Contacts of the helix formed by residues 34 - 53 (chain D) in PDB entry 4QPQ
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 34 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 4.1 1.8 - - - -
24D ARG* 5.8 1.3 - - - +
31D LYS* 4.0 16.5 + - - +
32D ASP 3.3 4.4 + - - -
33D VAL* 1.3 80.9 - - - +
35D PHE* 1.3 63.5 + - - +
37D ALA* 3.3 20.2 + - - +
38D THR* 3.2 23.0 + - - -
2P T 2.9 35.1 + - - -
3P A 3.2 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.5 36.3 - - + -
5A ASN 4.9 2.2 - - - -
6A LEU* 4.5 1.6 - - + -
8D ILE* 4.5 0.7 - - + -
13D TYR* 3.6 35.0 - + - -
16D ILE* 3.6 36.3 - - + -
17D ASN* 3.4 27.6 - - - -
20D ILE* 3.7 13.0 - - + +
34D SER* 1.3 69.0 - - - +
36D SER* 1.3 64.7 + - - +
38D THR* 3.3 1.7 + - - -
39D ALA* 3.0 39.0 + - + +
3P A 2.6 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN 3.8 6.5 - - - -
6A LEU* 3.8 13.9 - - - +
7A TYR* 2.8 36.1 + - - +
35D PHE* 1.3 74.2 - - - +
37D ALA* 1.3 57.3 + - - +
40D SER* 3.0 30.7 + - - -
2P T 2.8 29.0 + - - -
3P A 2.8 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ASP 4.3 9.9 - - - +
33D VAL* 5.2 0.2 - - - -
34D SER* 3.3 25.8 + - - +
35D PHE 3.2 0.6 - - - -
36D SER* 1.3 76.9 - - - +
38D THR* 1.3 62.5 + - + +
40D SER* 3.2 5.7 + - - -
41D MET* 2.8 29.6 + - - +
2P T 3.5 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 3.7 8.8 - - - +
19D ILE* 5.2 9.2 - - + -
20D ILE* 3.6 29.8 - - + +
23D ARG* 5.3 7.0 - - + +
33D VAL* 4.4 22.2 - - + -
34D SER 3.2 18.4 + - - +
35D PHE 3.3 4.7 + - - -
37D ALA* 1.3 77.5 - - + +
39D ALA* 1.3 59.0 + - - +
41D MET* 3.3 19.0 + - + +
42D LEU* 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.5 26.4 - - + +
43A LEU* 3.9 8.8 - - + +
16D ILE* 4.0 23.3 - - + -
35D PHE* 3.0 23.8 + - + +
38D THR* 1.3 75.7 + - - +
40D SER* 1.3 60.2 + - - +
42D LEU* 3.2 13.3 + - - +
43D LEU* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.2 5.8 - - - +
7A TYR 4.3 7.4 + - - -
8A ILE* 3.4 33.9 - - - +
36D SER 3.0 20.1 + - - -
37D ALA* 3.2 5.1 + - - -
39D ALA* 1.3 74.6 - - - +
41D MET* 1.3 65.1 + - - +
43D LEU* 3.5 6.8 - - - +
44D GLU* 3.1 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A HIS* 5.0 4.5 - - + -
19D ILE* 5.6 3.6 - - + -
23D ARG* 3.9 25.8 - - - +
37D ALA 2.8 13.5 + - - +
38D THR* 3.4 26.0 - - + +
39D ALA 3.2 0.2 - - - -
40D SER* 1.3 78.2 - - - +
42D LEU* 1.3 69.1 + - + +
44D GLU* 3.8 7.2 + - - +
45D LEU* 3.2 43.6 + - - +
48D ARG* 5.4 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 3.8 1.7 - - - +
43A LEU* 3.8 25.1 - - + +
46A GLY* 3.5 28.7 - - - +
47A LEU* 3.7 26.0 - - + +
50A HIS* 4.2 20.6 - - + +
16D ILE* 4.1 12.3 - - + -
19D ILE* 4.1 13.7 - - + -
38D THR* 3.1 20.5 + - - +
39D ALA* 3.2 7.8 + - - +
41D MET* 1.3 94.2 - - + +
43D LEU* 1.3 59.6 + - - +
45D LEU* 3.4 7.6 - - + +
46D GLY 3.0 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.1 22.2 - - + -
8A ILE* 4.2 16.4 - - + -
12A ALA* 5.7 1.6 - - + -
