Contacts of the strand formed by residues 330 - 337 (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 ALA 330 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TYR* 4.3 2.7 - - + +
218B ALA 3.2 12.8 - - - +
219B PHE* 3.6 14.8 - - + -
221B LEU* 4.0 1.2 - - - +
264B ASP* 3.5 7.8 - - - +
265B LEU* 3.0 38.3 + - + +
328B THR* 3.7 0.8 - - - +
329B GLU* 1.3 86.5 - - + +
331B ILE* 1.3 69.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLY 3.7 0.4 - - - +
217B TYR* 3.6 9.2 - - - -
218B ALA* 2.9 44.7 + - + +
221B LEU* 3.5 20.4 - - + -
245B VAL* 5.4 3.6 - - + -
262B ALA* 3.8 19.3 - - + -
263B PHE 3.0 18.6 - - - +
265B LEU* 3.8 9.2 - - - +
324B VAL* 4.1 11.7 - - + -
328B THR* 3.8 15.5 - - + -
330B ALA* 1.3 79.9 - - - +
332B ALA* 1.3 76.9 + - - +
333B LEU* 4.7 6.5 - - + +
377B LEU* 6.0 0.4 - - + -
380B LEU* 4.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 3.9 24.7 - - + -
215B LEU* 4.8 10.5 - - + -
216B GLY 3.2 9.0 - - - +
261B HIS 3.8 1.0 - - - +
262B ALA* 3.6 0.3 - - - -
263B PHE* 2.9 37.6 + - + +
265B LEU* 4.2 12.1 - - + +
268B VAL* 4.9 6.3 - - + -
272B ILE* 5.2 5.2 - - + -
331B ILE* 1.3 79.7 - - - +
333B LEU* 1.3 60.6 + - - +
334B GLU 3.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR 3.3 4.5 - - - +
215B LEU* 3.3 3.8 - - - +
216B GLY* 2.9 23.4 + - - +
249B THR* 4.8 4.7 - - + -
260B MET* 4.1 20.6 - - + -
261B HIS 3.4 23.1 - - - +
262B ALA* 4.2 9.4 - - + +
331B ILE* 4.3 6.7 - - + +
332B ALA* 1.3 71.6 - - - +
334B GLU* 1.3 58.5 + - - +
335B VAL* 3.9 6.7 - - + -
373B GLN* 3.1 41.5 + - - +
376B ALA* 3.8 28.0 - - + -
377B LEU* 4.2 17.3 - - + -
380B LEU* 4.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE* 4.4 21.8 - - + -
214B THR 3.9 4.5 - - - -
215B LEU* 4.1 8.2 - - + +
259B PRO* 4.2 5.7 - - - +
260B MET* 3.1 34.8 - - - +
261B HIS* 2.8 36.0 + - - +
263B PHE* 4.0 23.4 - - + -
300B ILE* 4.4 12.5 - - + +
314B ALA* 5.2 0.3 - - - -
315B GLY* 4.5 7.3 + - - -
332B ALA 3.9 1.8 + - - -
333B LEU* 1.3 70.0 - - - +
335B VAL* 1.3 62.2 + - - +
336B ALA 4.7 3.5 + - - +
338B PHE* 4.0 21.7 - - + -
360B PHE* 4.7 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR* 2.6 40.4 + - - +
258B GLN* 3.8 23.6 - - + +
259B PRO 4.6 0.7 - - - -
260B MET* 3.6 22.9 - - + -
333B LEU* 3.9 10.1 - - + -
334B GLU* 1.3 81.6 - - - +
336B ALA* 1.3 61.8 + - - +
369B GLN* 3.5 36.6 - - - +
372B ALA* 4.1 2.9 - - + -
373B GLN* 3.4 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B HIS 3.1 15.3 - - - +
213B PHE* 3.5 30.1 - - + -
258B GLN* 3.0 19.8 + - - +
259B PRO 4.7 2.0 + - - -
334B GLU* 4.1 4.9 + - + +
335B VAL* 1.3 77.3 - - - +
337B CYS* 1.3 62.9 + - - +
338B PHE* 4.1 16.8 - - + -
360B PHE* 3.3 15.2 - - - -
369B GLN* 3.3 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA* 3.9 1.6 - - - -
211B PRO* 3.1 30.9 - - - +
212B HIS* 2.8 28.0 + - + +
336B ALA* 1.3 77.5 - - - +
338B PHE* 1.3 67.4 + - - +
340B PRO* 6.3 0.2 - - - -
360B PHE* 4.3 3.4 - - - -
364B VAL* 4.1 28.0 - - - -
366B PRO* 4.2 14.6 - - + -
369B GLN* 3.6 14.6 - - - +
----------------------------------------------------------
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