Contacts of the helix formed by residues 38 - 50 (chain D) in PDB entry 3KDO
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 38 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PRO* 4.3 1.8 - - - -
36D GLY 5.5 1.3 - - - +
37D TYR* 1.3 77.1 - - - +
39D ILE* 1.3 64.4 + - - +
40D GLU* 2.9 21.7 + - - +
41D GLN* 2.9 35.4 + - - +
42D ALA* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 3.9 22.4 - - + +
33D PRO* 3.9 12.9 - - + +
38D THR* 1.3 72.9 - - - +
40D GLU* 1.3 75.8 - - - +
42D ALA 3.1 0.9 + - - -
43D ALA* 2.6 34.9 + - + +
77D PHE* 3.6 26.5 - - + -
85D TRP* 3.6 64.2 - - + +
87D VAL* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 5.6 0.2 - - - +
10D ASP* 6.0 0.7 - - - -
13D VAL* 3.8 22.0 - - + +
15D LYS* 5.1 13.8 + - + +
38D THR* 2.9 19.4 + - - +
39D ILE* 1.3 91.5 - - + +
41D GLN* 1.3 57.8 + - + +
43D ALA* 4.4 0.2 - - - -
44D GLY* 2.8 28.8 + - - -
77D PHE* 4.3 20.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 4.5 3.2 - - - +
36D GLY 3.8 3.9 + - - +
37D TYR* 3.2 26.2 - - + -
38D THR* 2.9 42.4 + - - +
40D GLU* 1.3 78.7 - - + +
42D ALA* 1.3 59.9 + - - +
44D GLY* 4.3 0.2 - - - -
45D ALA 3.4 11.1 + - - -
117D ARG* 3.2 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 4.0 15.3 - - + -
33D PRO* 3.9 28.0 - - + -
37D TYR* 5.3 0.4 - - + -
38D THR 3.0 11.8 + - - +
39D ILE 3.5 6.3 - - - +
41D GLN* 1.3 77.7 - - - +
43D ALA* 1.3 64.5 + - - +
45D ALA* 3.4 2.8 + - - +
46D VAL* 3.1 29.0 + - - +
117D ARG* 4.2 18.4 - - + +
118D VAL* 4.2 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D VAL* 4.9 0.4 - - + -
31D VAL* 5.3 3.1 - - - -
39D ILE* 2.6 21.2 + - + +
40D GLU 4.0 2.0 - - - +
42D ALA* 1.3 73.1 - - - +
44D GLY* 1.3 58.4 + - - +
46D VAL* 3.3 7.6 + - - +
47D ALA* 2.9 31.5 + - - +
74D ALA* 4.2 4.3 - - + -
77D PHE* 3.5 31.0 - - + -
87D VAL* 3.9 22.7 - - + -
89D ILE* 4.4 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 3.7 21.3 - - - +
12D TYR* 3.9 7.7 - - - +
13D VAL* 4.0 15.6 - - - +
40D GLU 2.8 17.4 + - - -
43D ALA* 1.3 76.3 - - - +
45D ALA* 1.3 55.7 + - - +
47D ALA* 3.3 1.8 + - - +
48D ALA* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 3.8 28.8 - - + +
41D GLN 3.4 19.0 + - - +
42D ALA* 3.7 4.7 - - - +
43D ALA 3.3 0.2 - - - -
44D GLY* 1.3 74.8 - - - +
46D VAL* 1.3 59.3 + - - +
48D ALA* 3.2 1.2 + - - +
49D GLU* 2.8 34.5 + - - +
115D MET* 4.0 16.8 - - + +
117D ARG* 3.8 18.8 - - + -
118D VAL* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 4.1 23.8 - - + -
31D VAL* 4.9 5.4 - - + -
42D ALA 3.1 19.1 + - - +
43D ALA* 3.6 6.5 - - - +
45D ALA* 1.3 77.1 - - - +
47D ALA* 1.3 60.9 + - - +
50D SER* 2.9 28.7 + - - +
89D ILE* 3.8 17.9 - - + -
112D ILE* 3.5 15.1 - - + +
115D MET* 3.4 25.6 - - + -
118D VAL* 4.2 7.6 - - + -
121D LEU* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TYR* 3.8 27.6 - - + +
43D ALA 2.9 17.4 + - - +
44D GLY 3.7 3.1 - - - +
46D VAL* 1.3 76.9 - - - +
48D ALA* 1.3 60.6 + - - +
50D SER* 3.2 16.4 + - - -
51D SER* 2.8 21.4 + - - -
72D ALA* 4.1 3.9 - - - +
74D ALA 4.5 2.7 - - - +
89D ILE* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 3.6 22.7 - - + -
12D TYR* 3.4 35.4 - - + -
44D GLY 2.8 18.3 + - - +
45D ALA 3.7 0.9 - - - +
47D ALA* 1.3 78.4 - - - +
49D GLU* 1.3 60.8 + - - +
51D SER 3.2 8.0 + - - -
52D THR 3.4 0.2 + - - -
53D GLY* 2.7 34.4 + - - -
165J LYS* 3.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 5.6 1.7 - - + -
45D ALA 2.8 21.3 + - - +
48D ALA* 1.3 72.6 - - - +
50D SER* 1.3 58.6 + - - +
51D SER 3.4 0.2 - - - -
53D GLY 4.7 4.6 - - - +
54D THR* 5.1 4.3 - - - -
107D SER* 4.7 1.6 - - - +
111D ASN* 3.2 35.3 + - + +
112D ILE* 3.7 20.1 - - + +
115D MET* 3.9 17.3 - - + -
163J LYS* 5.6 0.3 + - - -
165J LYS* 3.0 43.6 + - - +
192J GLU* 3.6 1.4 - - - +
193J ASN* 5.0 1.0 + - - -
322J LYS* 3.8 19.4 + - - -
323J LEU* 6.4 0.4 - - - -
600J CAP 3.3 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D VAL* 2.9 19.5 + - - +
47D ALA* 3.2 8.1 + - - -
49D GLU* 1.3 77.8 - - - +
51D SER* 1.3 59.7 + - - +
91D TYR* 2.7 35.9 + - - -
96D PHE* 5.0 1.4 - - - -
107D SER* 3.0 49.5 + - - +
108D ILE* 4.4 2.9 - - - -
112D ILE* 4.0 10.1 - - - -
193J ASN* 4.6 2.0 - - - -
----------------------------------------------------------
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