Contacts of the helix formed by residues 1 - 13 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C MET* 1.3 87.0 + - - +
2C LEU* 1.3 65.4 + - - +
3C GLU* 3.8 1.6 - - - -
4C ASN* 2.8 27.8 + - - +
5C VAL* 2.8 31.1 + - - +
21C GLU* 3.7 11.1 + - - -
1F SER* 3.4 30.5 - - - -
3F GLU* 3.5 7.6 - - - -
21F GLU* 5.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 2 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER* 1.3 71.2 - - - +
3C GLU* 1.3 66.0 + - - +
5C VAL* 3.5 7.4 + - - +
6C ALA* 2.9 28.6 + - - +
24C VAL* 3.6 29.4 - - + -
26C ILE* 3.4 32.3 - - + -
31C VAL* 4.6 5.2 - - + -
52C ASN* 4.5 13.2 - - + +
55C PHE* 3.7 26.7 - - + -
2F LEU* 3.8 23.6 - - + -
3F GLU* 3.1 20.5 + - - +
52F ASN* 4.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 3 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER* 2.9 2.6 - - - -
2C LEU* 1.3 90.3 + - - +
4C ASN* 1.3 60.1 + - - +
6C ALA* 3.6 1.3 - - - +
7C TYR 3.0 21.5 + - - -
21C GLU* 3.4 22.9 - - + -
22C ALA 3.0 37.4 + - - +
23C PRO* 4.6 5.2 - - + -
24C VAL* 4.5 13.4 + - + +
1F SER* 3.5 11.7 - - - +
2F LEU* 3.0 34.1 + - - +
52F ASN* 4.5 7.6 + - - -
56F GLU* 5.1 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 4 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C MET* 3.8 22.3 - - - +
1C SER* 2.8 27.5 + - - +
3C GLU* 1.3 75.0 - - - +
5C VAL* 1.3 65.9 + - - +
7C TYR* 3.4 1.7 + - - +
8C ASN* 2.8 32.0 + - - -
15C PHE* 3.3 29.9 - - - -
17C GLY 6.1 0.2 - - - -
18C HIS 3.2 21.5 + - - +
19C ALA* 4.2 2.3 - - - -
20C GLY 3.3 21.6 + - - +
21C GLU* 3.9 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 5 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C MET 5.5 0.9 - - - +
1C SER 2.8 19.5 + - - +
2C LEU* 3.6 9.6 - - - +
4C ASN* 1.3 77.0 - - - +
6C ALA* 1.3 62.5 + - - +
8C ASN* 3.2 5.5 + - - +
9C VAL* 3.0 25.3 + - - +
15C PHE* 4.1 19.7 - - + -
55C PHE* 3.6 23.8 - - + -
56C GLU* 3.2 37.5 - - + +
59C ALA* 3.5 28.7 - - + -
60C LYS* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU 2.9 18.3 + - - +
3C GLU 3.6 7.2 - - - +
5C VAL* 1.3 76.7 - - - +
7C TYR* 1.3 61.3 + - - +
9C VAL* 3.1 3.9 + - - +
10C VAL* 3.0 27.0 + - - +
22C ALA* 4.0 11.9 - - + +
24C VAL* 3.6 28.0 - - + -
33C THR* 5.4 0.7 - - - +
42C ILE* 4.5 5.6 - - + -
55C PHE* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU 3.0 19.1 + - - +
4C ASN 3.7 2.0 - - - +
6C ALA* 1.3 74.7 - - - +
8C ASN* 1.3 69.0 + - - +
10C VAL* 3.4 1.2 - - - +
11C ASN* 3.0 69.3 + - + +
12C LYS* 5.4 3.4 - - + -
18C HIS* 4.6 10.5 - - + -
19C ALA 3.5 24.3 + - - -
20C GLY* 3.5 19.1 - - - +
21C GLU 3.4 21.1 - - - +
22C ALA* 3.6 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ASN* 2.8 25.0 + - - +
5C VAL 3.2 8.7 + - - +
7C TYR* 1.3 85.6 - - - +
9C VAL* 1.3 56.6 + - - +
12C LYS* 2.8 29.0 + - - -
13C GLY 3.1 1.4 + - - -
14C HIS 2.9 21.2 - - - +
15C PHE* 3.5 19.3 - - + -
16C ASP* 2.7 29.7 + - - +
17C GLY 2.9 12.0 + - - -
18C HIS* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.2 33.3 - - + +
5C VAL 3.0 14.8 + - - +
6C ALA* 3.1 6.9 + - - +
8C ASN* 1.3 78.3 - - - +
10C VAL* 1.3 62.2 + - - +
13C GLY* 3.2 12.7 + - - +
14C HIS* 3.9 11.9 - - - +
42C ILE* 4.6 14.8 - - + -
55C PHE* 4.0 16.6 - - + -
58C TRP* 3.7 28.3 - - + -
59C ALA* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.3 22.1 - - - -
269B ILE* 4.0 24.7 - - + +
6C ALA 3.0 21.0 + - - +
7C TYR* 3.4 11.7 - - - +
9C VAL* 1.3 76.6 - - - +
11C ASN* 1.3 75.6 + - - +
22C ALA* 4.1 11.2 - - + -
33C THR* 3.8 30.5 - - + -
35C VAL* 6.0 0.4 - - + -
42C ILE* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 4.6 2.6 - - - -
291B VAL* 4.3 17.0 - - - +
7C TYR* 3.0 59.7 + - + +
10C VAL* 1.3 91.7 + - - +
12C LYS* 1.3 77.2 + - + +
13C GLY 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 4.8 1.3 - - - -
290B CYS* 3.5 14.2 - - - +
291B VAL* 4.2 21.5 - - + +
7C TYR* 5.4 2.9 - - + -
8C ASN* 2.8 21.6 + - - +
11C ASN* 1.3 92.1 - - + +
13C GLY* 1.3 57.2 + - - +
14C HIS* 3.4 17.7 - - + +
16C ASP* 3.4 37.3 + - + +
18C HIS* 3.5 40.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B GLU* 5.3 0.9 - - - +
268B PHE* 3.8 33.4 - - - +
279B PHE* 4.0 14.0 - - - -
290B CYS* 4.7 0.7 - - - -
8C ASN 3.1 2.8 + - - -
9C VAL* 3.2 21.3 + - - +
11C ASN 3.7 1.0 - - - -
12C LYS* 1.3 76.7 - - - +
14C HIS* 1.3 64.7 + - - +
58C TRP* 5.0 0.9 - - - -
61C ARG* 3.6 11.1 + - - -
----------------------------------------------------------
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