Contacts of the helix formed by residues 41 - 58 (chain C) in PDB entry 4QKB
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 SER 41 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 1.3 74.3 - - - +
42C THR* 1.3 54.4 + - - +
43C ALA* 3.5 10.0 + - - +
44C GLU* 2.9 32.4 + - - +
45C GLU* 2.7 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C SER* 1.3 72.7 - - - +
43C ALA* 1.3 51.4 + - - +
45C GLU* 3.2 15.2 + - + +
46C GLU* 2.7 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C SER* 3.1 9.0 + - - +
42C THR* 1.3 78.2 - - - +
44C GLU* 1.3 55.2 + - + +
46C GLU* 3.5 15.6 + - - +
47C THR* 2.6 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE 3.9 0.3 - - - +
40C LEU* 3.5 14.9 - - + -
41C SER* 2.9 36.0 + - - +
43C ALA* 1.3 77.3 - - + +
45C GLU* 1.3 65.3 + - - +
47C THR* 4.0 1.8 - - - +
48C LEU* 3.3 29.5 + - - +
87C ALA* 6.2 0.2 - - - +
88C ILE* 3.6 34.4 - - + +
91C ARG* 2.8 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 4.5 5.6 - - + +
41C SER 2.7 22.1 + - - +
42C THR* 3.4 16.5 + - + +
44C GLU* 1.3 70.4 - - - +
46C GLU* 1.3 64.4 + - - +
48C LEU* 3.2 4.3 + - - +
49C SER* 3.0 29.0 + - - +
137C LEU* 4.3 18.1 - - + +
138C LEU 5.3 2.9 + - - -
161C PRO* 3.7 17.5 - - - +
162C GLY* 3.4 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C THR* 2.7 23.6 + - + +
43C ALA* 3.8 15.1 - - - +
45C GLU* 1.3 73.4 - - - +
47C THR* 1.3 75.0 + - - +
49C SER* 4.6 4.7 - - - -
50C ARG* 2.9 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA 2.6 30.8 + - - -
44C GLU* 3.8 8.1 - - - +
46C GLU* 1.3 82.0 + - - +
48C LEU* 1.3 62.2 + - - +
50C ARG* 3.6 3.4 + - - +
51C GLU* 3.2 26.9 + - - +
84C ALA* 3.6 33.5 - - + +
85C SER* 3.7 18.8 - - - +
88C ILE* 4.2 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.7 30.5 - - + -
44C GLU 3.3 11.2 + - - +
45C GLU 3.2 5.2 + - - +
47C THR* 1.3 75.6 - - - +
49C SER* 1.3 64.7 + - - +
51C GLU* 3.3 3.0 + - - -
52C LEU* 2.9 39.0 + - + +
81C TRP* 4.5 16.2 - - + -
85C SER* 4.0 19.3 - - - +
88C ILE* 4.0 19.3 - - + -
89C MSE 5.2 5.8 - - - -
135C LEU* 4.1 16.2 - - + -
137C LEU* 4.0 24.0 - - + -
200C VAL* 4.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLU* 3.0 18.4 + - - +
46C GLU* 3.9 4.0 - - - -
48C LEU* 1.3 74.5 - - - +
50C ARG* 1.3 77.5 + - - +
52C LEU* 5.0 1.8 - - - -
53C GLU* 3.1 32.6 + - - +
137C LEU* 4.9 9.8 - - - +
138C LEU* 3.7 25.3 - - - +
198C ILE* 5.4 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 2.9 60.7 + - + +
47C THR* 3.9 4.0 - - - +
49C SER* 1.3 89.7 - - - +
51C GLU* 1.3 61.0 + - - +
53C GLU* 5.4 0.7 - - - -
54C PRO* 3.3 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.2 18.2 + - - +
48C LEU* 3.9 3.1 - - - +
49C SER 3.2 0.8 - - - -
50C ARG* 1.3 78.5 - - - +
52C LEU* 1.3 63.1 + - + +
54C PRO* 3.5 12.4 - - - +
55C GLU* 3.4 15.8 - - - +
78C LYS* 3.5 29.7 + - - +
81C TRP* 3.8 2.1 - - + -
82C SER* 2.7 42.4 + - - -
85C SER* 2.5 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 2.9 34.7 + - + +
49C SER* 4.4 1.6 - - - +
51C GLU* 1.3 78.9 - - + +
53C GLU* 1.3 64.2 + - - +
55C GLU* 3.2 11.3 + - - +
56C LEU* 3.0 36.4 + - + +
76C THR* 5.3 3.4 - - + -
78C LYS* 3.6 33.0 - - + -
81C TRP* 4.1 8.1 - - + -
109C VAL* 3.8 33.0 - - + -
137C LEU* 4.6 1.6 - - + -
198C ILE* 4.5 9.6 - - + -
200C VAL* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C SER* 3.1 18.3 + - - +
50C ARG* 5.1 0.9 - - - +
52C LEU* 1.3 74.0 - - - +
54C PRO* 1.4 72.7 - - + +
56C LEU* 3.2 3.9 + - - +
57C ARG* 2.8 53.0 + - + +
74C ARG* 4.8 0.9 + - - -
196C ARG* 2.7 43.0 + - - -
198C ILE* 4.3 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ARG 3.3 23.8 - - - +
51C GLU 3.5 10.5 - - - +
53C GLU* 1.4 93.8 - - + +
55C GLU* 1.3 63.5 + - + +
57C ARG* 3.6 4.6 + - + +
58C ARG* 3.4 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLU* 3.4 19.9 - - - +
52C LEU* 3.2 12.0 + - + +
53C GLU 3.2 0.8 - - - -
54C PRO* 1.3 78.0 - - + +
56C LEU* 1.3 64.8 + - - +
58C ARG* 3.4 36.8 - - - +
59C ARG* 4.2 12.6 + - - +
76C THR* 4.8 19.7 + - + +
77C GLU 5.7 0.5 - - - +
78C LYS* 3.1 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 3.0 29.0 + - + +
53C GLU 4.0 2.7 - - - +
55C GLU* 1.3 75.2 - - - +
57C ARG* 1.3 60.5 + - - +
59C ARG* 3.1 20.3 + - - +
74C ARG* 3.2 32.9 - - + +
75C GLU 4.5 5.8 - - - +
76C THR* 4.1 24.5 - - + -
109C VAL* 4.4 11.9 - - + +
111C ASP* 3.8 33.9 - - + +
196C ARG* 4.1 7.4 - - - +
198C ILE* 3.8 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLU* 2.8 50.2 + - + +
54C PRO* 4.1 4.5 - - + +
56C LEU* 1.3 71.8 - - - +
58C ARG* 1.3 58.1 + - - +
59C ARG 2.9 16.6 + - - +
74C ARG* 3.5 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 4.9 2.4 + - - -
54C PRO* 3.4 21.5 + - - +
55C GLU* 3.4 30.7 + - - +
56C LEU 3.2 0.4 - - - -
57C ARG* 1.3 76.9 - - - +
59C ARG* 1.3 62.7 + - + +
----------------------------------------------------------
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