Contacts of the helix formed by residues 47 - 58 (chain U) in PDB entry 4QLC
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 ARG 47 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J G 3.2 38.3 + - - -
85J C 2.9 42.2 + - - -
46U SER* 1.3 77.0 - - - +
48U GLN* 1.3 84.8 + - - +
50U ILE* 3.6 2.9 + - - +
51U GLN* 2.9 71.4 + - + +
68U ILE* 4.6 8.4 - - + +
69U LYS* 5.8 6.0 - - + +
72U ILE* 4.8 10.8 - - + -
89U ALA* 3.6 23.0 + - + +
90U SER* 3.7 16.4 + - - +
91U GLY 3.7 5.1 + - - +
93U PHE* 4.0 6.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I T 5.1 3.8 + - - -
86I G 3.1 36.4 + - - +
87I T 3.7 24.6 + - - +
83J A 6.0 2.0 - - - -
46U SER* 2.9 25.8 + - - -
47U ARG* 1.3 104.8 + - - +
49U SER* 1.3 64.6 + - - +
51U GLN* 3.3 14.2 + - - +
52U LYS* 3.3 22.9 + - - +
90U SER* 5.7 2.4 + - - +
91U GLY 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I T 2.8 24.1 + - - -
39U GLU* 4.0 28.1 + - - +
45U SER* 4.5 1.5 - - - -
46U SER* 2.9 20.7 + - - -
48U GLN* 1.3 78.4 - - - +
50U ILE* 1.3 61.9 + - - +
52U LYS* 3.5 3.3 + - - +
53U TYR* 3.2 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32U ILE* 4.0 18.8 - - + -
35U ALA* 3.9 24.5 - - + +
36U ILE* 3.7 28.0 - - + +
39U GLU* 5.5 0.7 - - - +
45U SER* 3.8 18.4 - - - +
46U SER 3.2 21.7 + - - +
47U ARG* 4.0 3.6 - - - +
48U GLN 3.4 0.4 - - - -
49U SER* 1.3 78.7 - - - +
51U GLN* 1.3 59.2 + - - +
53U TYR* 3.1 3.4 + - - +
54U ILE* 2.8 31.8 + - + +
68U ILE* 3.9 27.4 - - + -
72U ILE* 4.8 10.8 - - + -
81U LEU* 6.0 0.2 - - + -
93U PHE* 4.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47U ARG* 2.9 53.0 + - - +
48U GLN* 3.3 17.5 - - - +
50U ILE* 1.3 78.4 - - - +
52U LYS* 1.3 60.0 + - - +
54U ILE* 4.0 5.0 - - - +
55U LYS* 3.0 45.6 + - - +
64U ALA* 6.4 0.7 - - + -
65U ASP* 3.4 32.7 + - - +
68U ILE* 4.0 26.8 - - + +
69U LYS* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I C 4.8 13.9 - - - +
48U GLN 3.3 13.4 + - - +
49U SER* 4.2 3.4 - - - +
50U ILE 3.3 0.2 - - - -
51U GLN* 1.3 76.2 - - - +
53U TYR* 1.3 63.8 + - - +
55U LYS* 3.6 10.6 + - + +
56U SER* 3.0 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34U ALA* 4.3 2.8 + - - +
35U ALA* 3.4 39.3 - - + +
38U ALA* 3.3 32.3 - - + +
39U GLU* 5.9 6.3 - - + +
49U SER 3.2 13.5 + - - +
50U ILE* 3.1 7.5 + - - +
52U LYS* 1.3 77.8 - - - +
54U ILE* 1.3 62.2 + - + +
56U SER* 3.2 4.6 + - - -
57U HIS* 2.9 82.6 + + + +
58U TYR* 4.2 12.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28U TYR* 5.3 1.1 - - + -
31U MET* 3.2 52.7 - - + +
35U ALA* 3.8 7.6 - - + -
50U ILE* 2.8 32.3 + - + +
51U GLN* 4.0 6.1 - - - +
53U TYR* 1.3 76.7 - - + +
55U LYS* 1.3 60.1 + - + +
58U TYR* 3.0 53.8 + - + +
60U VAL* 4.2 20.6 - - + +
64U ALA* 5.2 2.5 - - + -
68U ILE* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51U GLN* 3.0 32.8 + - - +
52U LYS* 4.0 10.6 - - + +
53U TYR 3.2 0.4 - - - -
54U ILE* 1.3 78.8 - - + +
56U SER* 1.3 57.6 + - - +
58U TYR 3.5 14.2 - - - +
60U VAL* 4.5 18.1 - - + +
64U ALA* 4.7 11.0 - - + -
65U ASP* 3.6 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52U LYS* 3.0 22.8 + - - +
53U TYR* 3.2 7.5 + - - -
55U LYS* 1.3 78.9 - - - +
57U HIS* 1.3 75.6 + - - +
58U TYR 3.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 57 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53U TYR* 2.9 68.8 + + + +
56U SER* 1.3 89.7 + - - +
58U TYR* 1.3 89.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U HIS* 5.4 0.2 - - + -
26U PRO* 4.6 14.4 - - + -
30U GLU* 4.8 2.6 + - - -
31U MET* 3.5 38.8 - - + -
34U ALA* 3.5 23.7 - - + +
53U TYR* 4.2 9.6 + + - -
54U ILE* 3.0 48.5 + - + +
55U LYS 3.5 16.6 - - - +
56U SER 3.4 1.0 - - - -
57U HIS* 1.3 103.4 - - + +
59U LYS* 1.3 65.5 + - - +
60U VAL* 3.3 8.0 + - + +
----------------------------------------------------------
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