Contacts of the helix formed by residues 117 - 121 (chain F) in PDB entry 4X6D
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 ASP 117 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LYS* 4.9 5.7 - - - +
115F VAL* 3.3 14.9 - - - +
116F GLU* 1.3 81.6 - - - +
118F LEU* 1.3 81.1 + - - +
119F ASN* 3.2 35.3 + - - +
120F LYS* 3.4 25.9 + - + +
150G LYS* 4.2 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.4 11.0 - - + +
13F LEU* 4.8 0.7 - - - +
14F LYS* 4.4 30.0 - - + +
17F GLN* 5.6 2.9 - - - +
115F VAL* 3.8 20.9 - - + -
117F ASP* 1.3 76.0 + - - +
119F ASN* 1.3 58.2 + - - +
120F LYS 3.0 9.8 + - - -
121F VAL* 3.3 20.9 + - + +
218F LEU* 3.7 33.7 - - + +
222F ASP* 3.9 30.1 - - + +
223F GLU 4.6 9.6 - - - +
224F TRP* 3.6 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ASP* 3.2 26.3 + - + +
118F LEU* 1.3 74.4 - - - +
120F LYS* 1.3 56.0 + - + +
121F VAL 3.1 5.4 - - - -
122F PHE* 3.9 6.6 - - - -
224F TRP* 3.7 11.7 - - - -
225F THR 5.7 0.2 + - - -
226F GLN* 3.3 44.4 + - + +
228F ARG* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F VAL* 4.5 10.5 - - + -
116F GLU* 4.5 6.3 - - - +
117F ASP* 3.4 31.4 - - + +
118F LEU 3.0 0.8 - - - -
119F ASN* 1.3 77.9 - - - +
121F VAL* 1.3 60.5 + - + +
122F PHE* 3.4 19.2 - - - -
152F TYR* 3.1 32.6 - - + +
186F ASP* 2.3 52.4 + - + +
188F ARG* 5.1 0.3 - - - +
150G LYS 3.3 27.0 + - - -
151G ASP* 3.5 16.8 + - - +
152G SER* 3.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.4 17.9 - - + -
115F VAL* 5.2 2.5 - - + -
118F LEU* 3.3 23.1 - - + +
119F ASN 3.1 1.8 - - - -
120F LYS* 1.3 81.1 - - + +
122F PHE* 1.3 60.7 + - - +
152F TYR* 3.3 22.2 - - + +
153F PRO* 4.3 3.1 - - + -
215F PHE* 3.8 16.4 - - + -
217F GLY* 4.3 8.7 - - - -
218F LEU* 3.9 15.5 - - + -
228F ARG* 2.9 25.1 + - - -
231F PRO* 3.4 28.4 - - + +
----------------------------------------------------------
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