Contacts of the helix formed by residues 148 - 164 (chain J) 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 THR 148 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J PRO* 3.7 8.5 - - + -
132J ALA* 3.6 41.1 - - + +
135J ALA* 3.9 13.5 - - - +
147J THR* 1.3 70.0 - - - +
149J GLU* 1.3 70.6 + - - +
151J LEU* 2.8 5.8 + - - +
152J LYS* 2.5 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J THR* 3.4 21.1 - - - +
148J THR* 1.3 99.2 + - - +
150J SER* 1.3 62.5 + - - +
152J LYS* 3.6 18.3 + - + +
153J ALA* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J THR* 4.1 8.5 - - - +
147J THR* 2.8 38.9 + - - -
149J GLU* 1.3 77.4 - - - +
151J LEU* 1.3 63.8 + - - +
153J ALA* 3.3 8.3 + - - +
154J VAL* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J PRO* 3.7 13.2 - - + +
134J ALA* 3.5 20.6 - - + +
135J ALA* 3.4 33.4 - - - +
138J ALA* 5.2 0.2 - - + -
146J THR* 3.9 16.6 - - + -
147J THR 3.8 11.0 - - - +
148J THR 2.8 7.7 + - - +
150J SER* 1.3 80.6 + - - +
152J LYS* 1.3 65.5 + - - +
153J ALA 3.0 1.1 - - - -
154J VAL* 3.1 14.0 + - - +
155J GLN* 3.2 9.4 + - - +
190J LEU* 3.7 21.4 - - + +
191J ILE* 4.6 9.6 - - + -
194J ALA* 3.6 30.5 - - + -
195J HIS* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J PRO* 3.6 20.8 - - + +
132J ALA* 5.8 0.4 - - - +
148J THR* 2.5 42.4 + - + +
149J GLU* 3.6 19.3 + - + +
151J LEU* 1.3 72.7 - - - +
153J ALA* 1.3 57.3 + - - +
155J GLN* 3.3 16.0 + - - +
156J ALA* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J GLU 2.9 17.7 + - - +
150J SER* 3.3 9.6 - - - +
152J LYS* 1.3 76.0 - - - +
154J VAL* 1.3 63.3 + - + +
156J ALA* 3.2 9.8 + - - +
157J LYS* 3.2 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J SER 3.2 17.0 - - - +
151J LEU* 3.1 7.5 + - - +
153J ALA* 1.3 72.8 - - - +
155J GLN* 1.3 61.1 + - - +
157J LYS* 3.2 16.3 + - - +
158J VAL* 3.1 26.8 + - + +
190J LEU* 4.2 11.9 - - + -
193J THR* 3.9 27.4 - - + -
194J ALA* 3.8 31.4 - - + +
197J LEU* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 155 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J ALA* 3.0 27.9 + - - +
127J LEU* 3.4 29.2 + - + +
129J ALA* 2.8 32.7 + - - +
131J PRO* 4.0 19.7 - - - +
151J LEU 3.2 5.8 + - - +
152J LYS* 3.3 13.8 - - - +
154J VAL* 1.3 81.8 - - - +
156J ALA* 1.3 57.4 - - - +
158J VAL* 3.5 3.5 + - - +
159J LYS* 3.0 27.6 + - - +
190J LEU* 4.2 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J LYS 3.1 12.2 + - - +
153J ALA* 3.4 13.0 - - - +
154J VAL 3.1 0.2 - - - -
155J GLN* 1.3 75.0 - - - +
157J LYS* 1.3 60.5 + - - +
159J LYS* 3.7 11.1 - - + +
160J ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ASP* 5.7 4.8 + - - +
37I LEU* 4.5 24.0 - - + +
153J ALA* 3.2 13.7 + - - +
154J VAL* 3.3 20.7 - - + +
156J ALA* 1.3 76.2 - - - +
158J VAL* 1.3 62.9 + - + +
160J ALA* 3.3 6.1 + - - +
161J LEU* 2.9 28.9 + - - +
197J LEU* 4.3 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J VAL* 4.3 26.5 - - + +
124J ALA* 5.2 2.5 - - - -
126J ALA* 5.3 4.0 - - + -
127J LEU* 3.8 24.9 - - + -
154J VAL* 3.1 17.4 + - + +
155J GLN* 3.8 6.5 - - - +
156J ALA 3.4 0.2 - - - -
157J LYS* 1.3 83.1 - - + +
159J LYS* 1.3 62.3 + - - +
161J LEU* 3.1 9.9 + - + +
162J VAL* 2.9 31.5 + - + +
190J LEU* 6.4 0.2 - - + -
193J THR* 3.9 26.2 - - + -
197J LEU* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J LEU* 4.2 21.5 - - + -
155J GLN 3.0 19.0 + - - +
156J ALA* 3.7 10.3 - - + +
158J VAL* 1.3 75.3 - - - +
160J ALA* 1.3 66.2 + - - +
162J VAL* 3.9 3.4 - - + +
163J GLU* 3.0 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J ALA 2.9 20.0 + - - +
157J LYS* 3.6 7.0 - - - +
159J LYS* 1.3 76.4 - - - +
161J LEU* 1.3 61.8 + - - +
163J GLU* 4.0 10.2 - - - +
164J SER* 3.6 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ARG* 3.3 21.1 - - - +
36I ILE 5.1 0.4 - - - +
37I LEU* 4.1 28.7 - - + +
157J LYS 2.9 16.4 + - - +
158J VAL* 3.6 9.4 - - + +
159J LYS 3.0 0.4 - - - -
160J ALA* 1.3 77.1 - - - +
162J VAL* 1.3 66.0 + - + +
164J SER* 2.7 24.0 + - - -
165J GLY 3.7 2.1 + - - -
166J GLN 3.3 24.8 + - - +
167J LEU* 4.1 27.7 - - + +
170J PHE* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J ALA* 6.2 5.6 - - + -
127J LEU* 4.6 14.1 - - + -
158J VAL* 2.9 28.7 + - + +
159J LYS* 3.9 5.8 - - + +
161J LEU* 1.3 77.9 - - + +
163J GLU* 1.3 64.4 + - + +
165J GLY* 3.3 15.4 + - - -
167J LEU* 3.8 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159J LYS* 3.0 27.0 + - + +
160J ALA* 4.0 10.2 - - - +
162J VAL* 1.3 81.3 - - + +
164J SER* 1.3 56.6 + - - -
165J GLY 3.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I LYS* 3.3 24.3 - - - +
5I LYS* 5.4 9.2 - - - -
6I ARG* 3.3 21.5 + - - -
160J ALA 3.6 10.8 + - - -
161J LEU* 2.7 21.7 + - - -
162J VAL 3.2 0.6 - - - -
163J GLU* 1.3 75.8 - - - +
165J GLY* 1.3 57.3 + - - +
166J GLN* 3.1 20.4 + - - +
----------------------------------------------------------
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