Contacts of the helix formed by residues 210 - 218 (chain A) in PDB entry 1ANF
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 TYR 210 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 4.9 10.7 - - + +
150A ASN* 3.5 24.9 - - + +
156A PHE* 4.1 20.9 - + - -
209A ASP* 1.3 76.4 - - - +
211A SER* 1.3 61.5 + - - +
213A ALA* 3.8 1.9 - - - +
214A GLU* 2.8 58.2 + - + +
227A ASN* 3.2 34.9 + - - -
230A TRP* 3.2 31.5 + + - -
231A ALA* 3.9 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 3.4 10.6 + - - -
210A TYR* 1.3 79.2 - - - +
212A ILE* 1.3 66.5 + - - +
214A GLU* 3.3 7.7 + - - +
215A ALA* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 4.5 12.6 - - + -
207A ASP* 4.9 11.7 - - - +
208A THR* 3.9 20.9 - - + +
209A ASP* 3.1 32.2 + - - +
211A SER* 1.3 80.0 - - - +
213A ALA* 1.4 58.6 + - - +
215A ALA* 3.9 4.8 - - + +
216A ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 3.7 12.0 - - - +
149A PHE* 3.6 34.3 - - - +
150A ASN 4.0 1.6 - - - +
208A THR* 3.9 6.0 - - + +
209A ASP 2.9 18.3 + - - +
210A TYR* 3.9 2.7 - - - +
212A ILE* 1.4 72.4 - - - +
214A GLU* 1.3 68.4 + - - +
216A ALA* 3.3 5.9 + - - +
217A PHE* 3.0 25.6 + - - +
222A THR* 4.8 0.5 - - - +
225A THR* 4.1 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 2.8 48.8 + - + +
211A SER* 3.8 6.3 + - - +
213A ALA* 1.3 82.1 - - - +
215A ALA* 1.3 62.9 + - - +
217A PHE* 3.9 1.9 - - - +
218A ASN* 3.1 41.0 + - - +
225A THR* 5.6 1.8 - - - -
227A ASN* 5.5 6.3 - - - +
231A ALA* 4.8 9.3 - - + +
234A ASN* 2.9 34.7 + - - +
235A ILE* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER 2.8 20.5 + - - +
212A ILE* 4.0 4.3 - - - +
214A GLU* 1.3 68.3 - - - +
216A ALA* 1.3 62.1 + - - +
218A ASN* 4.6 4.3 - - - -
219A LYS* 2.8 57.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 3.1 36.6 - - + -
212A ILE 2.9 15.5 + - - +
213A ALA 3.7 4.0 - - - +
214A GLU 3.2 0.2 - - - -
215A ALA* 1.3 80.9 - - - +
217A PHE* 1.4 62.8 + - - +
219A LYS* 3.4 2.5 + - - +
221A GLU* 3.0 43.2 + - + +
222A THR* 3.6 10.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 3.6 37.5 - - + -
117A TYR 3.7 14.4 - - - -
118A ASN* 3.7 6.6 + - + -
213A ALA 3.0 15.2 + - - +
214A GLU* 4.0 2.7 - - - +
216A ALA* 1.4 77.2 - - - +
218A ASN* 1.3 76.2 + - - +
220A GLY* 3.3 11.4 + - - -
222A THR* 3.6 25.5 - - + +
223A ALA 3.6 21.5 - - - -
224A MET 3.9 9.0 - - - -
225A THR* 3.7 23.8 - - + -
235A ILE* 4.0 13.7 - - + -
240A VAL* 3.6 34.3 - - + +
242A TYR* 4.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLU* 3.1 28.8 + - - +
215A ALA* 4.1 4.5 - - - +
217A PHE* 1.3 94.6 - - - +
219A LYS* 1.3 62.1 - - + +
234A ASN* 3.5 36.4 - - - +
235A ILE* 3.5 22.3 + - - +
238A SER* 3.4 29.4 + - - +
240A VAL* 3.6 7.2 - - - +
----------------------------------------------------------
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