16A ILE* 3.8 31.0 - - + -
39A ALA* 3.9 23.1 - - + +
42A LEU* 3.8 24.6 - - + +
43A LEU* 4.4 11.4 - - + +
4D VAL* 6.0 1.8 - - + -
6D LEU* 4.4 2.7 - - + -
39D ALA 3.0 11.9 + - - +
40D SER* 3.3 10.1 + - - +
42D LEU* 1.3 74.0 - - - +
44D GLU* 1.3 61.7 + - + +
46D GLY* 2.9 4.7 + - - -
47D LEU* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 6.3 0.2 - - + -
9A SER* 3.5 24.8 + - - -
12A ALA* 4.3 18.2 - - + +
40D SER* 3.1 27.0 + - - +
41D MET* 4.2 5.1 - - - +
43D LEU* 1.3 76.9 - - + +
45D LEU* 1.3 61.6 + - - +
47D LEU* 3.2 13.1 + - + +
48D ARG* 3.1 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 3.7 17.5 - - - +
49A VAL* 3.6 39.5 - - + -
50A HIS* 5.0 11.0 - - + +
41D MET* 3.2 36.2 + - - +
42D LEU* 3.4 11.9 - - + +
43D LEU 3.1 0.4 - - - -
44D GLU* 1.3 78.5 - - - +
46D GLY* 1.3 59.2 + - - +
48D ARG* 3.6 25.7 + - - +
49D VAL* 3.3 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.5 27.2 - - - +
45A LEU* 3.7 21.9 - - - +
46A GLY* 3.9 3.8 - - - -
42D LEU 3.0 7.5 + - - -
43D LEU 2.9 8.3 + - - -
45D LEU* 1.3 75.6 - - - +
47D LEU* 1.3 57.6 + - - +
49D VAL 3.6 0.3 + - - -
50D HIS* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 4.1 31.2 - - + +
15A LYS* 4.3 24.5 - - + +
16A ILE* 4.6 2.7 - - + -
19A ILE* 4.2 15.9 - - + -
42A LEU* 3.6 25.8 - - + -
43D LEU* 2.9 21.2 + - + +
44D GLU* 3.2 24.4 + - + +
46D GLY* 1.3 76.9 - - - +
48D ARG* 1.3 65.6 + - + +
50D HIS* 3.2 15.2 + - + +
51D GLU* 3.3 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 6.3 0.9 - - - +
41D MET 5.4 1.0 + - - -
44D GLU* 3.1 38.6 + - + +
45D LEU* 4.0 27.4 - - - +
46D GLY 3.4 0.2 - - - -
47D LEU* 1.3 76.6 - - + +
49D VAL* 1.3 60.1 + - + +
51D GLU* 3.7 18.2 + - - +
52D ALA* 3.5 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.5 27.6 - - + -
49A VAL* 4.0 27.4 - - + -
45D LEU* 3.3 19.2 + - + +
46D GLY 3.8 1.1 - - - +
47D LEU 3.2 0.4 - - - -
48D ARG* 1.3 76.9 - - + +
50D HIS* 1.3 64.1 + - - +
51D GLU 3.1 1.8 - - - -
52D ALA* 3.1 18.4 + - + +
53D GLN* 3.3 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.8 32.4 - - + +
23A ARG* 3.6 28.5 + - - -
41A MET* 4.9 5.2 - - + +
42A LEU* 4.2 16.3 - - + +
45A LEU* 4.8 10.7 - - + +
46D GLY 3.1 15.0 + - - +
47D LEU* 3.2 12.3 + - + +
49D VAL* 1.3 77.3 - - - +
51D GLU* 1.3 63.8 + - + +
53D GLN* 3.9 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 3.8 28.2 + - - +
47D LEU* 3.3 21.9 - - + +
48D ARG* 3.9 17.0 - - - +
49D VAL 3.1 0.6 - - - -
50D HIS* 1.3 81.8 - - + +
52D ALA* 1.3 64.2 + - - +
53D GLN 3.2 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ARG 3.5 10.4 + - - +
49D VAL* 3.1 13.6 + - + +
51D GLU* 1.3 80.6 - - - +
53D GLN* 1.3 63.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL* 3.3 19.2 + - + +
50D HIS* 3.9 13.2 - - - +
51D GLU 3.2 4.2 - - - -
52D ALA* 1.3 85.5 - - + +
----------------------------------------------------------
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