Contacts of the strand formed by residues 236 - 242 (chain N) in PDB entry 3HOU
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 HIS 236 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225N VAL* 5.7 2.0 - - + -
226N PHE 3.5 10.8 - - - +
227N LYS* 3.7 36.3 + - + +
228N LYS* 4.5 0.9 - - - +
234N ILE* 3.2 7.1 - - - +
235N SER* 1.3 117.5 + - - +
237N VAL* 1.3 75.2 + - - +
257N LYS 3.6 13.7 - - - -
258N LEU* 3.6 5.5 + - + +
261N ARG* 5.3 3.2 + - - -
267N ARG* 6.0 0.2 + - - -
385N LEU* 3.9 17.9 + - + +
388N CYS* 3.3 21.2 - - + +
389N ALA* 3.3 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224N GLN 3.6 1.2 - - - +
225N VAL* 2.9 27.7 - - - +
226N PHE* 3.0 17.1 + - + +
228N LYS* 4.5 12.6 - - - -
234N ILE* 3.5 17.9 - - + -
236N HIS* 1.3 87.1 - - - +
238N ALA* 1.3 76.1 + - - +
239N GLU* 3.9 11.2 + - + +
255N GLN* 3.6 31.2 - - + +
256N VAL 3.6 9.4 - - - +
257N LYS* 3.7 19.1 - - + -
385N LEU* 4.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223N VAL* 6.2 1.8 - - + -
224N GLN 3.4 6.3 - - - +
225N VAL* 3.7 16.4 - - + -
237N VAL* 1.3 76.6 - - - +
239N GLU* 1.3 61.1 + - - +
254N LEU 3.4 5.9 - - - +
255N GLN* 3.6 1.2 - - - -
256N VAL* 3.0 45.5 + - + +
381N MET* 4.5 21.3 - - + +
384N ARG* 5.9 0.2 - - + -
385N LEU* 4.1 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222N ILE 3.1 5.2 - - - +
223N VAL* 3.3 5.0 - - - +
224N GLN* 2.7 39.9 + - + +
226N PHE* 3.9 28.3 - - + +
228N LYS* 5.8 2.1 + - - -
237N VAL* 3.9 18.5 - - + +
238N ALA* 1.3 73.6 - - - +
240N ILE* 1.3 62.1 + - - +
241N ARG* 5.3 11.5 - - + +
253N THR* 6.4 2.2 - - - -
254N LEU 3.5 2.2 - - - +
255N GLN* 4.0 26.1 + - + -
381N MET* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221N ASN* 3.2 12.3 - - + -
222N ILE* 2.8 48.5 - - - +
223N VAL* 3.8 8.7 - - + +
239N GLU* 1.3 76.2 - - - +
241N ARG* 1.3 66.9 + - - +
242N SER* 3.6 6.2 + - - +
253N THR* 3.5 2.6 - - - -
254N LEU* 2.9 50.9 + - + +
361N LEU* 5.0 2.0 - - + -
363N HIS* 4.7 10.8 - - + +
377N PHE* 4.5 11.9 - - + -
381N MET* 3.4 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217N ARG* 5.4 2.4 - - - +
218N SER* 3.2 29.0 + - - +
219N ALA 3.0 24.7 + - - -
220N GLY* 3.5 8.9 - - - -
221N ASN* 2.4 35.8 + - - +
222N ILE 3.9 4.0 + - - +
239N GLU* 5.3 10.5 - - + +
240N ILE* 1.3 75.9 - - - +
242N SER* 1.3 58.7 + - - +
243N ALA* 3.7 1.5 + - - +
251N ILE* 5.3 16.6 - - + +
253N THR* 3.0 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221N ASN* 2.9 10.5 - - - +
240N ILE* 3.6 9.2 + - - -
241N ARG* 1.3 71.3 - - - +
243N ALA* 1.3 60.0 + - - +
250N PHE 3.2 9.7 - - - +
251N ILE* 3.5 6.6 - - - -
252N SER* 2.6 36.0 + - - +
253N THR* 4.7 0.9 - - - -
254N LEU* 5.2 3.0 + - - +
361N LEU* 4.5 4.0 + - - -
362N PRO* 3.4 35.3 - - - +
363N HIS* 3.9 17.5 - - - -
----------------------------------------------------------
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