - - +
115E SER* 2.6 14.8 + - - +
117E PHE* 1.3 72.6 - - + +
119E ASP* 1.3 59.4 + - - +
120E MET 2.8 3.6 - - - -
121E ILE* 2.3 30.6 + - + +
122E LYS* 2.8 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 3.0 38.2 + - + +
100A GLN* 5.9 2.0 - - - +
104A ARG* 3.3 25.7 + - - +
115E SER* 3.3 8.6 + - - +
116E GLY* 4.0 4.7 - - - +
118E ILE* 1.3 74.8 - - - +
120E MET* 1.3 58.7 - - - +
122E LYS* 4.5 15.8 - - - +
123E PHE 4.2 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 3.5 10.8 - - + +
98A CYS* 3.4 50.5 - - - +
101A TRP* 3.9 23.1 - - + -
117A PHE* 4.0 17.0 - - + -
116E GLY 3.2 14.2 + - - +
117E PHE* 3.2 44.6 - - + +
118E ILE 2.7 2.2 + - - -
119E ASP* 1.3 74.3 - - - +
121E ILE* 1.3 72.6 + - + +
123E PHE* 3.1 22.3 + - - +
124E PHE* 3.6 14.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET* 4.9 0.7 - - + -
121A ILE* 3.8 23.1 - - + -
124A PHE* 3.5 35.2 - - + -
137A VAL* 3.9 28.0 - - + -
141A LEU* 4.6 3.4 - - + -
117E PHE* 3.2 33.9 + - + +
118E ILE* 2.3 25.7 + - + +
120E MET* 1.3 78.4 - - + +
122E LYS* 1.3 55.0 + - - +
124E PHE* 2.6 40.1 + - + +
125E ILE* 3.2 13.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL 4.0 10.8 + - - +
136A ASN* 4.8 0.8 - - - +
137A VAL* 3.1 40.0 - - + +
138A GLU* 3.4 25.6 + - - -
83E LEU* 4.8 6.7 - - - +
118E ILE* 2.8 32.3 + - - +
119E ASP* 4.6 12.3 - - - +
121E ILE* 1.3 72.4 - - - +
123E PHE* 1.3 62.2 + - - +
124E PHE 2.9 0.9 + - - -
125E ILE* 3.1 9.5 + - + +
126E LYS* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A CYS* 3.5 27.8 - - - -
93A GLU* 3.1 48.2 - - + -
94A ALA* 3.4 30.5 - - + -
97A LYS* 3.9 23.7 - - + +
119E ASP 4.2 1.8 + - - +
120E MET 3.1 10.8 + - - +
122E LYS* 1.3 78.4 - - - +
124E PHE* 1.3 86.4 + + - +
126E LYS* 4.1 19.6 - - - +
127E VAL* 2.9 30.2 + - + +
140E LEU* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 4.7 6.1 - - + -
97A LYS* 6.5 0.2 - - + -
98A CYS* 4.6 13.2 - - - -
121A ILE* 3.3 54.3 - - + -
124A PHE* 2.9 24.1 - - + +
125A ILE* 3.3 6.3 - - + -
120E MET* 4.5 15.0 - - + -
121E ILE* 2.6 28.8 + - + +
123E PHE* 1.3 102.5 - + - +
125E ILE* 1.3 57.6 + - - +
127E VAL* 2.9 13.2 - - + +
128E GLY 2.9 20.4 + - - -
140E LEU* 4.6 11.4 - - + -
141E LEU* 3.4 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 3.1 19.5 - - + +
127A VAL* 3.4 13.0 - - + +
128A GLY* 3.0 29.9 - - - +
132A GLY 4.6 0.9 - - - +
133A GLU* 5.4 1.6 - - - -
135A VAL* 3.7 27.6 - - + +
137A VAL* 4.1 32.1 - - + -
140A LEU* 4.4 11.7 - - + -
121E ILE* 3.6 20.0 - - + +
122E LYS* 3.6 8.7 - - - +
124E PHE* 1.3 72.0 - - - +
126E LYS* 1.3 57.6 + - - +
128E GLY 2.6 21.1 + - - -
129E ALA* 2.8 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A CYS* 5.7 1.0 - - - -
93A GLU* 3.6 22.6 + - - -
133A GLU* 3.3 48.9 + - + +
122E LYS 2.9 19.1 + - - +
123E PHE* 4.1 17.1 - - - +
125E ILE* 1.3 72.7 - - - +
127E VAL* 1.3 59.6 + - - +
129E ALA* 3.4 7.1 + - - +
130E GLU* 3.0 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 4.7 9.2 - - + -
90A CYS* 3.4 33.2 - - - -
125A ILE* 3.4 24.6 - - + +
123E PHE* 2.9 26.2 + - + +
124E PHE* 2.9 27.8 - - + +
125E ILE 3.0 0.4 - - - -
126E LYS* 1.3 77.8 - - - +
128E GLY* 1.3 61.1 + - - +
130E GLU* 3.5 9.3 - - - +
131E TYR* 3.3 29.3 + - + +
135E VAL* 5.1 1.4 - - + +
140E LEU* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.0 34.8 - - - -
129A ALA* 3.0 12.3 + - - -
124E PHE 2.9 6.9 + - - -
125E ILE 2.6 12.7 + - - -
127E VAL* 1.3 70.5 - - - +
129E ALA* 1.3 58.2 + - - +
132E GLY* 2.6 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY 2.9 19.5 + - - +
129A ALA* 3.9 4.5 - - - +
132A GLY* 3.6 19.5 - - - -
133A GLU* 3.6 16.2 - - + +
125E ILE 2.8 11.5 + - - +
126E LYS 3.4 9.6 + - - +
128E GLY* 1.3 77.5 - - - +
130E GLU* 1.3 64.3 + - - +
131E TYR 3.2 0.3 + - - -
132E GLY* 3.4 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 5.4 1.7 - - - -
90A CYS* 4.4 5.2 - - - -
126E LYS* 3.0 45.7 + - - +
127E VAL* 3.5 17.7 - - - +
129E ALA* 1.3 75.9 - - - +
131E TYR* 1.3 87.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 3.1 50.3 - - + +
85A THR 4.2 3.1 - - - -
86A VAL* 3.4 41.3 - - + +
87A SER* 2.9 30.8 + - - -
90A CYS* 3.9 5.5 - - - +
127E VAL* 3.3 17.2 + - + +
130E GLU* 1.3 108.9 - - + +
132E GLY* 1.3 64.5 + - - +
134E HIS 3.8 4.3 - - - +
135E VAL* 4.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.5 1.6 - - - +
129A ALA* 3.5 11.4 - - - -
128E GLY* 2.6 28.1 + - - -
129E ALA 3.4 3.8 + - - -
131E TYR* 1.3 71.0 - - - +
133E GLU* 1.3 55.0 + - - -
134E HIS 2.7 17.5 + - - -
135E VAL* 3.1 20.1 - - - +
----------------------------------------------------------
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