Contacts of the helix formed by residues 103 - 109 (chain A) 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 VAL 103 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.7 22.7 - - + -
55A CYS 3.4 21.8 - - - +
56A TYR* 4.0 18.2 - - + -
91A ALA 3.0 15.9 + - - +
93A LYS* 3.8 29.6 - - + -
101A ALA 3.5 1.0 + - - -
102A HIS* 1.3 72.2 - - - +
104A VAL* 1.3 58.1 + - - +
106A ALA* 3.1 5.4 + - - +
107A LEU* 2.9 29.9 + - + +
114A PHE* 4.7 2.5 - - + -
120A MET* 3.8 20.0 - - + -
123A ILE* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A CYS 4.6 4.5 - - - +
27A VAL* 3.7 25.9 - - - +
102A HIS* 4.0 15.0 - - + -
103A VAL* 1.3 77.1 - - - +
105A CYS* 1.3 69.8 + - - +
107A LEU* 3.3 6.2 + - - -
108A TYR* 3.1 53.9 + - + -
168A VAL* 3.3 12.4 - - + +
169A THR* 4.1 13.9 - - + -
172A GLN* 4.1 23.6 - - - +
177A LEU* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A CYS* 4.0 0.9 - - - -
84A LEU* 3.7 27.1 - - + -
85A CYS* 3.9 13.9 - - - -
102A HIS* 3.5 8.6 + - + +
103A VAL 3.3 0.2 - - - -
104A VAL* 1.3 84.1 - - - +
106A ALA* 1.3 60.7 + - - +
109A ILE* 3.0 32.7 + - + +
168A VAL* 3.9 23.8 - - + -
169A THR* 4.0 5.8 - - - -
303A ZN 2.3 37.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.3 2.1 - - + +
102A HIS 3.1 13.1 + - - +
103A VAL 3.1 9.5 + - - +
105A CYS* 1.3 76.4 - - - +
107A LEU* 1.3 51.7 + - - +
109A ILE 3.4 5.4 - - - +
112A VAL* 3.5 29.0 - - + +
114A PHE* 3.4 24.4 - - + -
123A ILE* 3.7 12.3 - - + -
27D LYS* 2.7 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.0 24.0 - - + +
103A VAL* 2.9 20.9 + - + +
104A VAL* 3.7 9.0 - - - +
105A CYS 3.3 0.2 - - - -
106A ALA* 1.3 76.4 - - - +
108A TYR* 1.3 70.9 + - + +
109A ILE 4.3 0.2 - - - -
110A PRO* 4.8 0.3 - - - +
114A PHE* 3.8 21.5 - - + -
120A MET* 4.8 0.9 - - + -
179A GLU* 5.7 0.7 - - - +
190A TYR* 3.6 45.4 - - + +
23D LYS* 3.7 37.0 - - + +
24D ALA* 4.2 1.8 - - - -
27D LYS* 3.2 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL 4.9 5.4 + - - -
28A CYS* 5.9 0.9 - - - -
104A VAL* 3.1 37.5 + - + -
107A LEU* 1.3 84.0 - - + +
109A ILE* 1.3 63.3 + - - +
110A PRO* 3.5 9.3 - - - +
155A MET* 3.8 21.6 - - - +
168A VAL* 3.6 23.8 - - + -
177A LEU* 3.8 22.7 - - + +
178A CYS* 3.6 11.1 + - - -
179A GLU* 3.4 26.2 + - - +
190A TYR* 3.4 35.8 - + + +
191A CYS 3.2 35.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.0 22.9 - - + +
105A CYS* 3.0 21.6 + - + +
106A ALA 3.4 2.1 - - - +
108A TYR* 1.3 76.2 - - - +
110A PRO* 1.3 73.4 - - + +
111A GLU* 3.7 13.7 - - - +
112A VAL* 3.1 22.5 + - + +
128A VAL* 4.8 7.2 - - + -
132A ARG* 3.8 13.9 - - - -
153A ALA* 3.8 33.7 - - + +
154A CYS 4.8 2.5 - - - +
155A MET* 4.7 7.9 - - + +
168A VAL* 3.8 15.7 - - + -
27D LYS* 2.9 18.0 + - - -
----------------------------------------------------------
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