Contacts of the helix formed by residues 19 - 26 (chain S) 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 GLY 19 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L GLY* 3.6 26.0 - - - -
218L PRO* 3.7 7.2 - - - +
17S CYS* 3.2 15.6 + - - -
18S THR* 1.3 77.9 - - - +
20S CYS* 1.3 58.0 + - - +
22S GLU* 3.9 3.1 - - - -
23S SER 3.1 19.8 + - - -
149S PRO* 3.4 14.2 - - - +
267S SF4 3.9 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 20 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S TYR* 4.0 2.2 - - - -
19S GLY* 1.3 76.2 - - - +
21S SER* 1.3 62.2 + - - +
23S SER* 3.0 20.9 + - - -
24S VAL* 3.5 9.9 + - - +
73S GLU* 3.1 26.7 + - + +
109S ILE* 3.7 16.8 - - + +
110S GLY* 3.2 31.4 - - - -
149S PRO* 3.9 3.8 - - - -
150S PRO* 3.8 14.8 - - - -
267S SF4 2.3 33.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S TYR* 3.6 6.0 + - - -
13S HIS* 2.9 21.6 - - - -
16S GLU* 4.1 0.3 + - - -
18S THR* 3.5 11.8 + - - +
19S GLY 3.4 0.2 - - - -
20S CYS* 1.3 74.2 - - - +
22S GLU* 1.3 64.9 + - - +
24S VAL* 3.0 22.0 + - - +
25S LEU* 3.5 13.5 + - - +
45S HIS* 3.8 21.9 - - - -
47S THR* 4.7 3.4 - - - -
73S GLU* 2.4 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L GLY 3.7 12.8 - - - +
67L VAL* 3.7 34.4 - - + +
106L HIS* 4.0 7.6 - - - -
110L VAL* 4.6 13.4 - - - +
115L LEU* 6.1 0.7 - - - +
218L PRO* 3.8 11.7 - - + -
18S THR* 3.2 18.0 + - + +
19S GLY 4.2 0.7 - - - +
20S CYS 3.5 0.2 - - - -
21S SER* 1.3 76.0 - - - +
23S SER* 1.3 62.4 + - - +
24S VAL 3.1 0.5 + - - -
25S LEU* 3.3 26.6 + - - +
26S ARG* 2.8 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L PRO* 3.8 14.3 - - - +
19S GLY 3.1 18.6 + - - -
20S CYS* 3.0 11.8 + - - -
21S SER 3.2 0.8 - - - -
22S GLU* 1.3 75.4 - - - +
24S VAL* 1.3 67.8 + - - +
26S ARG* 3.2 8.3 + - - +
109S ILE* 4.6 2.6 - - - +
149S PRO* 3.9 13.7 - - - +
150S PRO* 3.8 25.9 + - - +
151S ASN 5.2 0.2 - - - -
152S PRO* 3.1 34.2 - - - +
155S PHE* 6.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S TYR* 4.5 12.1 - - + +
20S CYS 3.6 14.4 - - - +
21S SER* 3.0 9.9 + - - +
23S SER* 1.3 80.0 + - - +
25S LEU* 1.3 58.1 + - + +
26S ARG 3.0 6.7 + - - -
27S THR* 3.0 33.1 + - - +
32S VAL* 4.4 6.9 - - + +
35S LEU* 4.5 19.3 - - + -
36S ILE* 6.1 0.2 - - + -
42S MET* 6.0 5.6 - - + -
45S HIS* 6.3 0.4 - - - +
109S ILE* 4.0 11.0 - - + -
152S PRO* 5.1 3.4 - - + -
155S PHE* 3.7 39.5 - - + -
156S VAL* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L VAL* 5.4 10.5 - - + -
114L HIS* 6.3 1.3 - - + +
200L LEU* 5.3 7.0 - - + -
203L GLN* 2.8 34.4 + - - +
204L VAL* 3.7 4.2 - - - +
21S SER* 3.5 11.0 + - - +
22S GLU* 3.3 39.2 + - - +
24S VAL* 1.3 74.9 - - + +
26S ARG* 1.3 64.4 + - - +
27S THR* 3.4 4.0 + - - +
32S VAL* 4.1 33.6 + - + +
45S HIS* 6.1 1.1 - - - +
47S THR* 6.3 2.7 - - + -
48S LEU* 4.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L GLY 5.1 1.8 + - - -
67L VAL 5.8 1.4 + - - -
69L THR* 5.7 1.4 - - - +
106L HIS* 3.4 19.1 - - - -
203L GLN* 3.1 25.9 + - - -
204L VAL* 4.4 11.8 - - + +
207L ALA* 3.3 20.3 - - - +
217L ASN* 2.8 46.8 + - - +
218L PRO* 4.0 2.8 - - + +
22S GLU* 2.8 57.7 + - - +
23S SER* 3.5 11.7 - - - +
24S VAL 3.0 1.4 - - - -
25S LEU* 1.3 79.0 - - - +
27S THR* 1.3 67.4 + - - +
28S VAL* 3.4 12.1 + - - +
152S PRO* 4.0 12.3 - - + +
234S ASN* 4.3 10.1 - - - +
235S GLN* 4.7 6.6 + - - +
----------------------------------------------------------
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