Contacts of the helix formed by residues 223 - 230 (chain G) in PDB entry 6BAA
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 223 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G TRP* 3.6 5.5 - - + -
67G HIS* 4.5 3.8 - - - -
75G TRP* 3.6 27.9 - - + +
125G HIS* 3.1 34.4 + - + +
128G GLU* 5.7 1.3 - - - +
222G VAL* 1.3 87.6 - - - +
224G LEU* 1.3 60.9 + - - +
225G LEU* 3.8 15.8 - - - +
226G SER* 2.5 45.7 + - - -
227G LYS* 3.1 10.7 + - - +
231G TRP* 5.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G HIS* 5.4 1.0 - - - -
72G ASN* 4.0 33.2 - - + +
75G TRP* 3.7 35.1 - - + +
76G ILE* 4.2 14.8 - - + -
79G PHE* 3.7 26.0 - - + -
222G VAL 3.8 1.0 + - - -
223G ASN* 1.3 70.0 - - - +
225G LEU* 1.3 61.1 + - - +
227G LYS* 3.4 19.7 - - + +
228G GLY* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G TRP* 3.6 35.0 - - + -
79G PHE* 3.6 31.4 - - + -
121G VAL* 6.5 0.2 - - + -
223G ASN* 3.1 17.0 - - - +
224G LEU* 1.3 73.6 - - - +
226G SER* 1.3 55.9 + - - +
228G GLY* 3.3 2.1 + - - -
229G THR* 2.6 51.0 + - + +
231G TRP* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G GLN* 3.9 5.2 + - - -
222G VAL* 3.5 25.8 - - - +
223G ASN* 2.5 27.8 + - - -
225G LEU* 1.3 77.7 - - - +
227G LYS* 1.3 63.3 + - - +
228G GLY 2.9 0.7 + - - -
229G THR* 3.5 8.1 - - - -
230G TYR* 2.5 27.2 + - - -
231G TRP* 3.3 27.3 - - - +
232G TRP* 3.9 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 227 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G HIS* 5.4 0.9 - - - -
71G HIS* 5.9 1.3 - - + -
72G ASN* 5.4 10.5 - - - +
219G GLN* 2.5 56.5 + - - +
220G PRO* 3.1 24.3 + - - +
222G VAL* 3.5 23.1 - - + +
223G ASN 3.1 10.5 + - - +
224G LEU* 3.1 25.0 + - + +
226G SER* 1.3 76.7 - - - +
228G GLY* 1.3 55.0 + - - +
230G TYR* 4.8 4.9 + - - -
375G ALA* 5.5 8.3 - - - +
378G TYR* 4.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G LEU* 2.9 13.6 + - - +
225G LEU 3.8 1.6 - - - -
226G SER 3.5 1.3 - - - -
227G LYS* 1.3 80.2 - - - +
229G THR* 1.3 58.4 + - - +
230G TYR* 3.7 17.9 + - - -
371G THR* 4.1 27.4 + - - +
374G GLN* 4.9 3.3 - - - +
375G ALA* 6.2 2.0 - - - -
1250G VAL* 3.7 11.5 - - - +
1254G TYR* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G LEU* 2.6 43.0 + - + +
226G SER* 3.5 0.2 - - - -
228G GLY* 1.3 72.4 - - - +
230G TYR* 1.3 72.5 + - - +
231G TRP* 3.3 28.4 + - + +
234G ASN* 5.0 0.9 + - - -
1247G TRP* 3.8 11.6 + - - -
1250G VAL* 4.1 11.9 - - - +
1251G CYS* 5.1 2.6 - - - -
1254G TYR* 3.2 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 230 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G GLN* 3.1 39.7 - - - -
226G SER 2.5 19.9 + - - -
227G LYS 4.8 2.9 + - - -
228G GLY 3.7 8.5 - - - -
229G THR* 1.3 75.7 - - - +
231G TRP* 1.3 65.3 + - - +
232G TRP* 3.1 13.7 - + + +
233G MET* 2.9 31.0 + - + +
234G ASN* 3.7 4.7 + - - -
374G GLN* 3.9 10.9 + - - +
375G ALA* 5.2 0.5 - - - -
378G TYR* 3.3 33.3 - + - +
1243G ALA* 4.7 7.9 - - + +
1246G ARG* 3.3 29.9 - - + +
1247G TRP* 3.6 26.8 - - + -
1250G VAL* 3.5 20.9 - - + -
----------------------------------------------------------
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