Contacts of the helix formed by residues 18 - 27 (chain D) in PDB entry 4PJO
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 18 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C VAL* 4.6 18.8 - - - +
16D LEU* 3.3 24.0 + - + +
17D GLN* 1.3 76.7 - - - +
19D ARG* 1.3 55.9 + - - +
20D GLU* 2.6 9.2 - - + +
21D GLU* 2.8 51.1 + - - +
22D GLU* 3.0 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D MET* 5.7 11.4 - - - +
12D THR* 3.7 23.7 + - + +
17D GLN* 2.9 10.7 - - + +
18D LYS* 1.3 79.9 - - - +
20D GLU* 1.3 62.5 + - - +
22D GLU* 3.9 23.3 + - + +
23D GLU* 3.1 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C VAL* 5.2 12.1 - - + +
17D GLN* 3.1 19.8 + - + +
18D LYS* 4.2 5.2 - - + +
19D ARG* 1.3 80.9 - - - +
21D GLU* 1.3 55.7 + - - +
23D GLU* 3.5 14.9 - - - +
24D PHE* 2.9 67.1 + - + -
61D ARG* 3.3 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2C SER* 5.8 4.0 - - - +
18D LYS* 2.8 45.1 + - + +
20D GLU* 1.3 75.7 - - - +
22D GLU* 1.3 59.1 + - + +
24D PHE* 3.2 12.2 + - + +
25D ASN* 2.9 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LYS 3.0 16.5 + - - +
19D ARG* 3.3 25.6 + - + +
21D GLU* 1.3 76.0 - - + +
23D GLU* 1.3 54.1 + - - +
25D ASN* 3.3 5.3 + - - +
26D THR* 2.6 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251 A 5.6 3.6 + - - -
19D ARG* 3.1 31.0 + - + +
20D GLU* 3.5 17.1 - - - +
22D GLU* 1.3 77.7 - - - +
24D PHE* 1.3 67.2 + - + +
26D THR* 4.0 2.0 - - - -
27D GLY* 2.6 39.7 + - - +
28D PRO* 4.8 0.8 - - + +
29D LEU* 4.7 1.6 + - - +
30D SER 4.6 0.2 + - - -
37F ASP* 3.9 28.3 - - + +
38F GLY* 4.1 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251 A 6.1 0.9 - - - -
-2C SER* 5.3 2.9 - - - -
-1C GLY* 4.1 23.3 - - - -
0C SER 4.2 9.0 - - - -
1C VAL* 5.9 0.2 - - - -
20D GLU* 2.9 50.5 + - + +
21D GLU* 3.2 13.2 + - + +
23D GLU* 1.3 87.2 - - + +
25D ASN* 1.3 57.6 + - - +
29D LEU* 3.7 32.1 - - + -
30D SER* 3.2 17.1 + - - +
33D THR* 2.7 35.0 + - + +
59D PHE* 4.1 22.2 - + - -
60D ASP 4.4 0.4 - - - -
61D ARG* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2C SER* 5.9 3.0 - - - -
21D GLU* 2.9 41.4 + - - +
22D GLU* 3.3 5.8 + - - +
24D PHE* 1.3 81.2 - - - +
26D THR* 1.3 63.5 + - + +
30D SER* 3.7 12.9 - - - -
33D THR* 4.4 9.9 - - - +
34D GLN* 5.4 4.0 + - - +
37D LYS* 4.2 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLU* 2.6 27.7 + - + +
23D GLU* 4.0 1.7 - - - -
25D ASN* 1.3 85.6 - - + +
27D GLY* 1.3 67.5 + - - +
30D SER* 4.1 4.2 + - - -
34F VAL* 5.6 1.6 - - - +
35F SER* 3.9 10.7 + - - -
43F GLN* 4.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU* 2.6 28.5 + - - -
26D THR* 1.3 86.8 + - - +
28D PRO* 1.3 70.8 - - - +
29D LEU 3.3 2.5 - - - -
30D SER* 3.0 18.9 + - - -
35F SER* 3.4 11.8 + - - -
36F VAL 5.0 3.4 - - - -
----------------------------------------------------------
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