Contacts of the helix formed by residues 105 - 110 (chain O) in PDB entry 2D2C
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 PRO 105 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122N VAL* 4.4 12.3 - - + +
126N VAL* 4.7 13.7 - - + -
101O MET 3.1 7.2 - - - +
102O ALA* 2.9 20.6 - - - +
104O VAL* 1.3 93.5 - - + +
106O LEU* 1.3 75.5 + - - +
108O LEU* 3.0 9.8 + - + +
109O ILE* 3.0 17.3 + - - +
1201O CLA 3.6 51.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O LEU* 6.6 0.2 - - + -
102O ALA* 3.4 16.4 - - + +
103O SER* 4.8 0.9 - - - -
105O PRO* 1.3 77.3 - - + +
107O GLY* 1.3 57.1 + - - +
108O LEU 2.6 16.4 + - - -
109O ILE* 2.7 39.4 + - + +
110O LEU* 3.5 18.8 + - + +
1201O CLA 4.7 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 107 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O SER* 3.4 23.8 + - - +
105O PRO 3.5 0.4 - - - -
106O LEU* 1.3 78.7 - - - +
108O LEU* 1.3 59.9 + - - +
110O LEU* 3.7 24.5 + - - +
111O VAL* 4.4 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101N VAL* 5.8 3.6 - - + -
118N TRP* 2.9 32.1 - - + -
122N VAL* 3.6 18.4 - - + -
302N HEM 5.1 4.7 - - + -
103O SER 4.2 1.0 + - - -
104O VAL 3.2 19.3 + - - +
105O PRO* 3.0 11.1 + - + +
106O LEU 2.6 4.9 + - - -
107O GLY* 1.3 71.3 - - - +
109O ILE* 1.3 54.3 + - - +
110O LEU 2.6 17.4 + - - -
111O VAL* 2.6 34.8 + - + +
1201O CLA 4.6 46.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N TRP* 3.2 21.2 - - + -
119N ILE* 3.2 52.8 - - + +
122N VAL* 4.1 11.2 - - + -
123N ILE* 4.6 10.8 - - + -
105O PRO 3.0 9.6 + - - +
106O LEU* 2.7 36.8 + - + +
108O LEU* 1.3 72.5 - - - +
110O LEU* 1.3 76.4 + - + +
111O VAL 3.3 1.3 + - - -
112O PRO* 3.6 7.8 - - - +
113O PHE* 4.3 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O LEU* 3.5 28.9 - - + +
107O GLY* 3.7 16.2 - - - +
108O LEU 2.6 5.4 + - - -
109O ILE* 1.3 92.7 - - + +
111O VAL* 1.3 62.0 + - - -
112O PRO* 3.7 0.7 - - - -
113O PHE* 3.5 26.3 - - + +
114O ILE* 3.3 26.3 + - + +
----------------------------------------------------------
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