Contacts of the helix formed by residues 152 - 164 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G SER* 3.1 35.9 - - - +
24G VAL* 5.0 2.7 - - + +
26G ARG* 4.0 16.4 - - + +
27G THR* 3.9 24.5 - - - +
150G PRO 3.5 5.8 - - - +
151G ASN* 1.3 90.5 - - - +
153G MET* 1.3 60.3 + - - +
155G PHE* 3.2 6.2 + - + +
156G VAL* 3.1 29.9 + - + +
233G PHE* 4.7 11.9 - - + -
234G ASN 5.8 3.8 - - - +
217H ASN 6.0 0.4 - - - +
218H PRO* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G THR* 5.9 0.4 - - - -
151G ASN* 3.5 14.3 + - - +
152G PRO* 1.3 80.0 - - - +
154G ASN* 1.3 66.9 + - - +
156G VAL* 5.1 2.2 - - - -
157G GLY* 3.0 29.3 + - - +
179G PHE* 3.9 19.9 - - + -
227G ASN* 4.0 1.8 - - - +
231G GLN* 3.1 48.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G ILE* 3.7 22.6 - - + +
151G ASN* 2.9 22.1 + - + +
153G MET* 1.3 86.8 - - - +
155G PHE* 1.3 61.0 + - - +
158G THR* 3.0 25.8 + - - -
179G PHE* 3.5 32.8 - - + +
180G PHE* 3.7 17.3 - - + -
226G ASN* 3.7 2.3 - - - +
227G ASN* 2.9 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 6.0 0.4 - - + -
11G TYR* 4.5 7.2 - + - -
23G SER* 6.0 0.9 - - - +
24G VAL* 3.7 35.4 - - + -
35G LEU* 5.6 3.6 - - + -
42G MET* 6.4 1.6 - - + -
71G VAL* 3.7 42.0 - - + -
107G ILE* 3.8 24.2 - - + -
109G ILE* 4.0 23.1 - - + -
145G ILE* 4.0 14.5 - - + +
150G PRO* 5.5 1.3 - - + -
151G ASN 3.6 4.3 + - - +
152G PRO* 3.2 7.6 + - + +
154G ASN* 1.3 78.5 - - - +
156G VAL* 1.3 76.6 + - + +
158G THR* 3.0 6.2 + - - -
159G VAL* 3.0 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 4.8 4.3 - - + -
27G THR* 3.5 37.0 - - + +
30G PRO* 4.1 22.4 - - + -
35G LEU* 4.4 19.7 - - + -
152G PRO* 3.1 14.4 + - + +
153G MET* 4.7 2.0 - - - +
155G PHE* 1.3 89.6 - - + +
157G GLY* 1.3 58.4 + - - +
159G VAL* 3.8 5.9 - - - +
160G VAL* 3.0 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G MET* 3.0 22.2 + - - -
156G VAL* 1.3 76.3 - - - +
158G THR* 1.3 58.3 + - - +
160G VAL* 4.4 5.5 - - - +
161G HIS* 3.2 25.2 + - - +
165G LYS* 5.1 1.9 + - - -
178G MET* 5.2 1.7 - - - +
179G PHE* 4.0 16.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ILE* 4.0 16.4 - - + -
143G ILE* 4.0 22.2 - - + -
145G ILE* 3.7 22.9 - - + +
154G ASN 3.0 22.3 + - - -
155G PHE 3.0 5.4 + - - -
157G GLY* 1.3 78.2 - - - +
159G VAL* 1.3 66.4 + - - +
161G HIS* 3.5 4.9 + - - +
162G LEU* 2.9 27.5 + - + +
168G PRO* 4.7 8.4 - - + +
176G PRO* 3.7 8.3 - - - +
178G MET* 5.3 1.1 - - - -
179G PHE* 3.3 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 5.6 5.8 - - + -
35G LEU* 5.1 8.1 - - + -
39G VAL* 5.4 0.2 - - + -
40G ILE* 4.0 18.6 - - + -
69G VAL* 5.5 4.7 - - + -
71G VAL* 5.2 4.5 - - + -
107G ILE* 3.7 23.8 - - + -
155G PHE* 3.0 33.2 + - + +
156G VAL* 3.4 9.6 + - - +
158G THR* 1.3 75.0 - - - +
160G VAL* 1.3 70.5 + - + +
162G LEU* 3.1 8.2 + - + +
163G LEU* 3.0 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G PRO* 5.4 6.5 - - + -
35G LEU* 5.1 2.7 - - + -
39G VAL* 4.5 18.2 - - + -
156G VAL* 3.0 30.3 + - + +
157G GLY* 4.4 5.6 - - - +
159G VAL* 1.3 84.6 - - + +
161G HIS* 1.3 55.5 + - - +
163G LEU* 3.6 6.9 - - - -
164G THR* 2.7 50.2 + - + +
165G LYS* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G GLY 3.2 22.5 + - - +
158G THR* 3.5 7.6 - - - +
159G VAL 3.1 0.8 - - - -
160G VAL* 1.3 76.4 - - - +
162G LEU* 1.3 60.8 + - - +
164G THR* 3.6 4.9 - - - -
165G LYS* 2.7 81.5 + - + +
166G GLY 2.8 33.4 + - - -
167G MET 3.9 2.9 - - - -
168G PRO* 3.5 38.8 - - + +
178G MET* 4.6 15.4 - - + -
426J GLU* 4.9 3.8 - - + +
427J VAL* 6.4 0.4 - - + -
430J ASP* 4.3 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G VAL* 4.6 10.5 - - + -
105G ALA* 4.1 20.2 - - + -
107G ILE* 3.7 32.3 - - + -
143G ILE* 3.9 26.7 - - + -
158G THR 2.9 12.5 + - - +
159G VAL* 3.2 7.4 - - - +
161G HIS* 1.3 83.0 - - - +
163G LEU* 1.3 62.9 + - + +
166G GLY* 3.3 29.9 + - - +
167G MET* 4.1 16.4 - - + -
168G PRO* 4.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G PRO* 3.6 39.0 - - + -
9G VAL* 6.4 1.6 - - + -
39G VAL* 4.1 15.7 - - + +
40G ILE* 3.9 19.1 - - + -
69G VAL* 4.8 17.3 - - + -
159G VAL* 3.0 26.3 + - + +
160G VAL* 3.7 5.8 - - - +
162G LEU* 1.3 81.9 - - + +
164G THR* 1.3 65.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G VAL* 2.7 39.1 + - + +
161G HIS 3.5 0.2 + - - -
163G LEU* 1.3 87.2 - - + +
165G LYS* 1.3 92.8 + - - +
166G GLY 3.8 0.2 - - - -
247J LYS* 4.9 9.0 + - - -
----------------------------------------------------------
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