Contacts of the helix formed by residues 29 - 51 (chain A) in PDB entry 3DC6
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 LYS 29 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 2.9 37.9 + - + +
28A GLN* 1.3 91.6 - - + +
30A HIS* 1.3 64.9 + - + +
31A HIS 3.6 0.4 - - - -
32A ALA* 4.0 0.3 - - - +
33A THR* 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.0 32.1 + - + +
26A HIS* 3.4 20.9 - - + +
29A LYS* 1.3 79.2 - - + +
31A HIS* 1.3 67.9 + - - +
33A THR* 3.2 6.5 + - - -
34A TYR* 3.1 37.2 + - + -
160A TRP* 6.1 0.2 - - - -
162A HIS* 3.4 51.0 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.5 7.5 - - + +
5A PRO* 3.5 18.2 - - + -
26A HIS 2.9 14.9 + - - +
27A HIS 3.5 11.4 - - - +
30A HIS* 1.3 74.2 - - - +
32A ALA* 1.3 63.8 + - - +
34A TYR* 3.1 10.1 + - + +
35A VAL* 3.0 29.8 + - + +
70A GLY 4.4 0.9 - - - -
71A HIS* 2.9 38.4 + - - -
74A HIS* 3.5 11.1 - - + +
75A SER* 3.3 27.6 - - - -
78A TRP* 2.9 34.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.7 19.9 - - + +
27A HIS 3.2 6.2 + - - +
28A GLN 3.0 29.8 - - - +
29A LYS* 4.0 1.1 - - - +
30A HIS 3.3 0.6 - - - -
31A HIS* 1.3 76.5 - - - +
33A THR* 1.3 57.7 + - - +
35A VAL* 3.3 5.6 + - - +
36A ASN* 2.9 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 2.8 23.6 + - - +
30A HIS* 3.6 5.8 - - - -
31A HIS 3.2 0.4 - - - -
32A ALA* 1.3 73.1 - - - +
34A TYR* 1.3 70.3 + - + +
36A ASN* 3.3 8.4 + - - +
37A ASN* 2.9 42.5 + - - +
67A ASN* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 3.1 31.5 + - + -
31A HIS* 3.1 9.0 + - - +
33A THR* 1.3 79.6 - - + +
35A VAL* 1.3 53.0 + - - +
38A LEU* 2.7 36.4 + - - +
66A PHE* 3.8 32.8 - + - -
67A ASN* 3.5 35.3 - - - +
70A GLY* 3.7 12.6 - - - -
71A HIS 3.9 7.9 - - - +
74A HIS* 3.4 30.5 - + - -
142A GLN* 2.8 26.0 + - + -
160A TRP* 3.5 21.0 - - - -
162A HIS* 4.2 4.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HIS* 3.6 33.2 - - + +
3A SER* 3.8 8.5 - - - -
4A LEU* 3.9 13.9 - - + +
31A HIS* 3.0 25.9 + - + +
32A ALA* 3.6 9.0 - - - +
34A TYR* 1.3 74.6 - - - +
36A ASN* 1.3 69.9 + - - +
38A LEU* 3.3 7.2 + - - +
39A ASN* 3.0 26.9 + - - +
71A HIS* 3.4 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 2.9 30.3 + - - +
33A THR* 3.8 7.8 + - - +
35A VAL* 1.3 83.8 - - - +
37A ASN* 1.3 67.6 + - - +
39A ASN* 3.3 8.8 + - - +
40A GLN* 3.3 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 2.9 33.9 + - - +
36A ASN* 1.3 76.1 - - - +
38A LEU* 1.3 65.5 + - - +
40A GLN* 3.1 23.1 + - - +
41A ILE* 2.9 31.3 + - + +
67A ASN* 3.2 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HIS* 3.5 34.8 - - + -
34A TYR 2.7 24.2 + - - +
35A VAL* 3.3 5.1 + - - +
37A ASN* 1.3 73.0 - - - +
39A ASN* 1.3 56.8 + - - +
41A ILE* 4.6 2.7 - - - -
42A GLU* 2.8 36.6 + - + +
64A LEU* 3.7 23.1 - - + -
67A ASN* 3.8 11.5 - - - +
68A GLY* 3.7 21.3 - - - +
71A HIS* 3.6 31.2 - - + -
54C VAL* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LYS* 2.9 43.4 + - + +
2A HIS* 2.9 44.0 + - - +
35A VAL* 3.0 23.2 + - - +
36A ASN* 3.7 10.7 + - - +
37A ASN 3.3 0.4 - - - -
38A LEU* 1.3 75.4 - - - +
40A GLN* 1.3 63.4 + - + +
42A GLU* 4.6 0.4 - - - -
43A GLU* 3.1 32.9 + - - +
----------------------------------------------------------
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 ASN* 3.3 14.7 + - - +
37A ASN* 3.1 29.2 + - - +
39A ASN* 1.3 79.0 - - + +
41A ILE* 1.3 62.8 + - + +
