Contacts of the helix formed by residues 46 - 57 (chain L) in PDB entry 2R1J
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 ASN 46 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A A 5.6 0.2 + - - -
32A T 4.5 20.4 + - - +
12B T 3.9 13.1 + - - +
13B C 2.8 21.9 + - - +
44L GLU 3.6 1.2 + - - -
45L PRO* 1.3 76.4 - - - +
47L GLY* 1.3 60.4 + - - +
48L GLU* 3.3 7.4 + - - +
49L ASN* 2.8 37.5 + - - +
50L LEU* 2.8 26.9 + - - +
46R ASN* 4.2 11.2 - - + +
47R GLY 3.5 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ASN* 1.3 76.4 - - - +
48L GLU* 1.3 63.9 + - - +
50L LEU* 3.4 0.9 + - - +
51L LEU* 3.2 28.2 + - - +
44R GLU* 6.4 0.2 - - - -
45R PRO 3.3 24.2 + - - -
46R ASN 3.9 6.7 - - - -
47R GLY* 3.4 5.4 - - - +
50R LEU* 3.7 20.9 - - - +
65R LEU* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ASN* 3.3 7.8 + - - +
47L GLY* 1.3 75.1 - - - +
49L ASN* 1.3 71.5 + - - +
51L LEU* 3.4 3.8 + - - +
52L ALA* 3.0 24.3 + - + +
44R GLU* 4.4 15.5 + - - +
65R LEU* 4.0 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B C 2.8 37.0 + - - +
28L VAL* 4.0 11.7 - - + +
29L GLY 5.1 1.2 - - - +
30L VAL* 3.6 27.6 - - - +
38L TRP* 3.8 14.0 - - + -
45L PRO* 4.2 2.0 - - - -
46L ASN* 2.8 24.8 + - - +
48L GLU* 1.3 84.1 - - - +
50L LEU* 1.3 59.8 + - - +
52L ALA* 3.3 5.0 + - - +
53L LEU* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L MET* 4.2 12.6 - - - -
45L PRO* 3.8 26.2 - - + +
46L ASN 2.8 21.1 + - - +
47L GLY 3.9 3.4 - - - +
48L GLU 3.4 0.2 - - - -
49L ASN* 1.3 72.7 - - - +
51L LEU* 1.3 64.3 + - + +
53L LEU* 3.3 4.5 + - + +
54L SER* 2.9 22.9 + - - -
61L PRO* 4.1 12.8 - - + +
64L LEU* 4.1 26.2 - - + -
65L LEU* 3.8 23.6 - - + -
47R GLY* 3.7 30.5 - - - +
51R LEU* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L GLY 3.2 11.6 + - - +
48L GLU 3.8 2.5 - - - +
50L LEU* 1.3 80.6 - - + +
52L ALA* 1.3 61.4 + - - +
54L SER* 2.6 21.4 + - - +
55L LYS* 3.2 36.6 + - - +
61L PRO* 3.8 27.1 - - + -
50R LEU* 4.0 7.6 - - + -
51R LEU* 4.1 9.2 - - + -
61R PRO* 3.9 27.1 - - + -
62R ASP* 3.7 15.5 - - - +
65R LEU* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L MET 5.2 2.8 - - - +
28L VAL* 3.9 30.4 - - + +
48L GLU* 3.0 19.2 + - + +
49L ASN* 3.9 5.4 - - - +
51L LEU* 1.3 75.8 - - - +
53L LEU* 1.3 57.8 + - - +
55L LYS* 3.4 10.5 + - - +
56L ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L ILE* 3.6 33.4 - - + -
24L LEU* 4.0 21.3 - - + -
28L VAL* 3.8 17.9 - - + +
38L TRP* 3.8 24.5 - - + -
45L PRO* 4.3 12.6 - - + -
49L ASN 2.8 18.4 + - - +
50L LEU* 3.5 3.6 - - + +
51L LEU 3.2 0.2 - - - -
52L ALA* 1.3 74.6 - - - +
54L SER* 1.3 65.2 + - - +
56L ALA* 3.2 1.4 + - - +
57L LEU* 2.9 46.1 + - + +
64L LEU* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L LEU 2.9 13.5 + - - -
51L LEU* 2.6 28.8 + - - +
53L LEU* 1.3 76.1 - - - +
55L LYS* 1.3 60.5 + - - +
57L LEU 3.5 0.5 + - - -
58L GLN 3.0 7.4 + - - -
59L CYS* 2.9 46.6 + - - +
60L SER 3.9 2.2 - - - -
61L PRO* 3.7 29.3 - - - +
64L LEU* 4.1 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L LEU* 3.2 29.8 + - - +
52L ALA* 3.7 9.9 - - - +
54L SER* 1.3 85.6 + - - +
56L ALA* 1.3 62.7 + - - +
58L GLN* 3.0 17.8 + - - +
59L CYS 5.0 0.2 - - - -
62R ASP* 3.2 37.9 + - - -
66R LYS* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L LEU* 4.6 8.3 - - - +
19L ILE* 5.8 0.9 - - - +
24L LEU* 3.7 25.2 - - + +
27L MET* 3.8 36.9 - - + +
28L VAL* 4.0 9.0 - - + -
52L ALA 3.0 17.2 + - - +
53L LEU 3.7 3.4 - - - +
55L LYS* 1.3 77.0 - - - +
57L LEU* 1.3 62.9 + - - +
58L GLN* 3.6 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L ILE* 4.1 20.0 - - + +
13L ARG* 2.8 57.3 + - + +
14L ARG* 4.0 25.4 - - + +
17L LEU* 5.0 6.7 - - + -
19L ILE* 5.5 1.3 - - + -
24L LEU* 3.8 25.8 - - + -
53L LEU* 2.9 43.2 + - + +
56L ALA* 1.3 75.8 - - - +
58L GLN* 1.3 63.7 + - - +
59L CYS* 3.4 8.5 + - - -
64L LEU* 4.2 11.0 - - + -
----------------------------------------------------------
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