Contacts of the helix formed by residues 41 - 52 (chain B) in PDB entry 2QQ6
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 41 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS* 3.2 30.5 - - + +
48A ILE* 4.1 13.2 - - + -
51A ASN* 3.2 34.1 - - + +
19B PRO* 6.2 0.4 - - + -
39B SER 3.8 0.9 - - - -
40B ALA* 1.4 92.5 - - + +
42B ALA* 1.3 52.1 + - - +
43B ALA* 2.6 12.4 + - + +
44B GLY* 2.6 36.9 + - - +
45B ILE* 3.4 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 4.1 15.0 - - + -
19B PRO* 3.8 36.8 + - + +
21B VAL* 3.0 21.8 - - + +
40B ALA 3.3 5.9 + - - -
41B PRO* 1.3 69.0 - - - +
43B ALA* 1.3 55.3 + - - +
44B GLY 3.3 0.2 - - - -
45B ILE* 3.5 15.0 - - - -
46B HIS* 2.9 25.3 + - - +
389B HIS* 4.9 4.7 - - + -
391B LYS 6.1 0.7 - - - +
394B VAL* 3.4 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS* 3.2 37.7 - - + +
41B PRO* 2.6 10.5 + - + +
42B ALA* 1.3 71.9 - - - +
44B GLY* 1.3 59.4 + - - +
46B HIS* 3.0 1.7 - - - +
47B HIS* 2.9 39.2 + - + +
391B LYS 5.6 2.6 - - - -
393B GLY* 4.2 11.2 - - - +
394B VAL* 3.3 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY* 4.4 23.5 - - - -
47A HIS* 4.2 4.4 - - - +
48A ILE* 5.0 5.2 - - - -
41B PRO* 2.6 21.8 + - - +
43B ALA* 1.3 70.6 - - - +
45B ILE* 1.3 64.5 + - - -
46B HIS 3.1 0.5 + - - -
47B HIS* 3.1 2.4 + - - +
48B ILE* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO 4.8 3.8 - - - +
21B VAL* 3.6 13.2 - - + +
36B CYS* 3.6 32.5 - - + -
37B TYR 3.8 8.3 - - - +
38B PRO 4.7 0.4 - - - -
39B SER* 2.8 49.6 - - - +
40B ALA* 4.7 0.9 - - + +
41B PRO 3.4 2.9 + - - +
42B ALA* 3.5 21.8 - - + +
44B GLY* 1.3 72.2 - - - +
46B HIS* 1.3 63.0 + - - +
48B ILE* 3.5 12.1 + - + +
49B VAL* 2.9 29.6 + - + +
84B ALA* 5.6 4.9 - - + +
87B THR* 5.1 2.0 - - + -
88B ALA* 4.1 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B THR* 2.5 35.1 + - + +
21B VAL* 3.9 11.4 - - + +
42B ALA 2.9 16.1 + - - +
43B ALA* 3.0 8.1 - - - +
45B ILE* 1.3 78.8 - - - +
47B HIS* 1.3 90.9 + + - +
49B VAL* 3.2 3.9 + - - +
50B MSE 2.9 40.4 + - + +
393B GLY 5.3 1.1 - - - -
394B VAL* 3.3 28.0 - - + +
395B PRO* 4.0 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 4.1 5.5 - - + +
43A ALA* 2.9 36.7 - - + +
44A GLY* 4.0 9.4 - - - +
47A HIS* 3.7 26.1 + + - -
393A GLY 4.1 15.0 - - - -
43B ALA* 2.9 36.9 + - + +
44B GLY 3.7 3.4 - - - +
46B HIS* 1.3 89.1 + + - +
48B ILE* 1.3 57.0 + - - +
50B MSE 3.0 7.3 + - - +
51B ASN* 2.7 37.2 + - - +
393B GLY 5.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 5.2 2.0 - - + -
41A PRO* 3.9 25.4 - - + -
44A GLY* 5.1 3.6 - - - -
48A ILE* 5.7 4.3 - - + -
84A ALA* 5.3 4.7 - - + -
44B GLY* 2.9 27.1 + - - +
45B ILE* 3.6 9.0 - - - +
47B HIS* 1.3 77.4 - - - +
49B VAL* 1.3 65.0 + - - +
51B ASN* 3.2 9.7 + - - +
52B MSE 3.3 24.6 + - + +
75B ASN* 5.9 0.9 - - - +
84B ALA* 4.0 30.1 - - + +
85B VAL* 4.0 32.3 - - + +
88B ALA* 3.6 17.3 - - + -
89B LEU* 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.5 14.0 - - + +
11B THR* 3.7 21.1 - - + -
21B VAL* 4.8 2.5 - - + -
23B VAL* 4.1 10.3 - - + -
36B CYS* 4.4 6.7 - - - -
45B ILE* 2.9 26.1 + - + +
46B HIS* 3.3 8.5 - - - +
48B ILE* 1.3 77.7 - - - +
50B MSE 1.3 61.2 + - - +
52B MSE 2.9 24.2 - - - +
53B GLU 3.8 1.9 + - - -
88B ALA* 3.8 27.4 - - + +
92B ILE* 3.8 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 2.8 48.5 - - + +
10B GLU* 4.4 3.1 - - - -
11B THR* 3.7 24.0 - - - -
46B HIS* 2.9 28.1 + - + +
47B HIS* 3.0 12.1 + - - +
49B VAL* 1.3 72.6 - - - +
51B ASN* 1.3 53.6 + - - +
52B MSE 2.8 15.0 + - - -
53B GLU* 2.8 46.0 + - + +
54B GLU* 3.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 4.4 5.0 + - - -
41A PRO* 3.5 40.9 - - + +
47B HIS 2.7 20.0 + - - +
48B ILE 3.5 5.6 - - - +
50B MSE 1.3 71.3 - - - +
52B MSE 1.3 74.1 + - - +
53B GLU 3.4 0.4 - - - -
54B GLU* 3.1 20.8 + - - +
55B GLN* 5.4 2.8 - - - +
74B TRP* 5.1 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 3.3 20.4 - - + +
49B VAL 2.9 13.7 + - - +
50B MSE 2.8 0.6 + - - -
51B ASN* 1.3 101.4 - - - +
53B GLU* 1.3 61.6 + - - +
54B GLU 3.4 1.3 - - - -
55B GLN* 3.3 19.9 + - + +
56B LEU* 3.1 18.7 - - + +
71B MSE 3.7 35.7 - - - -
74B TRP* 3.5 30.1 - - + +
75B ASN* 3.7 22.2 - - - +
89B LEU* 4.0 7.2 - - + -
92B ILE* 4.0 20.6 - - + -
----------------------------------------------------------
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