43A GLU* 3.5 8.7 + - - +
44A LYS* 3.1 39.5 + - - +
----------------------------------------------------------
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 ASN* 2.9 24.0 + - + +
38A LEU* 4.0 4.3 - - - +
40A GLN* 1.3 75.3 - - + +
42A GLU* 1.3 61.9 + - - +
44A LYS* 3.2 16.5 + - + +
45A LEU* 2.9 27.6 + - + +
60A LEU* 4.1 29.3 - - + +
63A ALA* 3.5 24.5 - - + +
64A LEU* 3.8 36.3 - - + +
67A ASN* 4.7 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LYS* 3.8 17.1 + - - +
2A HIS* 2.6 33.7 + - - -
38A LEU* 2.8 27.8 + - + +
39A ASN 4.0 3.6 - - - +
41A ILE* 1.3 73.6 - - - +
43A GLU* 1.3 55.1 + - - +
45A LEU* 3.3 6.0 + - - +
46A HIS* 2.8 29.9 + - + +
64A LEU* 4.4 9.6 - - + +
49C VAL* 4.1 23.1 - - + +
52C GLY* 3.7 19.5 - - - -
53C ASN 5.4 0.2 - - - -
54C VAL* 3.7 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LYS* 3.8 24.4 + - - +
39A ASN* 3.1 23.4 + - - +
40A GLN* 3.6 8.1 - - - +
41A ILE 3.3 0.2 - - - -
42A GLU* 1.3 76.8 - - - +
44A LYS* 1.3 63.0 + - + +
46A HIS* 3.4 7.5 + - - +
47A GLU* 3.2 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLN* 3.1 24.0 + - - +
41A ILE* 3.2 17.7 + - + +
43A GLU* 1.3 76.7 - - + +
45A LEU* 1.3 58.9 + - - +
47A GLU* 3.4 11.9 + - - +
48A ALA* 2.9 28.6 + - - +
60A LEU* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 2.9 17.8 + - + +
42A GLU* 3.7 6.5 - - + +
44A LYS* 1.3 75.3 - - - +
46A HIS* 1.3 59.3 + - - +
48A ALA* 4.3 0.4 - - - -
49A VAL* 2.8 51.2 + - + +
57A ALA* 3.8 31.9 - - + +
60A LEU* 3.5 15.7 - - + +
61A GLN* 6.0 1.3 - - + -
64A LEU* 3.7 35.0 - - + -
45C LEU* 4.6 12.3 - - + -
49C VAL* 3.7 26.9 - - + -
61C GLN* 5.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 2.8 18.4 + - + +
43A GLU* 3.6 8.9 - - - +
45A LEU* 1.3 74.9 - - - +
47A GLU* 1.3 57.2 + - - +
49A VAL* 4.0 2.0 - - - +
50A SER* 2.9 34.2 + - - -
46C HIS* 3.8 21.8 + + - -
49C VAL* 3.6 21.8 + - + +
50C SER* 3.5 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU 3.2 10.4 + - - +
44A LYS* 3.6 13.3 - - - +
45A LEU 3.2 0.2 - - - -
46A HIS* 1.3 77.2 - - - +
48A ALA* 1.3 67.3 + - - +
50A SER* 3.3 5.7 + - - -
51A LYS* 2.8 61.4 + - + +
56A GLU* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS 2.9 17.8 + - - +
45A LEU* 3.7 5.8 - - - +
47A GLU* 1.3 74.9 - - - +
49A VAL* 1.3 63.1 + - - +
51A LYS* 3.3 3.4 + - - -
52A GLY 3.1 3.1 + - - -
53A ASN* 2.9 31.6 + - - +
56A GLU* 3.8 40.2 - - + +
57A ALA* 3.9 15.9 - - - +
60A LEU* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 2.8 37.6 + - + +
46A HIS* 4.1 2.9 - - - +
48A ALA* 1.3 67.3 - - - +
50A SER* 1.3 66.7 + - - +
52A GLY* 3.0 14.8 + - - +
53A ASN 4.9 0.7 - - - +
57A ALA* 4.1 10.5 - - + -
0C MET* 4.9 0.7 - - - +
42C GLU* 3.7 30.6 - - + +
45C LEU* 3.7 28.9 - - + -
46C HIS* 3.7 37.4 - - + +
49C VAL* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS* 2.9 23.2 + - - -
47A GLU* 3.4 8.7 - - - -
48A ALA 3.3 0.2 - - - -
49A VAL* 1.3 77.4 - - - +
51A LYS* 1.3 63.1 + - - +
0C MET* 3.4 15.6 - - - +
46C HIS* 3.8 21.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
47A GLU* 2.8 51.6 + - + +
48A ALA* 3.3 3.6 + - - +
49A VAL 3.1 0.8 - - - -
50A SER* 1.3 82.3 - - - +
52A GLY* 1.3 63.3 + - - +
53A ASN* 3.2 7.9 + - + +
0C MET* 3.5 20.9 - - - +
----------------------------------------------------------
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