Contacts of the helix formed by residues 35 - 53 (chain A) in PDB entry 3QEL
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 THR 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.6 0.4 - - - +
34A SER* 1.3 92.0 + - - +
36A LYS* 1.3 64.0 + - - +
37A LYS* 3.2 11.2 + - - +
38A HIS* 2.9 34.0 + - + +
39A GLU* 3.0 21.0 + - - +
66A THR* 3.7 8.9 - - - +
96A PRO* 5.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 1.3 72.6 - - - +
37A LYS* 1.3 62.6 + - - +
39A GLU* 3.1 21.5 + - - +
40A GLN* 3.1 21.0 + - - +
43A ARG* 4.8 1.9 + - - -
66A THR* 4.0 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 3.1 11.5 + - - +
36A LYS* 1.3 74.9 - - - +
38A HIS* 1.3 67.4 + - + +
40A GLN* 3.1 10.3 + - - +
41A ILE* 3.1 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.4 14.5 - - + +
34A SER* 4.2 2.4 - - - -
35A THR* 2.9 34.1 + - + +
37A LYS* 1.3 77.6 - - + +
39A GLU* 1.3 63.6 + - - +
40A GLN 3.2 0.2 - - - -
41A ILE* 3.3 16.6 + - + +
42A PHE 3.1 17.7 + - - -
298A GLU* 3.5 57.6 + - + +
299A SER* 3.9 15.5 + - - -
302A ILE* 3.6 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.1 11.2 - - + +
35A THR 3.0 13.1 + - - +
36A LYS* 3.1 25.4 + - + +
38A HIS* 1.3 77.1 - - - +
40A GLN* 1.3 58.4 + - - +
42A PHE* 3.3 6.8 + - - +
43A ARG* 2.9 46.1 + - - +
64A SER* 2.7 46.3 + - - +
65A VAL* 3.7 14.3 + - - +
66A THR* 3.8 13.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS 3.1 10.4 + - - +
37A LYS* 3.1 11.6 + - - +
39A GLU* 1.3 75.5 - - - +
41A ILE* 1.3 59.8 + - + +
43A ARG* 2.8 43.8 + - - +
44A GLU* 3.0 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 3.1 16.7 + - + +
38A HIS* 3.6 22.2 - - + +
39A GLU 3.2 0.4 - - - -
40A GLN* 1.3 75.6 - - + +
42A PHE* 1.3 60.4 + - - +
44A GLU* 3.0 6.7 + - - +
45A ALA* 2.8 29.3 + - + +
299A SER* 3.6 38.1 - - - +
302A ILE* 4.2 20.4 - - + -
303A SER* 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.6 27.6 - - + -
30A GLY 3.7 11.7 - - - -
31A ALA* 3.7 13.9 - - + -
33A LEU* 3.6 17.9 - - + -
38A HIS 3.1 5.1 + - - -
39A GLU 3.4 7.2 - - - +
41A ILE* 1.3 76.1 - - - +
43A ARG* 1.3 64.2 + - - +
45A ALA* 3.1 3.5 + - - +
46A VAL* 3.0 29.2 + - + +
62A ALA* 3.5 24.0 - - + -
63A THR 3.7 20.9 - - - -
64A SER* 4.0 13.5 - - - -
91A LEU* 3.5 33.2 - - + -
302A ILE* 3.6 11.4 - - + +
306A VAL* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS 4.8 1.6 + - - -
39A GLU* 2.9 31.9 + - - +
40A GLN* 2.8 53.5 + - - +
41A ILE 3.3 0.2 - - - -
42A PHE* 1.3 76.7 - - - +
44A GLU* 1.3 57.6 + - - +
46A VAL* 3.4 2.8 + - - +
47A ASN* 3.1 26.9 + - - +
62A ALA* 3.9 26.2 - - + +
64A SER* 4.4 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLN* 3.0 31.3 + - - +
