Contacts of the helix formed by residues 22 - 33 (chain A) in PDB entry 3DAG
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 PHE 22 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.2 41.3 - + - -
21A ASN* 1.3 73.9 - - - +
23A MET* 1.3 63.5 + - - +
24A ARG 3.3 0.3 + - - -
25A ALA* 3.3 1.9 + - + -
26A CYS* 3.0 22.6 + - - -
38A ALA 3.4 21.3 - - - +
39A LEU* 3.6 13.7 - - - -
40A THR 3.2 28.9 - - - -
41A HIS* 4.2 1.3 - - + -
84A VAL* 4.4 4.0 - - + -
88A HIS* 2.9 23.1 + + + +
97A MET* 3.6 22.2 - - + -
100A ILE* 4.3 9.0 - - + -
121A LEU* 3.7 25.8 - - + -
207A GLU* 3.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 2.9 21.0 + - - +
22A PHE* 1.3 75.5 - - - +
24A ARG* 1.3 57.2 + - - +
26A CYS* 3.4 3.5 + - - +
27A GLU* 3.0 48.4 + - - +
88A HIS* 3.4 43.9 - - + +
89A LEU* 4.4 9.2 - - - -
91A GLY* 5.2 3.4 - - - -
93A PRO* 4.3 23.1 - - + -
207A GLU 3.2 2.0 + - - -
208A MET* 3.6 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET* 1.3 76.6 - - - +
25A ALA* 1.3 66.5 + - - +
27A GLU* 3.2 24.4 + - - +
28A VAL* 2.9 39.5 + - - +
45A THR* 4.8 0.7 - - + -
49A GLU* 2.9 19.4 + - - +
53A LEU* 3.8 8.1 - - - +
206A PRO 3.5 16.4 - - - +
207A GLU 3.0 9.0 + - - +
208A MET 3.4 17.7 + - - +
209A LYS 3.7 3.6 - - - +
210A GLY* 3.4 15.7 - - - +
233A ILE 4.4 1.0 + - - -
234A ALA 2.8 28.7 + - - -
235A ARG* 3.3 26.3 + - - +
236A GLY* 3.7 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.7 6.1 - - + +
24A ARG* 1.3 76.1 - - - +
26A CYS* 1.3 57.4 + - - +
28A VAL* 3.5 4.7 + - - -
29A ALA* 2.9 29.6 + - - +
37A ILE* 3.5 23.0 - - - +
38A ALA* 3.6 18.4 - - - +
40A THR* 3.9 20.0 - - - +
45A THR* 4.4 7.2 - - - +
207A GLU* 3.0 17.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.0 18.6 + - - -
23A MET 3.5 8.5 - - - +
25A ALA* 1.3 73.4 - - - +
27A GLU* 1.3 60.6 + - - +
29A ALA* 3.4 2.8 + - - +
30A LYS* 2.9 29.1 + - - +
38A ALA* 3.8 19.1 - - - -
84A VAL* 3.8 9.2 - - - -
85A MET* 3.7 21.0 - - + +
88A HIS* 3.7 28.5 - - + -
89A LEU* 3.9 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET* 3.0 32.5 + - - +
24A ARG* 3.5 36.1 + - - +
26A CYS* 1.3 72.8 - - - +
28A VAL* 1.3 60.9 + - - +
30A LYS* 3.4 6.2 + - - +
31A GLU* 3.0 28.4 + - - +
89A LEU* 3.8 19.2 - - + +
208A MET 5.5 0.2 - - - +
210A GLY 5.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.9 55.7 + - - +
25A ALA* 3.8 5.4 - - - +
27A GLU* 1.3 73.1 - - - +
29A ALA* 1.3 66.4 + - - +
31A GLU* 3.1 8.0 + - - +
32A VAL* 2.9 26.7 + - + +
37A ILE* 3.9 25.8 - - + -
45A THR* 5.6 0.7 - - + -
48A ALA 5.2 0.7 - - - +
49A GLU* 3.8 27.1 - - + +
52A HIS* 5.7 0.4 - - + -
53A LEU* 4.4 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 2.9 18.9 + - - +
26A CYS 3.4 6.1 - - - +
28A VAL* 1.3 76.0 - - - +
30A LYS* 1.3 57.5 + - - +
32A VAL* 4.4 1.8 - - - -
33A GLY* 3.0 23.7 + - - -
34A LYS 3.1 31.3 + - - +
35A PRO* 5.3 0.2 - - - +
37A ILE* 4.0 5.5 - - + +
38A ALA* 3.5 17.3 - - + +
85A MET* 3.9 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A CYS 2.9 17.1 + - - +
27A GLU* 3.8 5.2 - - - +
29A ALA* 1.3 72.8 - - - +
31A GLU* 1.3 67.5 + - - +
32A VAL 3.3 0.7 + - - -
33A GLY* 3.4 10.2 + - - -
85A MET* 3.7 17.2 - - + +
89A LEU* 3.8 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU 3.0 17.5 + - - +
28A VAL* 3.1 8.0 + - - +
30A LYS* 1.3 80.1 - - - +
32A VAL* 1.3 59.3 + - + +
33A GLY 3.7 0.2 + - - -
53A LEU* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 2.9 22.3 + - + +
29A ALA 4.1 0.4 - - - +
31A GLU* 1.3 80.0 - - + +
33A GLY* 1.3 60.8 + - - +
34A LYS* 3.5 20.5 + - + +
37A ILE* 3.5 29.4 - - + -
52A HIS* 4.0 26.9 - - + +
53A LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 3.0 8.6 + - - -
30A LYS* 3.4 9.2 + - - -
31A GLU 3.5 0.4 + - - -
32A VAL* 1.3 79.3 - - - +
34A LYS* 1.3 62.7 + - - +
35A PRO* 3.7 9.2 - - - +
----------------------------------------------------------
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