Contacts of the strand formed by residues 234 - 239 (chain G) in PDB entry 4A63
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 GLN 234 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G MET* 3.6 6.5 - - - +
179G PRO* 3.5 22.0 - - - +
190G VAL* 4.3 5.4 - - + +
191G VAL 4.1 6.8 - - - +
192G LYS* 3.4 30.9 - - - +
212G SER* 2.9 47.0 + - - +
213G HIS* 3.4 26.9 - - + +
214G LEU 4.7 0.8 + - - +
226G VAL 3.3 4.5 - - - -
227G ASP* 3.0 27.7 + - - +
232G GLY 3.6 8.7 + - - +
233G ARG* 1.4 73.7 - - - +
235G SER* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G ARG* 2.8 41.7 + - - -
177G ALA 3.5 16.2 - - - -
178G MET* 3.8 16.7 - - - +
179G PRO* 5.1 1.1 - - - -
213G HIS* 3.4 12.1 + - - -
215G ILE* 5.5 0.9 - - - -
225G TYR* 3.7 0.2 - - - -
226G VAL* 3.0 34.0 + - - +
233G ARG 5.0 0.7 + - - -
234G GLN* 1.3 76.1 - - - +
236G VAL* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175G ILE 3.9 1.4 - - - +
176G ARG* 3.6 1.4 - - - -
177G ALA* 3.1 37.7 + - + +
215G ILE* 3.6 35.2 - - + +
216G ARG 4.6 0.2 - - - +
217G VAL* 3.8 30.3 - - + +
223G SER* 4.2 10.8 - - - -
224G GLN 3.2 11.2 - - - +
225G TYR* 3.7 32.3 - - + -
235G SER* 1.3 76.5 - - - +
237G VAL* 1.3 63.5 + - - +
254G TYR* 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G ALA* 3.4 29.2 - - + -
175G ILE 3.4 10.5 - - - +
176G ARG* 3.4 44.0 - - + +
222G LEU 4.0 1.0 - - - +
223G SER* 3.3 4.0 - - - -
224G GLN* 2.8 46.6 + - + +
226G VAL* 3.8 15.9 - - + -
236G VAL* 1.3 77.5 - - - +
238G VAL* 1.3 65.2 + - - +
278G GLU* 5.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G ALA* 3.5 4.1 - - - -
175G ILE* 2.9 37.6 + - + +
217G VAL* 3.8 22.2 - - + -
220G ASN* 3.5 26.5 - - - +
222G LEU 4.6 0.2 - - - -
223G SER* 3.7 20.9 - - - -
237G VAL* 1.3 79.4 - - - +
239G PRO* 1.3 72.4 - - - +
252G ILE* 3.9 34.3 - - + -
254G TYR* 5.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 239 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G THR 3.7 7.6 - - - +
174G ALA* 4.2 4.5 - - + -
175G ILE* 5.1 1.1 - - - +
220G ASN* 4.6 6.5 + - - +
222G LEU* 3.7 48.5 - - + +
238G VAL* 1.3 96.2 - - + +
240G TYR* 1.3 68.6 + - - +
241G GLU* 3.5 6.3 + - + +
222I LEU* 3.9 20.2 - - + -
----------------------------------------------------------
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