Contacts of the helix formed by residues 204 - 213 (chain A) in PDB entry 4F2N
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 ARG 204 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 4.6 0.4 - - - -
200A ASP 3.8 8.9 + - - -
201A PHE* 2.9 54.5 + - - +
202A GLU* 3.2 6.5 + - - -
203A ASN* 1.3 90.7 + - - +
205A ARG* 1.3 61.6 + - - +
206A ALA* 3.3 3.1 - - - +
207A ASP* 2.7 53.9 + - + +
208A TYR 3.1 17.7 + - - -
211A GLU* 5.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLY 2.9 35.9 + - - -
149A VAL* 3.7 18.8 + - + +
151A ASN 2.7 25.5 + - - -
153A GLY* 2.9 25.7 + - - +
192A VAL* 3.0 28.7 + - + +
194A GLU* 4.5 7.9 + - - +
197A TYR* 3.0 49.6 + - + +
203A ASN 2.8 11.2 + - - +
204A ARG* 1.3 68.1 - - - +
206A ALA* 1.3 66.0 + - - +
208A TYR* 3.2 8.6 + - + +
209A LEU* 3.0 30.1 + - + +
193B TRP* 5.6 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN* 5.0 2.9 + - - +
149A VAL* 3.7 29.8 - - + +
204A ARG* 3.3 1.1 - - - -
205A ARG* 1.3 79.3 - - - +
207A ASP* 1.3 65.9 + - - +
209A LEU* 3.4 2.9 + - - +
210A LYS* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE* 3.9 6.7 - - + -
204A ARG* 2.7 54.4 + - - +
206A ALA* 1.3 76.8 - - - +
208A TYR* 1.3 61.4 + - - +
210A LYS* 3.3 7.5 + - - +
211A GLU* 2.8 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 5.0 4.4 - - + +
50A MET* 4.4 9.6 - - + +
111A PHE* 3.5 23.0 - - - -
191A ASP 2.7 30.3 + - - -
192A VAL* 4.4 2.5 - - + -
196A ALA* 3.8 14.5 - - + +
197A TYR* 3.4 45.3 - + + -
201A PHE* 3.6 26.4 - + + -
204A ARG 3.1 12.4 + - - +
205A ARG* 3.3 12.1 - - + +
207A ASP* 1.3 76.7 - - - +
209A LEU* 1.3 70.2 + - + +
211A GLU* 3.6 1.0 - - - +
212A LEU* 2.7 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 4.4 12.1 - - + -
145A GLN* 3.6 25.0 - - + +
148A GLY* 3.6 11.2 - - - -
149A VAL* 3.6 33.2 - - + +
190A ALA* 3.8 28.5 - - + -
192A VAL* 4.0 6.7 - - + -
205A ARG* 3.0 25.7 + - + +
206A ALA* 3.9 4.0 - - - +
208A TYR* 1.3 93.5 - - + +
210A LYS* 1.3 63.6 + - - +
212A LEU* 3.5 16.8 + - + +
213A TRP* 3.6 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN* 3.8 31.4 + - - +
206A ALA 3.1 16.9 + - - +
207A ASP* 3.5 9.6 - - - +
209A LEU* 1.3 76.6 - - - +
211A GLU* 1.3 65.4 + - + +
213A TRP* 3.2 25.6 + - + +
214A GLN* 5.0 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO 5.2 3.8 - - - +
49A VAL* 3.2 23.2 - - + +
201A PHE* 3.5 36.1 - - + -
204A ARG* 5.0 2.6 + - - -
207A ASP* 2.8 28.4 + - - +
208A TYR 3.9 2.2 - - - +
210A LYS* 1.3 75.0 - - + +
212A LEU* 1.3 66.0 + - - +
213A TRP 3.1 2.7 - - - -
214A GLN* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 4.4 7.6 - - + +
50A MET* 4.3 6.7 - - + -
111A PHE* 4.6 3.6 - - + -
115A LEU* 3.9 13.0 - - + -
144A PHE* 5.4 1.1 - - + -
188A PHE* 4.3 11.7 - - + -
190A ALA* 3.5 33.7 - - + -
208A TYR* 2.7 47.5 + - + +
209A LEU* 3.7 13.0 - - + +
210A LYS 3.4 1.0 - - - -
211A GLU* 1.3 74.2 - - - +
213A TRP* 1.3 64.7 + - + +
214A GLN 3.0 1.4 + - - -
215A ILE* 3.0 36.7 + - + +
216A VAL* 3.4 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY* 5.6 0.2 - - - -
140A PHE* 3.7 17.9 - + - -
141A MET* 3.6 52.2 - - + +
144A PHE* 3.5 30.7 - + - -
145A GLN* 2.7 29.0 + - + -
188A PHE* 3.7 17.9 - + - -
209A LEU 3.6 7.2 + - - -
210A LYS* 3.2 26.5 - - + +
211A GLU 3.1 1.0 + - - -
212A LEU* 1.3 78.3 - - + +
214A GLN* 1.3 61.4 + - + +
216A VAL* 3.3 24.2 + - + +
218A TRP* 3.5 45.6 + + + +
----------------------------------------------------------
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