Contacts of the helix formed by residues 50 - 61 (chain B) in PDB entry 6K0X
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 GLU 50 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 3.3 38.8 + - - +
7B ASN* 2.8 35.5 + - - +
21B PHE* 3.6 34.9 - - + -
48B LYS 3.4 0.7 + - - +
49B VAL* 1.3 71.9 - - - +
51B TRP* 1.3 64.3 + - - +
52B SER 3.5 1.6 - - - -
53B ALA* 3.5 3.4 + - + +
54B PHE* 3.1 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.0 22.4 - - + -
49B VAL* 3.4 39.6 + - + +
50B GLU* 1.3 71.4 - - - +
52B SER* 1.3 62.2 + - - +
54B PHE* 3.2 10.9 + + - +
55B LEU* 2.8 34.8 + - + +
67B PRO 3.0 21.2 + - - -
68B LYS 3.4 20.4 - - - +
69B GLY* 3.2 24.2 - - - +
70B PRO* 3.8 24.0 - - + -
80B PHE* 3.8 20.9 - + - -
84B MET* 3.7 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU 3.5 0.4 - - - -
51B TRP* 1.3 78.9 - - - +
53B ALA* 1.3 62.8 + - - +
55B LEU* 3.2 13.7 + - - +
56B GLU* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 3.7 9.2 - - + -
7B ASN* 4.0 5.8 - - - +
21B PHE* 3.8 22.7 - - + -
22B PRO* 3.5 31.2 - - + +
50B GLU* 3.5 9.9 + - + +
51B TRP 3.3 0.4 - - - -
52B SER* 1.3 80.1 - - - +
54B PHE* 1.3 61.1 + - - +
56B GLU* 3.5 10.5 - - - +
57B ALA* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.2 21.3 - - + -
6B HIS* 5.3 1.8 - - - -
7B ASN* 3.6 11.6 - - - +
49B VAL* 4.0 7.6 - - + -
50B GLU 3.1 12.4 + - - +
51B TRP* 3.3 24.9 - + - +
53B ALA* 1.3 76.4 - - - +
55B LEU* 1.3 61.2 + - - +
57B ALA* 3.3 4.1 + - - +
58B ALA* 2.8 31.8 + - + +
66B VAL* 3.4 31.2 - - + -
67B PRO 4.2 4.7 - - - -
84B MET* 3.5 30.7 - - + -
87B LEU* 3.8 26.2 - - + -
88B LEU* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TRP* 2.8 30.7 + - + +
52B SER* 3.2 14.6 + - - +
54B PHE* 1.3 76.4 - - + +
56B GLU* 1.3 57.3 + - - +
58B ALA* 3.9 3.1 - - - +
59B ASP* 3.0 27.4 + - - +
66B VAL* 3.7 20.1 - - + +
67B PRO 3.2 26.2 - - - +
68B LYS* 3.8 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 5.9 0.9 - - + -
22B PRO* 3.4 28.5 - - + +
23B LEU 5.8 2.9 - - - +
24B ARG* 5.3 11.3 - - - +
52B SER* 3.1 20.1 + - - +
53B ALA* 3.5 6.9 - - - +
55B LEU* 1.3 74.3 - - - +
57B ALA* 1.3 63.4 + - + +
59B ASP* 3.4 7.0 + - - +
60B ASN* 2.9 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.1 8.7 - - + -
6B HIS* 3.6 26.9 - - + +
25B LEU* 4.1 18.8 - - + +
53B ALA 3.1 19.0 + - - +
54B PHE* 3.8 4.3 - - - +
56B GLU* 1.3 78.8 - - - +
58B ALA* 1.3 63.4 + - - +
60B ASN* 3.1 18.5 + - - +
61B LEU* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.0 11.3 - - + +
54B PHE* 2.8 25.3 + - + +
55B LEU 3.9 2.7 - - - +
57B ALA* 1.3 71.5 - - - +
59B ASP* 1.3 63.4 + - - +
61B LEU 3.2 5.2 + - - -
63B LEU* 3.2 45.3 + - + +
66B VAL* 3.8 32.3 - - + -
87B LEU* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU 3.0 19.4 + - - +
56B GLU* 3.5 8.2 - - - +
57B ALA 3.2 0.2 - - - -
58B ALA* 1.3 76.2 - - - +
60B ASN* 1.3 67.2 + - - +
62B ARG* 2.9 19.1 + - - -
63B LEU 4.7 9.2 - - - +
66B VAL* 5.2 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 4.3 7.5 - - - +
25B LEU* 2.8 35.8 + - - +
26B GLN* 3.6 26.6 + - - +
27B ALA 5.5 2.8 + - - +
56B GLU* 2.9 31.9 + - - +
57B ALA* 3.1 8.3 + - - +
59B ASP* 1.3 79.7 - - - +
61B LEU* 1.3 63.1 + - + +
62B ARG* 3.3 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.9 23.6 - - + -
25B LEU* 3.8 16.4 - - + -
27B ALA* 3.7 31.6 - - + +
30B VAL* 4.1 16.9 - - + +
57B ALA 3.2 12.2 + - - +
58B ALA 3.7 7.2 - - - +
59B ASP 3.0 1.2 + - - -
60B ASN* 1.3 80.6 - - + +
62B ARG* 1.3 73.2 + - - +
63B LEU* 3.2 13.7 + - + +
91B VAL* 3.8 25.4 - - + -
93B VAL* 3.8 18.4 - - + -
----------------------------------------------------------
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