Contacts of the strand formed by residues 235 - 242 (chain E) in PDB entry 3H9S
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 235 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PRO* 3.8 24.4 - - - +
214E VAL 3.8 0.2 - - - +
215E GLN* 3.8 7.2 - - - +
216E PHE* 2.9 37.5 + - + +
231E LYS 4.6 1.7 - - - +
232E PRO* 4.3 1.2 - - - +
233E VAL* 3.3 33.0 + - + +
234E THR* 1.3 76.1 - - - +
236E ILE* 1.3 63.6 + - - +
237E VAL* 3.6 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E GLN* 3.7 45.5 - - + +
214E VAL 3.3 8.1 - - - +
215E GLN* 3.6 31.4 - - + +
235E GLN* 1.3 79.3 + - - +
237E VAL* 1.3 67.0 + - - +
238E SER* 4.1 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PRO* 4.9 0.4 - - + -
125E PRO* 3.6 38.6 - - + +
126E GLU* 4.9 0.7 - - - -
127E VAL* 3.5 31.7 - - + +
214E VAL 2.8 37.9 + - - +
235E GLN* 3.6 30.1 - - + +
236E ILE* 1.3 77.3 - - - +
238E SER* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 238 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D GOL 2.9 45.2 + - - -
127E VAL* 4.2 6.3 - - - +
211E ARG* 3.2 24.6 + - - -
212E CYS 3.3 5.6 + - - -
213E GLN* 3.6 15.8 - - - +
236E ILE* 4.1 4.9 + - - +
237E VAL* 1.3 77.7 - - - +
239E ALA* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LYS* 4.1 8.5 - - - +
207D GOL 4.3 5.4 - - - -
127E VAL* 3.4 35.9 - - + +
128E ALA* 3.9 4.7 - - - -
129E VAL* 3.6 18.7 - - + +
211E ARG* 3.4 5.2 - - - +
212E CYS 2.7 40.3 + - - +
238E SER* 1.3 74.6 - - - +
240E GLU* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D SER* 3.1 18.4 + - - -
132D LYS* 3.9 13.8 + - - +
207D GOL 3.9 29.3 - - - -
129E VAL* 4.0 7.9 - - - +
209E HIS* 2.6 34.3 + - - +
210E PHE 3.3 12.8 - - - +
211E ARG* 4.3 5.8 - - + -
239E ALA* 1.3 78.7 - - - +
241E ALA* 1.3 63.9 + - - +
242E TRP* 3.6 18.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D SER* 3.7 21.8 - - - +
129E VAL* 3.9 17.9 - - + +
131E GLU* 4.2 13.0 - - + +
145E LEU* 4.4 10.1 - - + -
203E TRP* 4.8 2.0 - - + -
209E HIS* 3.6 4.0 - - - -
210E PHE* 3.0 34.5 + - - +
240E GLU* 1.3 77.1 - - - +
242E TRP* 1.3 67.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E GLU* 4.1 8.5 + - - +
203E TRP* 3.6 15.9 - - - -
206E PRO 3.6 18.8 - - - +
207E ARG* 3.5 22.7 - - - -
208E ASN 3.6 13.7 - - - -
209E HIS* 3.4 38.8 - + + -
240E GLU* 3.6 20.1 + - + -
241E ALA* 1.3 80.0 - - - +
243E GLY* 1.3 69.1 + - - +
244E ARG* 3.4 3.5 + - - +
----------------------------------------------------------
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