Contacts of the strand formed by residues 212 - 219 (chain B) in PDB entry 1B70
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 212 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA 4.1 1.5 - - - +
211B PRO* 1.3 81.0 - - + +
213B PHE* 1.3 68.8 + - - +
214B THR* 4.0 6.1 - - + -
336B ALA* 3.1 4.7 - - - +
337B CYS* 2.8 46.4 + - + +
366B PRO 3.2 24.9 - - - +
367B LEU* 4.7 5.3 - - - +
369B GLN* 3.3 25.4 + - + +
370B VAL* 4.9 3.6 - - - +
394B GLU* 3.1 36.9 + - + -
395B ALA 3.4 1.5 + - - -
396B GLY 3.0 20.0 + - - -
398B PRO* 3.6 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 3.6 34.1 - - + -
204B VAL* 4.3 5.6 - - + -
210B ALA* 4.5 8.3 - - + +
212B HIS* 1.3 76.9 + - - +
214B THR* 1.3 68.1 + - - +
215B LEU* 3.7 28.3 - - + -
272B ILE* 4.4 4.9 - - + -
274B VAL* 3.5 32.5 - - + -
300B ILE* 4.3 19.1 - - + -
334B GLU* 4.4 11.2 - - + -
335B VAL 4.2 0.2 - - - -
336B ALA* 3.5 21.8 - - + -
338B PHE* 4.3 14.1 - + - -
393B LEU 3.5 1.0 - - - +
394B GLU* 3.5 2.8 - - - -
395B ALA* 2.9 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B HIS* 4.0 6.3 - - + -
213B PHE* 1.3 84.3 - - - +
215B LEU* 1.3 69.8 + - - +
333B LEU 3.3 1.6 - - - +
334B GLU* 3.9 0.2 - - - -
335B VAL* 2.6 47.5 + - - +
369B GLN* 3.8 19.3 - - + -
370B VAL* 4.5 6.5 - - + -
373B GLN* 2.9 24.8 + - - +
392B LEU* 4.6 7.2 - - + -
393B LEU 3.1 6.5 - - - -
394B GLU* 3.8 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 4.3 3.3 - - - +
200B PHE* 3.7 28.3 - - + -
202B LEU* 4.1 7.2 - - + -
213B PHE* 3.7 22.4 - - + -
214B THR* 1.3 82.4 - - - +
216B GLY* 1.3 60.4 + - - +
263B PHE* 6.2 2.2 - - + -
272B ILE* 3.8 33.2 - - + -
332B ALA* 4.8 4.3 - - + -
333B LEU 3.3 19.7 - - - +
334B GLU* 4.1 6.5 - - + -
373B GLN* 3.7 3.4 - - - -
392B LEU* 3.4 9.9 - - - +
393B LEU* 2.9 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 3.9 3.0 - - - -
215B LEU* 1.3 75.6 - - - +
217B TYR* 1.3 60.5 + - - +
218B ALA 4.2 0.2 - - - -
331B ILE* 3.7 0.6 - - - +
332B ALA* 3.2 11.3 - - - +
333B LEU* 2.9 36.3 + - - -
373B GLN* 3.5 18.3 - - - +
377B LEU* 4.8 4.9 - - - -
391B ALA 5.1 0.2 - - - -
392B LEU* 3.9 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 3.7 12.1 - - + +
198B LEU* 3.6 41.1 - - + +
199B PRO* 3.5 25.2 - - + +
200B PHE* 3.7 14.6 - + + -
216B GLY* 1.3 74.4 - - - +
218B ALA* 1.3 72.1 + - - +
219B PHE* 3.4 37.5 - + + +
265B LEU* 3.5 22.8 - - + +
330B ALA* 4.3 2.5 - - + +
331B ILE 3.6 8.5 - - - -
377B LEU* 4.9 3.2 - - - +
387B ARG 4.0 0.2 - - - +
388B VAL* 3.5 9.2 - - - +
389B ALA* 3.1 32.7 + - + +
391B ALA 4.9 3.4 + - - -
392B LEU* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLY 4.2 0.6 - - - -
217B TYR* 1.3 77.3 - - - +
219B PHE* 1.3 61.6 + - - +
221B LEU* 4.1 5.3 - - + +
330B ALA* 3.2 3.1 - - - +
331B ILE* 2.9 48.6 + - + +
377B LEU* 4.2 17.7 - - + -
380B LEU* 4.5 3.8 - - + -
386B ALA* 4.0 19.5 - - + -
387B ARG 3.3 9.2 - - - +
388B VAL* 4.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLU* 4.1 1.8 - - - -
196B LEU* 3.9 28.9 - - + -
217B TYR* 3.4 40.4 - + - +
218B ALA* 1.3 76.5 - - - +
220B GLY* 1.3 68.4 + - - +
221B LEU* 3.3 1.8 - - - -
329B GLU 3.1 8.5 - - - -
330B ALA* 3.6 15.0 - - + -
386B ALA* 3.8 1.6 - - - -
387B ARG* 2.7 91.5 + - + +
389B ALA 4.2 7.9 - - - -
----------------------------------------------------------
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