41A ILE* 3.0 6.7 + - - +
43A ARG* 1.3 73.4 - - - +
45A ALA* 1.3 66.5 + - - +
47A ASN* 3.5 19.1 + - - +
48A GLN* 3.0 53.8 + - - +
51A LYS* 5.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 2.8 17.2 + - + +
42A PHE* 3.1 6.5 + - - +
44A GLU* 1.3 76.9 - - - +
46A VAL* 1.3 57.8 + - - +
48A GLN* 3.4 11.5 + - - +
49A ALA* 3.0 26.5 + - - +
52A ARG* 4.1 4.5 + - - +
302A ILE* 4.6 1.8 - - + +
303A SER* 4.5 17.5 - - - +
306A VAL* 3.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.6 12.8 - - + -
42A PHE* 3.0 32.6 + - + +
43A ARG 3.8 4.0 - - - +
45A ALA* 1.3 73.8 - - - +
47A ASN* 1.3 66.8 + - - +
49A ALA* 3.0 6.3 + - - +
50A ASN* 2.9 23.5 + - - +
60A LEU* 3.8 35.9 - - + +
61A GLN* 4.3 0.4 - - - -
62A ALA* 3.9 29.4 - - + +
306A VAL* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG 3.1 17.6 + - - +
44A GLU* 3.7 26.2 - - - +
46A VAL* 1.3 77.0 - - - +
48A GLN* 1.3 59.0 + - - +
50A ASN* 3.3 15.6 + - - +
51A LYS* 3.1 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 3.0 49.0 + - - +
45A ALA* 3.7 10.4 - - - +
47A ASN* 1.3 71.7 - - - +
49A ALA* 1.3 61.1 + - - +
51A LYS* 2.9 18.2 + - + +
52A ARG* 2.8 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 3.0 13.0 + - - +
46A VAL* 3.0 11.1 + - - +
48A GLN* 1.3 74.7 - - - +
50A ASN* 1.3 64.7 + - - +
52A ARG* 3.3 20.5 - - - +
53A HIS* 2.9 31.8 + - - +
60A LEU* 4.2 8.3 - - + -
306A VAL* 4.5 4.7 - - + +
310A ALA* 3.7 29.4 - - + -
314A HIS* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 2.9 21.0 + - - +
47A ASN* 3.5 15.7 - - - +
48A GLN 3.2 0.2 - - - -
49A ALA* 1.3 77.2 - - - +
51A LYS* 1.3 60.8 + - + +
53A HIS 3.0 17.8 - - - +
55A THR* 3.4 21.4 + - + +
59A GLN* 3.8 21.6 + - - +
60A LEU* 2.9 52.9 + - - +
314A HIS* 5.5 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 5.8 1.7 + - - +
47A ASN* 3.1 34.4 + - - +
48A GLN* 2.9 21.4 + - + +
50A ASN* 1.3 79.2 - - - +
52A ARG* 1.3 61.3 + - + +
53A HIS 3.6 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 4.1 5.9 + - - -
48A GLN* 2.8 21.7 + - - +
49A ALA* 3.3 32.9 - - - +
51A LYS* 1.3 75.1 - - + +
53A HIS* 1.3 85.8 + - + +
54A PHE 4.2 0.2 + - - -
303A SER 5.8 0.2 + - - -
306A VAL* 5.4 0.6 - - - +
307A ALA* 4.0 26.0 + - - +
351A TYR* 4.0 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 2.9 34.4 + - - +
50A ASN 3.0 15.6 - - - +
51A LYS 3.8 4.2 - - - +
52A ARG* 1.3 104.7 + - + +
54A PHE* 1.3 63.2 + - - +
55A THR* 3.4 6.6 + - + -
307A ALA 5.0 0.6 + - - -
310A ALA* 3.9 16.4 - - + +
311A GLN* 4.1 23.7 + - + +
314A HIS* 3.5 44.1 + + + +
----------------------------------------------------------
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