Contacts of the helix formed by residues 219 - 230 (chain A) in PDB entry 3A4T
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 ASN 219 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 4.3 0.2 - - - -
211A THR* 3.5 6.1 - - - +
213A SER 2.9 20.6 + - - +
214A MET* 2.9 22.5 - - - -
215A GLU 3.1 12.5 + - - +
216A VAL 3.0 3.2 + - - +
217A GLU 3.4 0.6 - - - -
218A GLU* 1.3 92.8 + - - +
220A GLU* 1.3 79.8 + - - +
221A GLU 3.2 1.3 + - - -
222A VAL* 3.2 13.9 + - - +
223A ILE* 3.2 9.0 + - - +
258A ARG* 2.7 20.9 + - - +
267A PHE* 3.2 40.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 3.4 12.7 + - + +
219A ASN* 1.3 79.7 - - - +
221A GLU* 1.3 56.0 + - - +
223A ILE* 3.7 2.2 - - - -
224A LYS* 2.8 41.1 + - - +
251A GLY* 3.2 4.0 - - - -
252A TYR* 2.7 29.3 + - + +
253A ILE* 3.4 39.8 - - + +
256A THR* 4.1 2.5 - - - +
258A ARG* 2.5 49.0 + - - -
267A PHE* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LYS* 4.1 12.8 + - - -
216A VAL* 3.1 27.4 + - + +
217A GLU* 3.4 42.5 - - - +
220A GLU* 1.3 77.4 - - - +
222A VAL* 1.3 58.5 + - - +
224A LYS* 2.4 43.6 + - - +
225A TYR* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 4.0 13.0 - - - +
190A GLN* 3.4 49.8 - - - +
191A LYS* 4.1 11.2 - - + +
194A ILE* 4.1 14.5 - - + +
209A TYR* 3.9 19.3 - - + +
217A GLU 3.5 15.7 - - - +
218A GLU 3.8 6.5 - - - -
219A ASN 3.2 6.3 + - - +
221A GLU* 1.3 73.4 - - - +
223A ILE* 1.3 66.4 + - - +
225A TYR* 3.6 3.5 - - - +
226A ILE* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 3.5 27.6 - - + -
209A TYR* 4.0 13.2 - - + -
219A ASN 3.2 13.8 + - - +
220A GLU* 3.8 7.2 - - - +
222A VAL* 1.3 76.6 - - - +
224A LYS* 1.3 62.0 + - - +
226A ILE* 3.1 7.3 + - - +
227A LEU* 3.0 33.1 + - + +
235A LEU* 3.9 26.2 - - + -
253A ILE* 4.1 13.2 - - + -
256A THR* 4.6 5.4 - - + -
267A PHE* 3.8 17.7 - - + -
269A ALA* 3.8 20.0 - - + -
271A LEU* 4.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 5.2 4.6 - - - +
220A GLU* 2.8 29.5 + - - +
221A GLU* 2.4 43.7 + - - +
223A ILE* 1.3 72.3 - - - +
225A TYR* 1.3 62.1 + - - +
227A LEU* 3.9 6.9 - - - +
228A GLN* 3.1 51.3 + - + +
253A ILE* 4.0 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LYS* 3.4 65.0 + - + +
192A GLU* 5.6 0.7 - - - -
194A ILE* 4.5 2.2 - - + -
195A ASP* 4.8 2.2 - - + +
221A GLU 2.9 19.4 + - - +
222A VAL 3.6 7.0 - - - +
224A LYS* 1.3 79.2 - - - +
226A ILE* 1.3 68.3 + - + +
228A GLN* 3.8 10.0 - - - +
229A LYS* 2.9 69.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 4.0 25.1 - - + -
195A ASP* 3.5 35.2 - - + +
198A ILE* 3.1 22.4 - - + -
222A VAL 3.2 11.5 + - - +
223A ILE* 3.1 20.2 + - - +
225A TYR* 1.3 81.3 - - + +
227A LEU* 1.3 58.3 + - + +
229A LYS* 4.5 4.5 - - + -
230A ARG* 3.1 59.2 + - + +
233A VAL* 4.2 3.4 - - + +
271A LEU* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 3.0 37.5 + - + +
224A LYS* 3.9 7.0 - - - +
226A ILE* 1.3 78.2 - - + +
228A GLN* 1.3 56.9 + - + +
230A ARG 2.9 21.3 - - - +
233A VAL* 3.8 27.7 - - + +
234A GLU* 4.9 0.2 - - - -
235A LEU* 4.1 35.7 - - + +
253A ILE* 5.2 8.5 - - + -
271A LEU* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LYS* 3.1 41.1 + - + +
225A TYR* 4.1 7.8 + - - +
227A LEU* 1.3 73.6 - - + +
229A LYS* 1.3 67.0 + - - +
230A ARG 3.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ASP* 3.5 34.9 + - + +
225A TYR* 2.9 57.3 + - + +
226A ILE* 3.3 5.3 + - + +
228A GLN* 1.3 81.1 - - - +
230A ARG* 1.3 64.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ASP* 2.8 35.1 + - - +
198A ILE* 3.2 22.9 - - - +
199A ASP* 2.7 31.5 + - - +
226A ILE* 3.1 40.1 + - + +
227A LEU 2.9 19.6 - - - +
228A GLN 4.7 0.6 - - - +
229A LYS* 1.3 86.8 - - + +
231A ASN* 1.3 58.9 + - - +
232A ASP* 2.7 45.1 + - - +
233A VAL* 4.2 10.4 - - + +
273A LYS* 4.0 7.1 - - - +
----------------------------------------------------------
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