Contacts of the helix formed by residues 1 - 13 (chain F) in PDB entry 2RHB
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 SER 1 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C MET 4.8 0.5 + - - -
1C SER* 3.4 31.5 - - - -
3C GLU* 3.5 20.0 - - - -
21C GLU* 4.9 12.4 + - - +
2F LEU* 1.3 63.5 + - - +
3F GLU* 4.1 0.9 + - - -
4F ASN* 3.5 26.8 + - - +
5F VAL* 3.3 27.6 + - - +
21F GLU* 4.4 7.3 + - - -
56F GLU* 5.4 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 2 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU* 3.8 23.1 - - + -
3C GLU* 3.0 22.3 + - - +
52C ASN* 5.0 1.3 - - - +
1F SER* 1.3 71.5 - - - +
3F GLU* 1.3 76.7 + - - +
5F VAL* 3.1 17.4 + - - +
6F ALA* 3.1 10.4 + - - +
24F VAL* 3.8 20.4 - - + -
26F ILE* 3.4 31.6 - - + -
31F VAL* 5.0 2.9 - - + -
52F ASN* 4.4 17.0 - - + +
55F PHE* 3.7 28.9 - - + -
56F GLU* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 3 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C MET* 3.7 19.5 - - - +
1C SER* 3.5 7.4 + - - -
2C LEU* 3.1 30.9 + - - +
52C ASN* 5.0 8.3 + - - +
103C THR* 6.1 3.6 - - + -
1F SER* 3.6 1.5 + - - +
2F LEU* 1.3 88.5 - - - +
4F ASN* 1.3 56.4 + - - +
6F ALA* 3.7 3.0 + - - -
7F TYR 3.1 12.3 + - - -
21F GLU* 3.7 11.4 - - + -
22F ALA 2.9 46.2 + - - +
23F PRO* 4.8 5.4 - - + -
24F VAL* 4.8 9.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 4 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F SER* 3.5 25.9 + - - +
2F LEU 3.1 0.4 - - - -
3F GLU* 1.3 76.7 - - - +
5F VAL* 1.3 65.2 + - - +
7F TYR* 3.0 10.9 + - - +
8F ASN* 2.8 24.5 + - - +
15F PHE* 3.3 33.5 - - - -
17F GLY* 5.6 1.0 - - - -
18F HIS 2.9 23.6 + - - +
19F ALA* 4.0 1.6 - - - -
20F GLY 2.9 27.8 + - - +
21F GLU* 4.1 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 5 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F SER 3.3 17.5 - - - +
2F LEU* 3.1 10.0 + - - +
4F ASN* 1.3 77.3 - - - +
6F ALA* 1.3 56.0 + - - +
8F ASN* 3.4 4.5 + - - +
9F VAL* 3.0 27.0 + - - +
15F PHE* 4.2 22.0 - - + -
55F PHE* 3.6 24.7 - - + -
56F GLU* 4.1 32.5 - - + -
59F ALA* 3.5 28.2 - - + +
60F LYS* 4.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 6 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU 3.1 8.8 + - - +
3F GLU 3.8 9.2 - - - +
4F ASN 3.2 0.2 - - - -
5F VAL* 1.3 74.7 - - - +
7F TYR* 1.3 59.2 + - - +
9F VAL* 3.1 2.2 + - - +
10F VAL* 2.9 35.7 + - + +
22F ALA* 4.1 8.5 - - + -
24F VAL* 3.7 29.8 - - + -
33F THR* 5.5 0.4 - - - +
42F ILE* 4.3 6.1 - - + -
55F PHE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F GLU 3.1 10.7 + - - +
4F ASN 3.0 9.5 + - - +
6F ALA* 1.3 75.0 - - - +
8F ASN* 1.3 69.2 + - - +
10F VAL* 3.3 1.3 - - - +
11F ASN* 3.0 67.7 + - + +
12F LYS* 5.5 5.6 + - + -
18F HIS* 4.5 10.8 - + + -
19F ALA 3.3 23.0 + - - -
20F GLY* 3.5 21.5 - - - +
21F GLU 3.7 20.6 - - - -
22F ALA* 3.7 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 8 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ASN* 2.8 30.7 + - - -
5F VAL 3.5 7.4 - - - +
7F TYR* 1.3 80.1 - - - +
9F VAL* 1.3 56.2 + - - +
12F LYS* 2.7 33.2 + - - +
13F GLY 3.3 0.2 + - - -
14F HIS 3.0 22.6 - - - +
15F PHE* 3.6 24.4 - - + -
16F ASP* 3.0 23.4 + - + +
17F GLY 3.2 0.2 + - - -
18F HIS* 3.2 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E PHE* 3.2 25.7 - - + +
5F VAL 3.0 18.1 + - - +
6F ALA* 3.1 9.8 + - - +
8F ASN* 1.3 77.7 - - - +
10F VAL* 1.3 61.2 + - + +
13F GLY* 3.3 11.3 + - - +
14F HIS* 4.1 14.6 - - - +
42F ILE* 4.3 23.8 - - + -
55F PHE* 4.0 10.3 - - + -
58F TRP* 4.0 29.2 - - + -
59F ALA* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E PHE* 3.5 19.6 - - - +
269E ILE* 4.2 22.0 - - + +
277E ASN* 5.8 1.0 + - - -
6F ALA* 2.9 18.9 + - + +
7F TYR* 3.3 14.6 - - - +
9F VAL* 1.3 77.5 - - + +
11F ASN* 1.3 78.4 + - - +
22F ALA* 4.3 9.6 - - + -
33F THR* 3.9 31.4 - - + +
35F VAL* 6.3 0.9 - - + -
42F ILE* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E VAL* 3.4 17.6 - - - +
7F TYR* 3.0 65.6 + - + +
10F VAL* 1.3 93.1 - - - +
12F LYS* 1.3 76.9 + - + +
13F GLY 3.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E CYS* 3.6 12.6 - - - +
291E VAL* 4.0 20.8 - - + +
7F TYR* 5.5 5.2 + - + -
8F ASN* 2.7 22.1 + - - +
11F ASN* 1.3 91.1 - - + +
13F GLY* 1.3 55.2 + - - +
14F HIS* 3.0 28.2 + - - +
16F ASP* 3.8 26.5 - - + +
18F HIS* 3.5 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 13 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E GLU* 5.1 1.6 - - - +
268E PHE* 3.9 37.0 - - - +
279E PHE* 4.5 6.9 - - - -
290E CYS* 4.6 6.3 - - - -
9F VAL* 3.3 25.5 + - - +
11F ASN 3.8 1.4 - - - -
12F LYS* 1.3 74.4 - - - +
14F HIS* 1.3 61.1 + - - +
58F TRP* 5.0 1.9 - - - -
61F ARG* 3.5 12.6 + - - -
----------------------------------------------------------
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