Contacts of the helix formed by residues 22 - 27 (chain D) in PDB entry 5DAH
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 22 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 3.3 22.7 - - - +
57A GLY* 4.2 10.1 - - - -
117A VAL 2.5 21.9 + - - +
118A SER* 3.4 29.2 - - - +
120A MET* 3.6 7.4 - - - -
20D LEU 4.3 7.4 - - - +
21D ALA* 1.3 77.8 - - - +
23D LYS* 1.3 63.4 + - - +
24D ALA* 3.4 2.4 + - - +
25D ALA* 3.2 25.6 + - - +
26D ARG* 3.4 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 5.0 0.7 - - + -
28A CYS* 4.1 11.1 - - - +
54A ALA* 3.0 15.1 + - + +
55A CYS* 3.6 36.8 - - + -
107A LEU* 3.7 22.7 - - + -
120A MET* 4.4 6.5 - - + -
179A GLU* 3.0 34.5 + - - +
190A TYR* 2.7 36.5 + - + +
22D THR* 1.3 73.5 - - - +
24D ALA* 1.3 61.4 + - - +
26D ARG* 3.3 27.0 + - - +
27D LYS 3.3 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.2 6.1 - - - -
114A PHE* 3.4 34.5 - - + -
117A VAL* 3.8 17.3 - - + +
120A MET* 3.6 30.9 - - + +
22D THR* 3.2 2.3 + - - +
23D LYS* 1.3 81.1 - - - +
25D ALA* 1.3 61.0 + - - +
26D ARG 3.1 0.9 + - - -
27D LYS* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 3.6 28.2 - - + +
118A SER* 6.1 0.2 - - - -
187A ASN* 4.8 3.8 - - - +
21D ALA* 4.5 10.1 - - + -
22D THR* 3.2 27.8 + - - +
24D ALA* 1.3 76.0 - - - +
26D ARG* 1.3 60.4 + - - +
27D LYS 3.8 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 4.8 1.2 + - - -
186A ASP* 2.3 51.0 + - + +
187A ASN* 3.3 9.9 - - - +
188A VAL* 2.8 56.5 + - + +
190A TYR* 4.2 2.9 - - - +
21D ALA* 4.3 23.3 - - + -
22D THR 3.5 14.8 - - - +
23D LYS* 3.3 34.2 + - - +
24D ALA 3.1 0.8 - - - -
25D ALA* 1.3 80.3 - - - +
27D LYS* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA 2.7 23.0 + - - +
107A LEU* 3.2 23.1 + - + +
109A ILE 2.9 13.4 + - - -
110A PRO* 3.3 18.9 + - - -
112A VAL 2.7 28.8 + - - +
113A GLN* 5.9 0.4 - - - -
114A PHE* 5.1 7.0 - - + -
187A ASN* 4.2 3.5 - - - +
188A VAL 3.8 4.7 - - - -
190A TYR* 3.8 21.5 - - + +
23D LYS 3.3 4.9 + - - +
24D ALA* 3.2 18.7 + - - +
25D ALA 4.6 2.6 - - - +
26D ARG* 1.3 78.5 - - - +
28D SER* 1.3 72.0 + - - +
----------------------------------------------------------
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