Contacts of the helix formed by residues 21 - 29 (chain B) in PDB entry 1DWQ
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 21 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR* 6.3 1.3 - - + -
165A GLY* 4.8 7.6 - - - -
18B ILE 4.6 0.8 + - - -
19B TRP* 3.2 0.4 - - - +
20B HIS* 1.3 97.5 - - + +
22B LEU* 1.3 67.5 + - - +
24B PRO* 3.3 15.3 - - - +
25B ALA* 3.4 10.6 + - - +
28B ARG* 5.4 0.9 + - - -
163B THR* 6.3 0.2 - - - -
166B GLU* 3.8 14.9 + - - +
239B GLN 3.8 11.2 - - - +
240B LEU* 3.3 46.4 + - + +
243B THR* 3.7 13.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.3 9.0 - - + -
19B TRP* 3.5 42.6 + - + +
21B LYS* 1.3 75.8 - - - +
23B LYS* 1.3 65.4 + - - +
25B ALA* 3.1 2.9 + - - +
26B LEU* 3.1 30.7 + - + +
77B VAL* 5.3 0.2 - - + -
239B GLN* 4.1 11.3 + - + -
243B THR* 3.6 34.4 - - + +
246B VAL* 4.0 13.7 - - + -
247B ALA* 3.8 22.4 - - + +
250B LEU* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLU* 3.1 38.4 + - + +
171A LYS* 4.1 8.1 - - - +
172A MET* 4.0 11.9 - - + -
8B LEU* 4.3 5.8 - - + +
19B TRP 2.9 23.5 + - - +
22B LEU* 1.3 70.4 - - - +
24B PRO* 1.4 66.0 - - + +
26B LEU* 3.3 2.6 + - - +
27B GLU* 2.8 53.7 + - - +
33B VAL* 3.5 46.4 - - + -
34B THR* 5.1 0.2 - - - +
35B ALA* 4.5 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 3.9 38.4 - - + +
165A GLY* 4.3 1.3 - - - +
168A GLU* 3.6 14.6 - - + +
20B HIS 3.3 23.3 - - - +
21B LYS* 3.3 15.5 - - - +
23B LYS* 1.4 89.4 - - + +
25B ALA* 1.3 54.7 + - - +
27B GLU* 3.2 12.1 + - + +
28B ARG* 2.9 42.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
21B LYS 3.4 11.6 + - - +
22B LEU* 3.1 10.5 + - - +
24B PRO* 1.3 75.6 - - - +
26B LEU* 1.3 61.9 + - - +
28B ARG* 3.2 32.1 + - - +
29B ALA* 3.6 6.8 + - - +
243B THR* 4.0 10.5 - - + -
244B GLU* 3.3 25.5 - - - +
247B ALA* 4.1 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 4.1 17.7 - - + -
8B LEU* 4.3 13.2 - - + -
22B LEU* 3.1 30.0 + - + +
23B LYS 3.7 2.0 - - - +
25B ALA* 1.3 77.2 - - - +
27B GLU* 1.3 61.3 - - - +
29B ALA* 3.2 7.9 + - - -
31B HIS* 3.1 46.6 + - + -
33B VAL* 3.6 26.5 - - + -
247B ALA* 4.0 19.1 - - - +
250B LEU* 3.8 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLU* 4.0 7.6 - - - +
171A LYS* 5.5 0.7 + - - -
23B LYS* 2.8 54.0 + - - +
24B PRO* 3.2 10.7 + - + +
26B LEU* 1.3 73.0 - - - +
28B ARG* 1.3 64.7 + - - +
29B ALA 3.1 0.4 - - - -
30B GLY* 3.0 13.9 + - - -
31B HIS 3.9 14.1 - - - +
32B LYS* 5.4 0.4 - - - -
33B VAL* 3.9 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 3.7 26.5 + - - +
21B LYS 5.4 1.0 + - - -
24B PRO* 2.9 34.1 + - - +
25B ALA* 3.2 22.5 + - - +
27B GLU* 1.3 77.1 - - - +
29B ALA* 1.3 56.1 + - - +
30B GLY 3.3 1.2 + - - -
244B GLU* 2.9 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 5.9 1.0 + - - -
3B THR* 3.9 12.0 - - - +
25B ALA 3.6 5.2 + - - +
26B LEU* 3.2 11.8 + - - +
27B GLU 3.1 1.2 - - - -
28B ARG* 1.3 77.6 - - - +
30B GLY* 1.3 60.5 + - - +
31B HIS* 3.5 19.8 + - + +
247B ALA 6.2 0.2 - - - +
251B GLN* 4.1 11.3 - - + +
----------------------------------------------------------
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