Contacts of the helix formed by residues 152 - 164 (chain E) in PDB entry 2FRV
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 PRO 152 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E SER* 3.1 35.9 - - - +
24E VAL* 5.0 2.5 - - + +
26E ARG* 4.0 15.9 - - + +
27E THR* 3.9 24.0 - - - +
150E PRO 3.5 5.6 - - - +
151E ASN* 1.3 91.3 - - - +
153E MET* 1.3 59.9 + - - +
155E PHE* 3.2 6.8 + - + +
156E VAL* 3.1 29.8 + - + +
233E PHE* 4.7 11.4 - - + -
234E ASN 5.8 3.6 - - - +
217F ASN 6.0 0.9 - - - +
218F PRO* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E THR* 5.9 0.4 - - - -
151E ASN* 3.5 14.3 + - - +
152E PRO* 1.3 79.8 - - - +
154E ASN* 1.3 68.5 + - - +
156E VAL* 5.1 2.0 - - - -
157E GLY* 3.0 29.7 + - - +
179E PHE* 3.9 20.4 - - + -
227E ASN* 4.0 1.6 - - - +
231E GLN* 3.1 48.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E ILE* 3.7 22.8 - - + +
146E ALA 5.3 0.2 - - - +
151E ASN* 2.9 20.6 + - + +
153E MET* 1.3 87.4 - - - +
155E PHE* 1.3 60.3 + - - +
157E GLY 4.2 0.2 - - - -
158E THR* 3.0 25.6 + - - -
179E PHE* 3.5 33.9 - - + +
180E PHE* 3.7 17.5 - - + -
226E ASN* 3.7 1.7 - - - +
227E ASN* 2.9 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E VAL* 6.0 0.7 - - + -
11E TYR* 4.5 8.1 - + - -
23E SER* 6.0 0.7 - - - +
24E VAL* 3.7 34.5 - - + -
35E LEU* 5.6 3.6 - - + -
42E MET* 6.4 1.6 - - + -
71E VAL* 3.7 41.3 - - + -
107E ILE* 3.8 24.5 - - + -
109E ILE* 4.0 22.7 - - + -
145E ILE* 4.2 12.8 - - + -
150E PRO* 5.5 1.3 - - + -
151E ASN 3.6 3.9 + - - +
152E PRO* 3.2 8.0 + - + +
154E ASN* 1.3 79.7 - - - +
156E VAL* 1.3 76.6 + - + +
158E THR* 3.0 6.1 + - - -
159E VAL* 3.0 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E VAL* 4.8 4.3 - - + -
27E THR* 3.5 36.3 - - + +
30E PRO* 4.1 21.8 - - + -
35E LEU* 4.4 20.6 - - + -
152E PRO* 3.1 15.0 + - + +
153E MET* 4.7 2.2 - - - +
155E PHE* 1.3 89.6 - - + +
157E GLY* 1.3 56.9 + - - +
159E VAL* 3.8 5.6 - - - +
160E VAL* 3.0 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E MET* 3.0 21.7 + - - -
156E VAL* 1.3 76.4 - - - +
158E THR* 1.3 59.0 + - - +
160E VAL* 4.2 5.4 - - - +
161E HIS* 3.2 25.8 + - - +
165E LYS* 5.1 1.9 + - - -
178E MET* 5.2 1.6 - - - +
179E PHE* 4.0 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ILE* 4.0 16.8 - - + -
143E ILE* 4.0 21.8 - - + -
145E ILE* 3.7 22.3 - - + +
154E ASN 3.0 22.1 + - - -
155E PHE 3.0 6.0 + - - +
157E GLY* 1.3 77.6 - - - +
159E VAL* 1.3 65.9 + - - +
161E HIS* 3.5 5.8 + - - +
162E LEU* 2.9 26.8 + - + +
168E PRO* 4.7 8.4 - - + +
176E PRO* 3.7 9.2 - - - +
178E MET* 5.3 1.4 - - - -
179E PHE* 3.3 13.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E VAL* 5.6 6.7 - - + -
35E LEU* 5.1 7.9 - - + -
39E VAL* 5.4 0.4 - - + -
40E ILE* 4.0 18.8 - - + -
69E VAL* 5.5 4.5 - - + -
71E VAL* 5.2 4.0 - - + -
107E ILE* 3.7 23.6 - - + -
155E PHE* 3.0 32.8 + - + +
156E VAL* 3.8 9.2 - - - +
158E THR* 1.3 76.9 - - - +
160E VAL* 1.3 71.1 + - + +
162E LEU* 3.1 7.9 + - + +
163E LEU* 3.0 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E PRO* 5.4 6.7 - - + -
35E LEU* 5.1 2.7 - - + -
39E VAL* 4.5 18.6 - - + -
156E VAL* 3.0 31.9 + - + +
157E GLY* 4.4 5.6 - - - +
159E VAL* 1.3 84.0 - - + +
161E HIS* 1.3 55.8 + - - +
163E LEU* 3.6 6.7 - - - -
164E THR* 2.7 49.7 + - + +
165E LYS* 5.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLU* 4.8 3.8 - - + +
427B VAL* 6.3 0.7 - - + -
430B ASP* 4.4 11.0 + - - -
157E GLY 3.2 21.7 + - - +
158E THR* 3.5 8.1 - - - +
159E VAL 3.1 0.2 - - - -
160E VAL* 1.3 76.9 - - - +
162E LEU* 1.3 61.9 + - - +
164E THR* 3.6 4.7 - - - -
165E LYS* 2.7 81.4 + - + +
166E GLY 2.8 32.9 + - - -
167E MET 3.9 2.7 - - - -
168E PRO* 3.5 38.2 - - + +
178E MET* 4.6 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E VAL* 4.6 10.3 - - + -
105E ALA* 4.1 21.8 - - + -
107E ILE* 3.7 30.3 - - + -
143E ILE* 3.9 26.5 - - + -
158E THR 2.9 13.2 + - - +
159E VAL* 3.2 7.2 - - - +
161E HIS* 1.3 83.0 - - - +
163E LEU* 1.3 63.9 + - + +
166E GLY* 3.3 29.1 + - - +
167E MET* 4.1 17.3 - - + +
168E PRO* 4.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PRO* 3.6 38.6 - - + -
9E VAL* 6.4 1.6 - - + -
39E VAL* 4.1 15.9 - - + +
40E ILE* 3.9 19.3 - - + -
69E VAL* 4.8 17.5 - - + -
159E VAL* 3.0 27.1 + - + +
160E VAL* 3.7 5.2 - - - +
162E LEU* 1.3 81.5 - - + +
164E THR* 1.3 66.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS* 5.0 7.6 + - - -
250B ARG* 5.7 0.3 + - - -
160E VAL* 2.7 38.7 + - + +
161E HIS 3.5 0.3 + - - -
163E LEU* 1.3 87.5 - - + +
165E LYS* 1.3 92.2 + - - +
166E GLY 3.8 0.2 - - - -
----------------------------------------------------------
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