Contacts of the helix formed by residues 16 - 32 (chain B) in PDB entry 1DXO
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 16 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B HIS* 3.2 42.9 - - - -
13B GLU* 2.8 20.2 + - - +
14B ARG 4.5 0.5 - - - +
15B THR* 1.3 85.1 + - - +
17B PHE* 1.3 62.2 + - - +
19B TYR* 3.1 17.5 + - - +
20B ALA* 3.3 13.2 + - - +
301B FAD 3.4 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER* 1.3 70.8 - - - +
18B ASN* 1.3 56.3 + - - +
20B ALA* 3.1 3.3 + - + +
21B MET* 2.7 58.6 + - + +
147B THR* 4.1 9.6 - - + -
189B THR* 4.7 3.4 - - - -
192B ILE* 3.7 26.7 - - + -
200B ARG* 3.6 29.6 - - + -
203B ILE* 3.3 36.6 - - + -
204B LEU* 3.7 23.6 - - + -
301B FAD 2.7 59.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.1 5.6 - - + -
11B HIS* 3.6 28.9 - - + -
16B SER 3.2 0.2 - - - -
17B PHE* 1.3 78.3 - - - +
19B TYR* 1.3 57.4 + - - +
21B MET* 3.1 5.3 + - - +
22B LYS* 2.9 23.6 + - - +
100B GLN* 2.9 36.6 + - - +
101B PHE* 2.9 22.7 + - - +
102B PRO* 3.6 6.7 - - - +
147B THR* 3.1 22.7 + - - +
301B FAD 2.7 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.9 21.0 - - + +
11B HIS 5.9 0.7 - - - -
13B GLU 3.6 9.0 - - - +
14B ARG* 3.4 62.2 + - + +
16B SER* 3.1 19.3 + - - +
18B ASN* 1.3 78.2 - - - +
20B ALA* 1.3 66.2 + - - +
22B LYS* 2.9 30.6 + - - +
23B GLU* 2.9 49.1 + - + +
40B ASP* 4.2 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER 3.3 3.0 + - - +
17B PHE* 3.1 10.2 + - - +
19B TYR* 1.3 83.8 - - - +
21B MET* 1.3 55.3 + - - +
23B GLU* 3.4 6.8 + - - +
24B ALA* 3.0 29.8 + - - +
204B LEU* 3.5 11.3 - - + +
301B FAD 3.2 49.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 2.7 51.1 + - + +
18B ASN 3.1 7.2 + - - +
20B ALA* 1.3 72.0 - - - +
22B LYS* 1.3 62.2 + - - +
24B ALA* 4.0 0.6 - - - +
25B ALA* 3.2 17.2 + - - +
100B GLN* 3.1 27.4 - - - +
145B SER* 3.2 26.9 - - - +
147B THR* 4.9 1.1 - - + -
187B GLN* 4.2 4.7 - - + +
189B THR* 4.0 28.3 - - + +
203B ILE* 4.4 3.8 - - + -
204B LEU* 3.9 11.0 - - - -
207B TRP* 3.3 44.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.7 27.9 - - + +
9B LEU* 4.1 24.9 - - + -
18B ASN 2.9 11.8 + - - +
19B TYR* 2.9 39.2 + - - +
21B MET* 1.3 75.6 - - - +
23B GLU* 1.3 88.6 + - - +
25B ALA* 3.4 5.6 + - - +
26B ALA* 3.1 25.8 + - - +
38B GLU* 3.3 39.7 + - + +
40B ASP* 5.3 2.3 + - - -
100B GLN* 4.5 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 2.9 47.8 + - + +
20B ALA* 3.8 7.0 - - - +
22B LYS* 1.3 103.7 + - - +
24B ALA* 1.3 57.8 + - - +
26B ALA* 3.9 5.2 - - - +
27B ALA* 3.0 31.5 + - - +
38B GLU* 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 3.0 17.7 + - - +
21B MET* 4.0 4.9 - - - +
22B LYS 3.3 0.2 - - - -
23B GLU* 1.3 78.1 - - - +
25B ALA* 1.3 56.8 + - - +
27B ALA* 3.5 2.9 + - - -
28B ALA* 2.9 31.0 + - - +
204B LEU* 4.1 22.2 - - + +
207B TRP* 4.7 4.0 - - + -
208B LYS* 3.4 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.9 14.6 - - + -
21B MET 3.2 16.9 + - - +
22B LYS* 3.7 5.2 - - - +
24B ALA* 1.3 74.9 - - - +
26B ALA* 1.3 62.1 + - - +
28B ALA* 3.9 0.3 - - - +
29B LEU* 2.9 35.4 + - - +
98B ILE* 4.4 10.5 - - + -
207B TRP* 3.6 16.5 - - + +
211B LEU* 3.6 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.8 8.9 - - + +
22B LYS 3.1 17.7 + - - +
23B GLU* 3.9 8.3 - - - +
25B ALA* 1.3 76.8 - - - +
27B ALA* 1.3 57.7 + - - +
30B LYS* 2.9 47.4 + - - +
36B VAL* 3.9 23.2 - - + +
38B GLU* 4.2 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU 3.0 18.4 + - - +
24B ALA* 3.8 4.5 - - - +
26B ALA* 1.3 78.2 - - - +
28B ALA* 1.3 61.2 + - - +
30B LYS* 3.7 7.3 - - - +
31B LYS* 3.0 33.6 + - + +
208B LYS* 4.1 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 2.9 19.0 + - - +
25B ALA 3.9 2.9 - - - +
27B ALA* 1.3 76.6 - - - +
29B LEU* 1.3 63.0 + - - +
31B LYS* 3.2 26.1 + - - +
32B LYS* 3.2 15.3 + - - +
208B LYS* 3.7 39.9 - - + +
211B LEU* 4.4 8.7 - - + -
212B GLU* 5.8 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ALA* 3.6 30.5 - - + -
7B ILE* 5.5 1.1 - - + -
25B ALA 2.9 21.7 + - - +
28B ALA* 1.3 70.7 - - - +
30B LYS* 1.3 65.3 + - - +
32B LYS* 3.1 6.8 + - + +
34B TRP* 3.0 54.8 + - + +
36B VAL* 3.7 15.5 - - + -
96B LEU* 4.0 15.0 - - + -
98B ILE* 4.5 11.7 - - + -
211B LEU* 3.7 42.6 - - + +
214B ILE* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 2.9 37.4 + - - +
27B ALA* 3.7 7.6 - - - +
29B LEU* 1.3 75.7 - - - +
31B LYS* 1.3 56.4 + - + +
33B GLY* 2.7 27.0 + - - -
34B TRP 3.8 13.8 + - - +
36B VAL* 3.7 38.0 + - + +
38B GLU* 5.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 3.0 27.2 + - - +
28B ALA* 3.4 16.1 - - - +
30B LYS* 1.3 79.4 - - + +
32B LYS* 1.3 63.6 + - + +
33B GLY 3.2 3.3 + - - -
208B LYS* 2.7 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.2 10.8 + - - +
29B LEU* 3.1 10.4 + - - +
30B LYS 3.1 1.2 - - - -
31B LYS* 1.3 80.4 - - + +
33B GLY* 1.3 58.6 + - - +
34B TRP* 3.6 17.6 + - + +
211B LEU 5.4 1.1 - - - +
212B GLU* 3.8 62.7 + - + +
213B ASN* 4.7 4.0 + - - -
----------------------------------------------------------
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