Contacts of the helix formed by residues 149 - 166 (chain E) in PDB entry 3BVE
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 HIS 149 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E ASN 5.2 0.4 + - - -
147E GLU 3.2 0.6 + - - -
148E ASN* 1.3 97.8 + - - +
150E GLY* 1.3 64.0 + - - +
151E LEU 3.4 2.7 - - - -
152E TYR* 3.3 17.8 + + + +
153E LEU* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E ILE* 3.3 19.2 - - - +
145E GLY 3.3 24.0 - - - -
146E ASN 4.3 1.9 + - - -
147E GLU 2.8 17.4 + - - -
148E ASN 3.5 0.4 + - - -
149E HIS* 1.3 77.4 - - - +
151E LEU* 1.3 57.4 + - - +
153E LEU* 4.9 1.1 - - - -
154E ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B HIS* 3.6 34.5 - - + +
1006B HIS* 4.5 15.0 - - + +
36E LEU* 4.2 19.8 - - + +
83E LEU* 4.0 35.2 - - + +
84E THR* 6.0 1.1 - - - +
145E GLY 4.1 2.3 + - - +
146E ASN* 4.6 20.5 + - + +
149E HIS 3.4 0.4 - - - -
150E GLY* 1.3 74.0 - - - +
152E TYR* 1.3 58.3 + - - +
154E ALA* 3.7 4.5 - - + +
155E ASP* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E LEU* 5.7 1.1 - - - -
149E HIS* 3.3 21.9 + + + +
151E LEU* 1.3 79.3 - - - +
153E LEU* 1.3 74.0 + - + +
155E ASP* 3.2 5.8 + - + +
156E GLN* 2.9 68.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E ILE* 4.0 23.2 - - + +
148E ASN 5.7 0.9 - - - +
149E HIS* 3.0 29.8 + - + +
150E GLY* 3.7 2.9 - - - +
152E TYR* 1.3 93.0 - - + +
154E ALA* 1.3 57.0 + - - +
156E GLN* 3.4 5.8 + - + +
157E TYR* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E LEU* 3.8 19.7 - - + -
141E ILE* 4.3 16.4 - - + -
144E ILE* 3.7 23.9 - - + +
145E GLY 5.3 2.0 - - - +
150E GLY 2.9 18.8 + - - +
151E LEU* 3.7 4.5 - - + +
153E LEU* 1.3 78.4 - - - +
155E ASP* 1.3 56.6 + - - +
157E TYR* 3.3 4.0 + - - +
158E VAL* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E SER 4.2 2.3 - - - +
36E LEU* 3.3 32.1 - - + +
37E ASP* 3.4 13.0 + - - +
38E GLY* 2.9 21.4 + - - -
39E ALA* 2.8 29.2 + - - +
83E LEU* 4.4 4.4 - - + +
151E LEU 2.8 21.9 + - - +
152E TYR* 3.7 5.6 - - + +
154E ALA* 1.3 74.2 - - - +
156E GLN* 1.3 64.0 + - - +
158E VAL* 3.5 3.8 + - - +
159E LYS* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASP* 4.9 4.2 + - - -
152E TYR* 2.9 60.2 + - + +
153E LEU* 3.8 6.5 - - + +
155E ASP* 1.3 82.5 + - - +
157E TYR* 1.3 61.4 + - - +
159E LYS* 3.4 30.9 + - - +
160E GLY* 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E ASP* 5.0 5.6 + - - +
137E ILE* 5.0 6.1 - - + -
140E LYS* 3.5 50.0 + - + +
141E ILE* 6.3 0.9 - - + -
144E ILE* 4.7 6.3 - - + -
153E LEU 2.9 17.9 + - - +
154E ALA* 3.5 7.4 - - - +
156E GLN* 1.3 73.6 - - - +
158E VAL* 1.3 73.3 + - + +
160E GLY* 3.1 11.5 + - - -
161E ILE* 3.2 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ALA* 3.6 21.8 - - + +
42E PHE* 3.4 37.2 - - + +
83E LEU* 5.6 1.3 - - + -
87E PHE* 4.4 5.8 - - + -
137E ILE* 3.6 29.2 - - + -
141E ILE* 4.6 11.0 - - + -
154E ALA 3.0 20.9 + - - +
155E ASP* 3.9 5.4 - - - +
157E TYR* 1.3 81.5 - - + +
159E LYS* 1.3 57.3 + - - +
161E ILE* 3.2 8.9 + - - +
162E ALA* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASP* 4.6 16.5 + - - +
38E GLY* 3.5 24.6 - - - +
41E LEU* 5.4 9.0 - - + -
155E ASP 2.8 21.4 + - - +
156E GLN* 3.4 32.3 + - - +
157E TYR 3.2 0.2 - - - -
158E VAL* 1.3 74.4 - - - +
160E GLY* 1.3 61.9 + - - +
162E ALA* 3.2 4.9 + - - +
163E LYS* 3.0 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E GLN 3.0 14.0 + - - -
157E TYR 3.1 5.1 + - - -
159E LYS* 1.3 75.3 - - - +
161E ILE* 1.3 57.0 + - - +
163E LYS* 3.5 8.8 + - - +
164E SER* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.7 24.7 - - + -
133E LEU* 4.0 15.7 - - + -
136E ASP* 6.3 1.8 - - + -
137E ILE* 3.7 23.1 - - + -
157E TYR* 3.2 46.3 + - + +
158E VAL* 3.2 10.4 + - - +
160E GLY* 1.3 73.2 - - - +
162E ALA* 1.3 65.6 + - - +
164E SER* 3.0 11.4 + - - +
165E ARG* 3.0 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLY 4.3 0.2 - - - +
41E LEU* 4.0 17.5 - - + -
42E PHE* 3.8 38.1 - - - +
45E ASP* 4.4 4.7 - - - +
158E VAL 2.9 13.1 + - - +
159E LYS* 3.2 11.9 + - - +
161E ILE* 1.3 78.2 - - - +
163E LYS* 1.3 62.4 + - - +
165E ARG* 3.4 10.9 + - - +
166E LYS* 3.5 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU* 4.7 13.5 - - + -
159E LYS* 3.0 58.4 + - + +
160E GLY* 3.9 6.1 - - - +
162E ALA* 1.3 74.2 - - - +
164E SER* 1.3 65.4 + - - +
166E LYS* 3.5 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E GLY 3.0 16.6 + - - -
161E ILE* 3.0 18.2 + - - +
163E LYS* 1.3 76.6 - - - +
165E ARG* 1.3 63.8 + - - +
166E LYS 3.5 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 4.8 8.7 - - + -
46E HIS* 5.3 4.8 + - - -
49E GLU* 5.5 7.1 - - - +
129E GLU* 3.0 44.8 + - - +
130E GLU* 4.6 13.7 + - - +
133E LEU* 3.7 36.0 - - - +
161E ILE* 3.0 24.7 + - + +
162E ALA* 3.9 6.5 - - - +
163E LYS 3.3 0.4 - - - -
164E SER* 1.3 77.0 + - - +
166E LYS* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU* 3.8 28.7 - - - +
45E ASP* 2.8 38.0 + - - +
162E ALA 3.5 12.7 + - - +
163E LYS* 3.7 20.2 - - + +
164E SER 3.3 9.9 - - - +
165E ARG* 1.3 81.9 - - - +
----------------------------------------------------------
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