Contacts of the helix formed by residues 45 - 56 (chain B) in PDB entry 2I6A
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 HIS 45 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 3.7 17.4 + - - +
32B SER 5.5 0.9 - - - -
33B LEU* 4.1 13.0 - - + -
39B ILE* 3.7 12.4 - - + +
40B LEU 4.2 0.7 - - - -
41B ALA* 3.6 17.9 - - + -
42B GLU* 2.8 55.8 - - + +
43B ASP 2.9 0.6 - - - -
44B LYS* 1.3 105.9 + - - +
46B LYS* 1.3 57.4 + - - +
47B GLU 3.0 3.6 - - - -
48B LEU* 2.5 56.9 + - + +
49B PHE* 3.7 7.0 + - + -
135B ILE* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 3.8 3.2 + - - +
43B ASP* 3.2 39.3 + - + +
45B HIS* 1.3 77.6 - - - +
47B GLU* 1.3 59.3 + - - +
48B LEU 3.4 0.3 + - - -
49B PHE* 3.8 15.1 + - - +
50B ASP* 3.7 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 3.0 30.6 + - + +
44B LYS 5.3 1.1 - - - +
45B HIS 3.0 0.6 - - - +
46B LYS* 1.3 78.1 - - - +
48B LEU* 1.3 64.4 + - - +
49B PHE 3.3 0.4 - - - -
50B ASP* 3.6 9.9 + - + +
51B GLU* 3.4 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 3.8 19.8 - - + -
31B TYR* 3.4 30.3 - - + -
33B LEU* 3.8 31.0 - - + -
45B HIS* 2.5 38.7 + - + +
47B GLU* 1.3 73.6 - - - +
49B PHE* 1.3 70.5 + - + +
51B GLU* 4.0 0.3 - - - +
52B LEU* 3.2 23.8 + - + +
124B ALA* 3.9 28.3 - - + -
126B CYS* 4.4 4.7 - - - -
135B ILE* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 5.4 7.9 - - + -
41B ALA* 4.1 14.4 - - + -
45B HIS* 3.8 15.5 - - + -
46B LYS* 3.8 8.9 + - - +
47B GLU 3.3 0.8 - - - -
48B LEU* 1.3 82.2 - - + +
50B ASP* 1.3 61.1 + - - +
52B LEU* 3.6 7.2 + - + +
53B VAL* 3.0 32.9 + - + +
122B THR* 4.2 20.4 - - - -
123B CYS 4.4 1.8 - - - -
124B ALA* 3.6 34.3 - - + -
135B ILE* 3.5 28.7 - - + -
137B ASN* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS 3.7 13.9 - - - +
47B GLU* 3.6 11.7 + - + +
48B LEU 3.4 0.2 - - - -
49B PHE* 1.3 80.7 - - - +
51B GLU* 1.3 56.7 + - - +
53B VAL* 3.6 4.4 + - - +
54B LYS* 3.0 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 3.6 25.7 - - + -
30B LYS* 5.8 4.2 - - - +
31B TYR* 2.5 33.2 + - - +
47B GLU* 3.4 19.1 + - + +
48B LEU 4.0 0.4 - - - +
50B ASP* 1.3 75.1 - - + +
52B LEU* 1.3 62.3 + - - +
53B VAL 3.2 1.1 - - - -
54B LYS* 3.7 9.9 - - + -
55B LYS* 2.8 63.4 + - + +
56B PHE* 3.7 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 3.7 39.7 - - + +
21B ALA* 3.6 29.4 - - + +
23B VAL* 3.9 20.9 - - + -
27B PHE* 3.9 13.7 - - + -
48B LEU* 3.2 22.8 + - + +
49B PHE* 3.8 7.0 - - + +
50B ASP 3.4 0.4 - - - -
51B GLU* 1.3 75.8 - - - +
53B VAL* 1.3 61.6 + - + +
56B PHE* 3.1 39.8 + - + +
58B VAL* 4.2 5.0 - - + +
124B ALA* 4.1 19.3 - - + -
126B CYS* 4.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.6 17.3 - - + -
49B PHE* 3.0 21.7 + - + +
50B ASP* 4.0 4.3 - - - +
51B GLU 3.2 0.2 - - - -
52B LEU* 1.3 81.1 - - + +
54B LYS* 1.3 60.6 + - + +
56B PHE 3.5 13.2 - - - +
58B VAL* 3.5 19.9 - - + +
60B TYR* 3.4 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 3.0 50.1 + - - +
51B GLU* 4.0 7.9 - - + -
53B VAL* 1.3 79.2 - - + +
55B LYS* 1.3 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU* 2.8 54.7 + - + +
54B LYS* 1.3 80.2 - - + +
56B PHE* 1.3 79.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.8 15.7 - - + -
22B VAL 3.1 19.5 - - - +
23B VAL* 3.6 23.3 - - + -
24B ASP* 3.8 22.2 - - - -
27B PHE* 3.8 32.1 - + - -
51B GLU 3.7 4.9 - - - -
52B LEU* 3.1 23.8 + - - +
53B VAL 3.5 15.2 - - - +
54B LYS 3.6 0.4 - - - -
55B LYS* 1.3 102.8 - - + +
57B LYS* 1.3 63.2 + - - +
58B VAL* 3.0 7.9 + - - +
----------------------------------------------------------
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