Contacts of the helix formed by residues 113 - 121 (chain D) in PDB entry 4FZX
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 SER 113 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A C 3.5 25.1 + - - -
16A C 3.4 25.8 - - - -
80D HIS* 3.4 0.4 - - - -
111D LYS 3.7 0.8 - - - -
112D TYR* 1.3 82.4 - - - +
114D ASN* 1.3 65.5 + - - +
115D MSE 3.9 3.3 + - - +
116D ALA* 3.3 23.4 + - - +
117D LEU* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A C 2.8 18.3 + - - +
6D ASP* 5.4 1.6 + - - -
80D HIS* 3.3 24.8 + - + +
113D SER* 1.3 74.4 - - - +
115D MSE 1.3 58.5 + - + +
117D LEU* 3.6 3.5 + - - +
118D TYR* 3.2 23.0 + - - +
133D HIS* 5.2 7.2 - - + -
139D ASP* 3.5 27.5 + - - +
142D ILE* 3.6 18.8 - - - +
143D THR* 2.9 33.9 + - - -
146D LEU* 4.0 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D SER* 3.3 3.6 + - - +
114D ASN* 1.3 78.4 - - - +
116D ALA* 1.3 64.9 + - - +
118D TYR* 3.6 31.1 - - - +
119D LYS* 3.0 38.7 + - + +
133D HIS* 3.7 51.1 - - + +
138D TYR* 4.1 13.5 - - + +
142D ILE* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A C 5.6 0.2 - - - +
111D LYS* 3.8 30.7 - - + +
113D SER* 3.3 23.2 + - - +
115D MSE 1.3 75.6 - - - +
117D LEU* 1.3 53.6 + - - +
119D LYS* 3.2 7.7 + - - +
120D THR* 2.7 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D HIS* 3.6 16.4 - - + -
103D ALA* 3.7 24.5 - - + -
107D TRP* 4.5 5.4 - - + -
110D ILE* 3.6 31.9 - - + -
111D LYS 3.3 18.4 - - - +
112D TYR* 3.4 31.2 - - + +
113D SER 3.2 12.2 + - - +
114D ASN 3.8 3.4 - - - +
116D ALA* 1.3 74.8 - - - +
118D TYR* 1.3 61.8 + - - +
120D THR* 4.5 1.3 - - - +
121D ARG* 2.9 37.5 + - + +
146D LEU* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ASN 3.2 14.3 + - - +
115D MSE 3.6 22.7 - - - +
117D LEU* 1.3 80.7 - - - +
119D LYS* 1.3 64.5 + - + +
122D LYS 3.4 1.7 + - - -
123D LEU* 3.1 71.5 + - + +
124D ASN* 3.3 7.0 + - - -
125D VAL* 3.1 31.0 + - + +
127D THR* 4.9 2.4 - - - +
142D ILE* 3.7 46.4 - - + +
145D ALA* 3.9 15.0 - - + -
146D LEU* 4.9 2.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D MSE 3.0 40.3 + - + +
116D ALA* 3.2 6.3 + - - +
118D TYR* 1.3 78.4 - - + +
120D THR* 1.3 61.0 + - - +
122D LYS* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ILE* 3.7 35.8 - - + +
111D LYS* 5.2 1.7 + - - +
116D ALA* 2.7 25.8 + - - +
117D LEU 4.1 2.0 - - - -
119D LYS* 1.3 73.8 - - - +
121D ARG* 1.3 62.3 + - - +
122D LYS* 3.2 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D TRP* 3.3 48.8 - - + +
110D ILE* 5.3 2.5 - - - -
117D LEU* 2.9 25.5 + - + +
120D THR* 1.3 82.2 + - - +
122D LYS* 1.3 73.3 + - - +
123D LEU* 3.3 19.1 + - + +
146D LEU* 4.8 3.8 - - + -
149D ASP* 2.7 33.6 + - - +
153D THR* 3.3 24.7 + - - +
----------------------------------------------------------
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