Contacts of the helix formed by residues 47 - 63 (chain B) in PDB entry 1Q6X
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 47 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU 4.8 0.2 - - - +
46B VAL* 1.3 91.7 - - + +
48B GLU* 1.3 67.6 + - - +
49B GLU* 4.5 4.5 - - + +
50B GLN* 3.2 28.9 + - + +
51B PHE* 3.0 19.6 + - - +
541B MET* 5.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL 3.6 2.3 + - - -
47B PRO* 1.3 71.1 - - - +
49B GLU* 1.3 63.4 + - - +
51B PHE* 3.2 10.7 + - + +
52B ARG* 3.2 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO* 3.3 4.6 - - + +
48B GLU* 1.3 80.4 - - - +
50B GLN* 1.3 66.6 + - - +
52B ARG* 3.2 20.8 + - - +
53B LYS* 3.4 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.9 7.7 - - + +
47B PRO* 3.2 30.1 + - + +
49B GLU* 1.3 83.9 + - - +
51B PHE* 1.3 63.7 + - - +
53B LYS* 3.2 11.0 + - + +
54B SER* 3.1 19.1 + - - +
536B ASP* 4.9 3.3 - - - +
537B GLU* 4.3 9.6 - - + +
538B THR* 2.8 32.2 + - - +
541B MET* 2.8 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.4 43.5 - - + -
42B MET* 4.6 3.4 - - + -
43B GLN* 3.2 59.9 - - + +
46B VAL* 3.9 17.0 - - + +
47B PRO 3.0 12.7 + - - +
48B GLU* 3.2 13.9 + - + +
50B GLN* 1.3 75.8 - - - +
52B ARG* 1.3 66.3 + - + +
54B SER* 3.0 11.2 + - - -
55B GLN* 2.9 56.5 + - + +
538B THR* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 3.2 35.2 + - + +
49B GLU* 3.2 11.6 + - - +
51B PHE* 1.3 79.1 - - + +
53B LYS* 1.3 62.1 + - + +
55B GLN* 3.4 21.5 + - - +
56B ALA* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 3.4 37.9 + - - +
50B GLN* 3.2 11.1 + - + +
51B PHE 3.2 0.4 - - - -
52B ARG* 1.3 73.8 - - + +
54B SER* 1.3 61.6 + - - +
56B ALA* 3.1 9.0 + - - +
57B ILE* 2.8 40.0 + - + +
60B ARG* 4.8 0.2 + - - -
536B ASP* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 5.7 0.9 - - - -
39B LEU* 4.5 10.3 - - - -
50B GLN 3.1 7.6 + - - -
51B PHE* 3.0 13.7 + - - -
53B LYS* 1.3 76.7 - - - +
55B GLN* 1.3 53.7 + - - +
57B ILE* 3.5 2.8 - - - +
58B VAL* 2.7 43.0 + - - +
536B ASP* 2.5 24.0 + - - -
538B THR* 2.5 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.4 21.1 - - + +
43B GLN* 5.3 0.2 - - - +
51B PHE* 2.9 50.6 + - + +
52B ARG* 3.6 26.7 + - - +
54B SER* 1.3 75.9 - - - +
56B ALA* 1.3 58.5 + - - +
58B VAL* 3.9 1.7 - - - +
59B LYS* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG 3.4 8.9 + - - +
53B LYS* 3.1 11.5 + - - +
55B GLN* 1.3 77.3 - - - +
57B ILE* 1.3 66.5 + - - +
59B LYS* 3.3 8.2 + - - +
60B ARG* 2.9 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS* 2.8 27.9 + - + +
54B SER* 3.5 7.6 - - - +
56B ALA* 1.3 77.4 - - - +
58B VAL* 1.3 57.6 + - + +
60B ARG* 3.3 22.8 + - - +
61B PHE* 2.9 26.7 + - - +
532B GLU* 3.6 33.7 - - + +
533B MET* 3.8 26.5 - - + +
536B ASP* 3.7 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.9 34.5 - - + +
38B TYR* 3.9 21.1 - - + -
39B LEU* 3.8 35.0 - - + -
54B SER* 2.7 25.2 + - - +
55B GLN 3.9 2.9 - - - +
57B ILE* 1.3 69.5 - - + +
59B LYS* 1.3 56.8 + - - +
61B PHE* 3.1 6.9 + - - +
62B GLY* 2.7 33.1 + - - -
533B MET* 4.1 12.1 - - - -
536B ASP* 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN 2.9 19.2 + - - +
56B ALA* 3.6 8.3 - - - +
57B ILE 3.3 0.2 - - - -
58B VAL* 1.3 78.5 - - - +
60B ARG* 1.3 63.1 + - + +
62B GLY* 3.7 1.1 - - - +
63B ALA* 2.9 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS 4.8 0.2 + - - -
56B ALA* 2.9 36.4 + - - +
57B ILE* 3.7 21.0 - - - +
59B LYS* 1.3 78.5 - - + +
61B PHE* 1.3 63.8 + - - +
63B ALA* 3.5 15.6 + - - +
66B GLY* 4.7 6.8 - - - -
67B LEU 4.9 1.2 + - - -
532B GLU* 3.1 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.4 2.5 - - + -
35B LEU* 4.0 27.8 - - + -
57B ILE 2.9 17.7 + - - +
58B VAL* 3.1 7.4 + - - +
60B ARG* 1.3 78.6 - - - +
62B GLY* 1.3 59.3 + - - +
63B ALA 3.7 0.2 + - - -
66B GLY 4.4 1.0 - - - -
67B LEU* 3.8 32.2 + - + -
68B GLY* 3.0 58.0 + - - +
69B GLU 4.6 0.2 + - - -
71B LEU* 4.1 15.0 - - + -
519B LEU* 4.4 19.5 - - + -
533B MET* 3.7 45.3 - - + -
534B PHE* 4.5 9.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.6 7.0 - - - -
32B GLN* 3.1 25.7 + - - -
35B LEU* 3.8 19.5 - - - -
58B VAL 2.7 19.4 + - - -
59B LYS* 3.7 2.2 - - - -
61B PHE* 1.3 74.4 - - - +
63B ALA* 1.3 63.9 + - - +
64B PRO* 3.8 1.9 - - - +
69B GLU* 4.4 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LYS* 2.9 18.8 + - + +
60B ARG* 3.5 11.9 + - - +
61B PHE 3.5 2.8 - - - -
62B GLY* 1.3 79.1 - - - +
64B PRO* 1.3 72.3 - - + +
65B GLY 3.2 0.5 + - - -
66B GLY* 2.8 25.5 + - - +
69B GLU* 4.1 4.7 - - - +
----------------------------------------------------------
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