Contacts of the helix formed by residues 120 - 145 (chain E) in PDB entry 3BVI
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 LEU 120 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 4.4 14.8 - - + -
57E LEU* 4.5 2.2 - - + -
101E ILE* 5.3 2.0 - - + +
104E ILE* 3.7 33.0 - - + +
105E VAL* 3.9 30.5 - - + +
108E ALA* 5.1 0.7 - - + -
116E THR* 2.9 33.1 + - + +
117E PHE* 3.7 7.4 - - - +
118E ASN 3.3 0.6 - - - -
119E PHE* 1.3 89.7 - - + +
121E GLN* 1.3 58.3 + - - +
122E TRP 3.5 0.9 - - - -
123E TYR* 3.0 32.3 + - + +
124E VAL* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLN* 5.5 1.8 - - - +
105E VAL* 4.5 9.3 - - - +
117E PHE* 3.0 57.1 + - + +
118E ASN* 3.7 15.7 - - - +
119E PHE 3.2 2.4 - - - -
120E LEU* 1.3 74.1 - - - +
122E TRP* 1.3 67.0 + - - +
123E TYR 3.0 1.3 - - - -
124E VAL* 3.3 17.5 + - - +
125E ALA* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E HIS* 3.6 24.7 - + - -
56E LYS* 3.5 47.3 - - + -
57E LEU* 4.9 3.1 - - + -
118E ASN 4.9 0.6 + - - -
119E PHE* 2.8 58.4 + + - -
121E GLN* 1.3 76.9 - - - +
123E TYR* 1.3 88.9 + + + +
125E ALA* 3.6 5.2 + - - +
126E GLU* 3.0 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLN* 2.9 33.6 + - + +
17E GLU* 2.5 37.3 + - - +
53E HIS* 4.0 21.1 - + + -
57E LEU* 4.2 16.8 - - + -
101E ILE* 3.5 34.1 - - + +
104E ILE* 5.5 0.9 - - + -
120E LEU* 3.0 32.3 + - + +
121E GLN 3.0 0.4 - - - -
122E TRP* 1.3 115.1 - + + +
124E VAL* 1.3 64.5 + - - +
126E GLU* 4.5 0.4 - - - +
127E GLN* 3.0 28.5 + - + +
1006E FE 4.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ILE* 3.8 24.9 - - + -
102E ASN* 5.1 10.3 - - - +
105E VAL* 3.8 18.6 - - + -
120E LEU 2.9 20.4 + - - +
121E GLN* 3.8 20.2 - - - +
123E TYR* 1.3 77.2 - - - +
125E ALA* 1.3 62.5 + - - +
127E GLN* 3.5 3.0 + - - +
128E HIS* 3.1 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E GLN 3.1 15.6 + - - +
122E TRP* 3.9 5.8 - - - +
124E VAL* 1.3 77.0 - - - +
126E GLU* 1.3 65.9 + - + +
128E HIS* 3.4 7.8 + - - +
129E GLU* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLU* 4.1 5.8 - - - +
53E HIS* 3.2 28.8 + - + +
56E LYS* 4.1 11.3 + - - -
122E TRP* 3.0 44.8 + - + +
123E TYR* 4.3 2.0 - - - +
125E ALA* 1.3 77.4 - - + +
127E GLN* 1.3 63.1 + - - +
129E GLU* 3.4 10.6 + - - +
130E GLU* 3.1 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E HIS* 5.4 1.1 - - - -
94E GLU* 2.8 46.3 + - - +
97E ILE* 3.6 11.0 - - - +
98E SER* 3.3 21.9 + - - +
101E ILE* 3.5 22.2 - - + +
123E TYR* 3.0 22.7 + - + +
124E VAL* 3.9 3.4 - - - +
126E GLU* 1.3 76.2 - - - +
128E HIS* 1.3 57.9 + - - +
130E GLU* 3.1 4.6 + - - +
131E GLU* 2.8 27.3 + - - +
1006E FE 2.9 12.3 - - - -
1007E FE 2.5 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E SER* 5.2 0.2 - - - -
124E VAL* 3.1 19.8 + - + +
125E ALA* 3.7 7.2 - - - +
127E GLN* 1.3 77.2 - - - +
129E GLU* 1.3 64.2 + - + +
131E GLU* 3.2 15.4 + - - +
132E VAL* 3.0 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ALA 3.2 12.1 + - - +
126E GLU* 3.6 13.0 - - - +
128E HIS* 1.3 82.9 - - + +
130E GLU* 1.3 58.9 + - + +
132E VAL* 3.5 6.7 + - - +
133E LEU* 3.0 27.5 + - - +
165E ARG* 3.5 32.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
46E HIS* 3.4 22.9 - - + +
49E GLU* 3.9 12.8 - - - +
50E GLU* 2.9 6.4 - - - +
53E HIS* 2.9 28.8 + - - -
94E GLU* 4.2 2.7 - - - +
126E GLU* 3.1 18.4 + - - +
127E GLN* 3.4 8.9 - - - +
129E GLU* 1.3 78.6 - - + +
131E GLU* 1.3 61.2 + - - +
133E LEU* 3.3 7.9 + - + +
134E PHE* 3.1 32.7 + - - -
165E ARG* 5.6 4.5 - - - +
1007E FE 2.1 38.0 - - - -
1010E GOL 4.6 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TYR* 3.6 20.7 + - + -
94E GLU* 4.2 21.5 - - + -
95E GLN* 3.4 24.2 - - - +
98E SER* 2.6 35.1 + - - +
127E GLN* 2.8 21.2 + - - +
128E HIS* 3.2 14.2 + - - +
130E GLU* 1.3 73.5 - - - +
132E VAL* 1.3 58.5 + - + +
134E PHE* 3.5 0.9 + - - -
