Contacts of the helix formed by residues 52 - 65 (chain A) in PDB entry 4QBT
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 TYR 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 4.2 22.4 - + - -
42A THR* 3.6 17.3 - - + -
45A THR* 5.1 0.5 - - - +
46A GLY 4.4 2.3 + - - -
47A LYS 4.9 0.2 - - - -
48A PRO* 3.7 33.0 - - + -
49A HIS* 2.9 45.6 + + - +
51A ALA* 1.3 77.8 - - + +
53A PHE* 1.3 61.4 + - - +
54A VAL 3.1 0.8 + - - -
55A PRO* 3.3 12.7 - - + +
56A MET* 3.2 25.3 + - + +
97A TYR* 3.3 13.3 + + - -
101A ILE* 5.2 6.1 - - + -
104A MET* 3.4 17.7 - - + -
502A K 2.7 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 2.8 28.7 + - + +
52A TYR* 1.3 77.6 - - - +
54A VAL* 1.3 56.4 + - - +
56A MET* 3.7 2.0 - - + -
57A SER* 2.7 35.3 + - - -
104A MET* 3.4 39.4 - - + +
107A SER* 5.2 0.7 - - - -
108A ILE* 4.0 27.8 - - + -
234A LEU* 3.8 18.2 - - + -
263A PHE* 4.3 6.7 - + + -
267A VAL* 3.7 21.8 - - + -
317A LEU* 4.7 2.0 - - + -
320A LEU* 4.0 36.6 - - + -
321A LEU* 3.9 13.0 - - + -
324A ILE* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 3.0 17.0 + - + +
53A PHE* 1.3 79.0 - - - +
55A PRO* 1.3 69.9 - - + +
57A SER* 3.2 10.5 + - - -
58A LYS* 3.5 8.8 + - - +
212A ASN* 3.3 26.7 + - + +
213A PRO 5.5 0.7 - - - +
215A VAL* 4.1 32.5 - - + -
262A SER 5.6 0.4 - - - +
263A PHE* 5.1 7.0 - - + -
266A HIS* 4.2 18.2 - - + +
267A VAL* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.8 42.2 - - + +
51A ALA 3.5 7.0 - - - +
52A TYR* 3.3 21.1 - - + +
54A VAL* 1.3 97.3 - - + +
56A MET* 1.3 61.1 + - + +
58A LYS* 3.1 4.5 + - - +
59A ILE* 3.0 26.9 + - - +
183A PHE* 3.9 18.9 - - + -
212A ASN* 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.4 42.0 - - + -
52A TYR* 3.2 25.2 + - + +
53A PHE* 3.8 8.1 - - - +
54A VAL 3.2 0.2 - - - -
55A PRO* 1.3 77.1 - - - +
57A SER* 1.3 58.3 + - - +
59A ILE* 3.3 21.9 + - + +
60A ALA* 2.9 28.2 + - - +
71A ILE* 4.8 1.1 - - + -
101A ILE* 4.1 18.2 - - + +
104A MET* 3.5 26.2 - - + -
105A LEU* 3.8 32.3 - - + +
108A ILE* 4.0 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE 2.7 23.5 + - - -
54A VAL 3.2 3.3 + - - -
56A MET* 1.3 76.3 - - - +
58A LYS* 1.3 66.7 + - - +
60A ALA* 3.4 8.6 + - - +
61A ASP* 3.0 27.0 + - - +
108A ILE* 4.7 8.7 - - - +
266A HIS 3.2 26.4 + - - -
267A VAL* 3.5 20.6 + - - +
270A PRO* 4.8 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU 3.0 17.6 + - - -
14A ILE 3.1 18.5 + - - -
16A ARG 2.8 29.4 + - - +
17A ASN* 4.7 6.5 - - + +
18A LEU* 4.1 6.5 - - - -
54A VAL 3.5 3.5 + - - +
55A PRO 3.1 3.3 + - - +
57A SER* 1.3 76.6 - - - +
