Contacts of the helix formed by residues 46 - 51 (chain Q) in PDB entry 2QJK
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 PRO 46 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P ARG* 4.2 15.7 - - + +
86P ASN* 4.7 7.0 - - - +
44Q PHE 3.4 10.5 - - - +
45Q VAL* 1.3 84.1 - - + +
47Q ILE* 1.3 63.0 + - - +
48Q ARG* 3.2 37.5 - - + +
49Q SER* 2.2 50.3 + - - +
52Q GLU* 5.3 0.4 - - - +
85Q PRO 5.1 0.2 - - - +
86Q THR 5.8 1.6 - - - +
87Q ASP 3.9 5.2 - - - +
88Q HIS* 3.1 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Q VAL 3.3 1.4 + - - -
46Q PRO* 1.3 69.4 - - - +
48Q ARG* 1.3 52.5 + - - +
50Q LEU* 2.5 62.5 + - + +
63Q VAL* 4.2 8.7 - - + -
66Q TYR* 4.2 7.9 - - + -
67Q ALA* 4.1 26.5 - - + +
70Q PHE* 3.9 29.6 - - + -
83Q GLY* 5.7 0.9 - - - -
84Q LYS 4.1 4.7 - - - +
85Q PRO* 3.9 5.4 - - + +
87Q ASP* 2.8 34.5 + - + +
88Q HIS 4.3 6.5 - - - +
89Q PHE* 3.8 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P ASN* 3.1 27.7 + - - +
46Q PRO* 4.0 23.8 - - + +
47Q ILE* 1.3 71.9 - - - +
49Q SER* 1.3 61.8 + - - +
50Q LEU 3.0 0.9 - - - -
51Q SER* 3.4 24.1 + - - +
52Q GLU* 2.9 38.8 + - - +
63Q VAL* 4.3 1.3 - - - -
85Q PRO* 2.8 41.9 + - + +
86Q THR* 4.1 20.2 + - - +
88Q HIS* 5.8 0.6 - - - -
42R ALA* 3.4 22.4 + - - +
43R ASP* 3.3 28.7 + - - +
46R ALA* 5.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P ARG* 5.4 1.9 + - - -
45Q VAL* 3.6 15.1 - - - +
46Q PRO* 2.2 42.4 + - - +
47Q ILE 2.6 3.9 + - - -
48Q ARG* 1.3 72.8 - - - +
50Q LEU* 1.3 68.2 + - - +
51Q SER 2.9 3.7 + - - -
52Q GLU* 3.1 38.0 + - - +
56Q PRO* 4.6 0.2 - - - +
217Q TRP* 3.5 25.1 - - - -
221Q PRO* 5.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q LEU* 3.6 30.1 - - + -
47Q ILE* 2.5 42.1 + - + +
49Q SER* 1.3 80.2 + - - +
51Q SER* 1.3 53.7 + - - +
56Q PRO* 3.9 9.8 - - + +
57Q GLU 3.1 13.0 + - - -
58Q LEU* 3.0 26.7 + - + -
63Q VAL* 3.9 17.7 - - + -
66Q TYR* 4.2 17.5 - - + -
89Q PHE* 3.9 23.8 - - + -
214Q PHE* 4.7 1.8 - - + -
217Q TRP* 4.1 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q ARG* 3.4 13.8 + - - +
49Q SER 2.9 0.6 - - - -
50Q LEU* 1.3 75.5 - - - +
52Q GLU* 1.3 69.2 + - - +
53Q PRO* 3.6 0.9 - - - +
57Q GLU* 3.5 14.6 - - - +
58Q LEU 3.4 17.5 + - - +
60Q GLU* 4.2 20.8 + - - +
63Q VAL* 3.3 25.8 - - - +
----------------------------------------------------------
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