135E LYS* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E HIS* 3.0 48.5 + - + +
129E GLU* 3.8 6.3 - - - +
131E GLU* 1.3 74.1 - - + +
133E LEU* 1.3 61.4 + - - +
135E LYS* 3.3 23.2 + - - +
136E ASP* 2.8 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.6 31.4 - - + -
129E GLU 3.0 18.3 + - - +
130E GLU* 3.3 8.9 + - - +
132E VAL* 1.3 76.5 - - - +
134E PHE* 1.3 60.3 + - + +
136E ASP* 3.2 12.1 + - + +
137E ILE* 2.9 37.4 + - + +
161E ILE* 3.9 29.4 - - + -
165E ARG* 3.8 35.9 - - - +
1010E GOL 4.1 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TYR* 3.9 8.3 - + - -
42E PHE* 3.6 32.1 - + - -
43E LEU* 4.1 4.5 - - + -
46E HIS* 3.5 46.0 - + - -
87E PHE* 3.9 21.0 - + - +
90E ALA* 3.6 33.4 - - + -
91E TYR* 4.3 19.6 - - + +
94E GLU* 3.9 14.6 - - + -
130E GLU 3.1 28.3 + - - +
131E GLU 4.0 3.8 - - - +
132E VAL 3.3 0.2 - - - -
133E LEU* 1.3 76.3 - - + +
135E LYS* 1.3 60.6 + - - +
137E ILE* 4.0 4.3 - - - +
138E LEU* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TYR* 3.6 37.5 - - + +
131E GLU 3.1 14.8 + - - +
132E VAL* 3.4 24.9 - - - +
134E PHE* 1.3 76.2 - - - +
136E ASP* 1.3 79.1 + - - +
138E LEU* 3.7 3.4 - - - +
139E ASP* 2.9 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E VAL* 2.8 31.9 + - - +
133E LEU* 3.4 15.2 - - + +
135E LYS* 1.3 104.2 + - - +
137E ILE* 1.3 59.0 + - + +
139E ASP* 3.6 7.3 + - - +
140E LYS* 3.1 30.1 + - - +
157E TYR* 5.2 4.7 + - + +
161E ILE* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.2 46.9 - - + -
87E PHE* 3.6 27.4 - - + -
133E LEU* 2.9 26.9 + - + +
134E PHE* 4.0 4.7 - - - +
136E ASP* 1.3 71.5 - - - +
138E LEU* 1.3 65.8 + - - +
140E LYS* 3.1 8.0 + - - +
141E ILE* 2.9 28.4 + - + +
157E TYR* 5.1 2.7 - - + -
158E VAL* 3.6 24.9 - - + -
161E ILE* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E THR* 4.2 10.1 - - + +
87E PHE* 3.7 20.1 - - + +
88E GLN* 3.9 42.2 - - + +
91E TYR* 4.0 24.2 - - + -
134E PHE 2.9 19.0 + - - +
135E LYS* 3.7 4.9 - - - +
137E ILE* 1.3 76.9 - - - +
139E ASP* 1.3 64.8 + - - +
141E ILE* 3.3 10.3 + - + +
142E GLU* 3.0 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E LYS* 2.9 38.5 + - - +
136E ASP* 3.6 8.1 - - - +
138E LEU* 1.3 77.4 - - - +
140E LYS* 1.3 59.5 - - + +
142E GLU* 3.5 12.4 + - - +
143E LEU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E ASP 3.1 14.3 + - - +
137E ILE* 3.1 9.8 + - + +
139E ASP* 1.3 74.5 - - + +
141E ILE* 1.3 62.1 + - + +
143E LEU* 3.2 28.7 + - - +
144E ILE* 2.9 45.9 + - + +
157E TYR* 3.6 52.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E LEU* 4.1 24.5 - - + +
84E THR* 3.4 35.0 - - + +
87E PHE* 3.4 46.0 - - + -
137E ILE* 2.9 27.1 + - + +
138E LEU* 3.7 7.0 - - + +
140E LYS* 1.3 75.7 - - + +
142E GLU* 1.3 63.6 + - + +
144E ILE* 3.3 1.6 + - - +
145E GLY* 3.1 23.9 + - - +
151E LEU* 6.0 1.6 - - + -
154E ALA* 4.4 18.0 - - + +
158E VAL* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E THR* 4.1 20.7 - - + +
88E GLN* 4.1 15.1 + - - +
138E LEU* 3.0 45.1 + - + +
139E ASP* 3.9 12.4 - - - +
141E ILE* 1.3 78.0 - - - +
143E LEU* 1.3 60.6 + - - +
144E ILE 3.6 0.2 + - - -
145E GLY* 3.8 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E ASP 2.9 18.9 + - - +
140E LYS* 3.2 35.6 + - + +
142E GLU* 1.3 78.8 - - - +
144E ILE* 1.3 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E LYS* 2.9 39.0 + - + +
141E ILE* 3.9 3.8 - - + +
143E LEU* 1.3 81.2 - - + +
145E GLY* 1.3 63.3 + - - +
147E GLU* 5.5 0.7 + - - +
150E GLY* 3.2 34.5 - - - +
153E LEU* 4.1 19.7 - - + +
154E ALA* 3.6 29.2 - - + +
157E TYR* 4.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E ILE* 3.1 15.4 + - - +
142E GLU 3.8 6.9 + - - -
143E LEU 3.5 2.0 - - - -
144E ILE* 1.3 80.1 - - - +
146E ASN* 1.3 60.1 + - - +
147E GLU* 3.7 3.8 - - - -
150E GLY* 3.6 20.6 - - - +
151E LEU* 3.9 1.9 + - - +
154E ALA* 5.5 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