59A ILE* 1.3 63.2 + - - +
61A ASP* 2.8 25.1 + - - +
62A PHE* 2.8 46.6 + - + -
183A PHE* 3.5 35.4 - - + -
212A ASN* 3.8 21.8 - - - +
266A HIS 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.8 35.2 - - + -
55A PRO 3.0 20.2 + - - +
56A MET* 3.6 30.3 - - + +
58A LYS* 1.3 73.6 - - - +
60A ALA* 1.3 64.9 + - - +
62A PHE* 3.1 21.7 + - + +
63A LEU* 3.0 36.1 + - + +
69A VAL* 4.2 18.4 - - + -
71A ILE* 4.3 12.6 - - + -
105A LEU* 4.0 17.9 - - + -
115A LEU* 4.6 2.0 - - + -
183A PHE* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A MET 2.9 12.4 + - - +
57A SER* 3.5 12.6 - - - +
59A ILE* 1.3 77.7 - - - +
61A ASP* 1.3 63.3 + - - +
63A LEU* 3.3 5.7 + - - +
64A LYS* 3.1 36.1 + - - +
108A ILE* 4.6 6.5 - - + +
110A VAL* 3.3 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.1 23.2 - - + +
16A ARG* 2.8 42.4 + - - +
17A ASN* 5.9 0.3 + - - -
57A SER 3.0 19.6 + - - +
58A LYS* 2.8 34.6 + - - +
60A ALA* 1.3 77.8 - - - +
62A PHE* 1.3 64.7 + - + +
64A LYS* 3.4 14.5 + - - +
65A ALA* 3.0 24.4 + - - +
270A PRO* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.4 46.2 - - + -
18A LEU* 5.5 0.2 - - + -
38A ILE* 3.8 22.2 - - + -
39A TYR 6.4 0.2 - - - -
40A TRP* 5.8 0.9 - - + -
58A LYS* 2.8 32.3 + - + -
59A ILE* 3.1 19.2 + - + +
61A ASP* 1.3 77.0 - - - +
63A LEU* 1.3 62.8 + - - +
65A ALA* 3.1 8.4 + - - -
66A GLY 3.4 0.2 + - - -
67A CYS* 3.1 36.6 + - + +
69A VAL* 3.8 17.3 - - + -
183A PHE* 3.6 51.8 - + + -
210A LEU* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.0 19.3 + - + +
60A ALA 3.7 6.1 - - - +
62A PHE* 1.3 73.1 - - - +
64A LYS* 1.3 58.9 + - - +
66A GLY* 2.8 22.3 + - - -
67A CYS 3.6 20.9 - - - +
69A VAL* 3.9 15.3 - - + -
110A VAL* 3.3 33.4 - - + -
111A PRO* 3.9 21.3 - - + +
114A LYS* 4.4 20.0 - - + +
115A LEU* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.2 14.4 - - - +
13A LEU* 4.3 23.4 - - + +
16A ARG* 4.5 7.7 - - - +
60A ALA* 3.1 27.6 + - - +
61A ASP* 3.8 13.2 + - - +
62A PHE 3.4 0.2 - - - -
63A LEU* 1.3 76.0 - - + +
65A ALA* 1.3 60.3 + - - +
66A GLY 3.3 0.9 + - - -
110A VAL* 6.4 0.4 - - - -
270A PRO 3.6 21.8 + - - -
271A LEU* 4.7 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.7 2.2 - - - -
10A LYS* 3.2 44.1 - - - +
13A LEU* 4.1 12.7 - - + +
14A ILE* 3.7 31.6 - - + +
31A LEU* 5.8 0.3 - - - +
35A GLU* 3.6 0.9 - - - +
61A ASP 3.0 17.7 + - - +
62A PHE 3.5 6.5 - - - +
63A LEU 3.1 0.8 - - - -
64A LYS* 1.3 77.8 - - - +
66A GLY* 1.3 58.7 + - - +
67A CYS* 3.4 1.9 + - - -
----------------------------------------------------------
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