Contacts of the helix formed by residues 217 - 223 (chain A) in PDB entry 6YBO
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 GLU 217 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 2.9 9.3 - - - +
182A PRO 5.2 1.2 + - - -
215A ASN 3.7 0.6 + - - -
216A PRO* 1.3 73.0 - - - +
218A VAL* 1.3 70.7 + - - +
219A GLY 3.9 2.7 - - - +
220A HIS* 2.8 41.2 + - + +
221A GLU* 3.4 11.5 + - - +
228A PHE* 3.4 8.0 - - - -
245A ASP* 3.3 18.1 - - + +
247A ASN* 2.8 28.3 + - - +
255A ASP* 3.5 0.9 - - - +
257A ASP* 3.0 0.2 - - - +
287A ASP* 2.9 7.4 - - - +
401A MG 2.1 33.8 - - - -
402A MG 2.0 29.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 1.3 73.0 - - - +
219A GLY* 1.3 65.1 + - - +
220A HIS 3.3 0.2 + - - -
221A GLU 3.5 0.7 + - - -
222A GLN* 3.3 47.3 + - - +
228A PHE* 3.5 37.5 - - + -
245A ASP 3.1 14.0 + - - +
246A LEU* 4.0 4.3 - - + -
247A ASN* 3.4 33.7 - - - +
248A GLY* 4.8 2.0 - - - -
260A PHE* 4.7 3.6 - - + -
267A ALA* 6.2 0.2 - - + -
268A ALA* 6.5 0.4 - - - -
271A LEU* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 3.3 3.9 - - - +
218A VAL* 1.3 76.3 - - - +
220A HIS* 1.3 61.2 + - - +
222A GLN* 3.3 2.6 + - - +
223A MET* 3.0 33.3 + - - +
247A ASN* 3.0 19.4 + - - -
249A GLN* 3.5 30.1 - - - +
255A ASP* 4.7 1.6 - - - -
257A ASP 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 4.4 6.5 - + - -
181A GLU* 3.4 15.4 + - - -
182A PRO 3.0 27.1 + - - +
183A LYS* 3.5 34.8 - - + +
184A PRO* 3.3 21.9 - - - +
217A GLU* 2.8 43.1 + - + +
219A GLY* 1.3 74.1 - - - +
221A GLU* 1.3 69.0 + - - +
223A MET* 3.1 15.7 + - - +
224A ALA* 3.8 0.5 + - - +
255A ASP* 3.2 17.6 + - - -
287A ASP* 5.3 0.2 - - - -
401A MG 4.2 0.4 - - - -
402A MG 2.4 23.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
182A PRO* 4.0 11.6 - - - +
194A PRO 4.6 1.5 - - - +
195A THR* 3.5 20.2 - - - -
196A VAL* 3.2 48.2 + - + +
216A PRO* 5.1 1.4 - - + +
217A GLU 3.4 5.0 + - - +
220A HIS* 1.3 79.2 - - - +
222A GLN* 1.3 58.1 + - - +
224A ALA* 3.1 17.8 + - - +
226A LEU* 3.2 39.1 + - + +
228A PHE* 3.5 43.3 - - + -
231A GLY* 5.8 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 3.3 32.2 + - - +
219A GLY 3.3 9.1 + - - +
220A HIS 3.2 0.8 - - - -
221A GLU* 1.3 73.7 - - - +
223A MET* 1.3 56.0 + - - +
224A ALA 3.1 4.9 - - - -
225A GLY* 2.9 20.4 + - - +
226A LEU 4.1 14.8 - - - +
228A PHE* 4.2 12.9 - - + +
249A GLN* 3.5 37.1 + - + +
251A GLY* 3.8 12.2 - - - +
252A ILE* 3.7 9.0 - - - +
264A ASP* 4.1 14.9 + - - +
267A ALA* 3.9 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 4.0 13.7 - - - -
184A PRO* 3.8 12.5 - - + +
185A ASN* 3.5 47.5 + - - +
186A GLU* 4.2 3.4 - - + +
219A GLY 3.0 19.4 + - - +
220A HIS* 3.1 16.1 + - - +
222A GLN* 1.3 75.9 - - - +
224A ALA* 1.3 56.2 + - - +
225A GLY 3.4 0.4 - - - -
249A GLN* 3.9 10.3 - - - +
251A GLY 4.4 4.5 - - - -
252A ILE* 3.5 22.5 - - - +
253A LYS 3.6 25.4 - - - +
254A TYR* 4.7 0.9 - - - -
255A ASP* 3.8 34.1 - - + +
----------------------------------------------------------
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