Contacts of the helix formed by residues 322 - 333 (chain B) in PDB entry 6R7H
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 ASP 322 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA 3.7 13.0 + - - +
320B ASN* 4.4 19.5 - - + +
321B ASN* 1.3 77.8 - - - +
323B ILE* 1.3 63.3 + - - +
324B THR* 3.3 17.0 + - - -
325B GLU* 3.1 30.9 + - + +
326B PHE* 3.4 17.3 + - - +
354B ILE* 3.5 6.9 - - - +
358B VAL* 5.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP* 1.3 70.3 + - - +
324B THR* 1.3 68.5 + - - +
325B GLU 3.3 0.2 - - - -
326B PHE* 3.8 7.5 - - - +
327B GLU* 3.4 32.9 + - - +
351B LEU* 4.2 15.5 - - + +
354B ILE* 3.7 24.9 - - + -
355B ARG* 3.7 32.3 - - + +
358B VAL* 5.7 1.9 - - + +
378B LEU* 3.4 52.0 - - + +
380B ILE* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP* 3.3 16.4 + - - -
323B ILE* 1.3 85.6 - - - +
325B GLU* 1.3 58.8 + - - +
327B GLU* 4.1 5.9 + - - +
328B LYS* 3.8 21.2 + - - +
377B GLU 5.6 1.2 + - - -
378B LEU* 4.6 8.0 + - - -
379B ASN* 4.8 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASN* 5.2 5.7 + - - +
316B SER* 4.6 6.8 - - - +
317B ALA* 4.0 19.5 + - + +
320B ASN* 3.8 21.8 + - - -
322B ASP* 3.1 22.8 + - + +
324B THR* 1.3 75.3 - - - +
326B PHE* 1.3 63.8 + - - +
327B GLU 3.4 0.7 - - - -
328B LYS* 3.5 29.2 + - + +
329B ILE* 3.4 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B MET* 4.9 0.2 - - - -
314B LEU* 3.6 37.9 - - + +
317B ALA* 3.8 19.7 - - + +
318B TYR* 4.2 10.5 - + + -
322B ASP 3.4 14.6 + - - +
323B ILE* 3.5 4.9 + - - +
324B THR 3.5 0.4 - - - -
325B GLU* 1.3 80.1 - - - +
327B GLU* 1.3 61.1 + - - +
328B LYS 3.5 0.3 + - - -
329B ILE* 3.5 12.6 + - - +
330B LEU* 3.8 18.5 + - + +
347B ILE* 4.1 23.8 - - + -
350B LEU* 4.0 31.9 - - + -
351B LEU* 3.7 28.5 - - + -
354B ILE* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ILE* 3.4 20.0 + - - +
324B THR* 4.6 4.9 - - - +
325B GLU 3.4 0.2 - - - -
326B PHE* 1.3 75.2 - - - +
328B LYS* 1.3 64.2 + - - +
329B ILE 3.3 0.2 - - - -
330B LEU* 3.5 15.6 + - + +
331B LYS* 3.3 31.3 + - + +
351B LEU* 4.3 28.6 - - + +
355B ARG* 5.4 4.1 + - - -
379B ASN 5.7 0.7 - - - +
380B ILE* 5.4 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B THR* 3.8 16.0 + - - +
325B GLU* 3.5 26.6 + - + +
326B PHE 3.3 0.6 - - - -
327B GLU* 1.3 77.3 - - - +
329B ILE* 1.3 65.9 + - + +
331B LYS* 3.4 5.9 + - + +
332B THR* 3.0 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ALA 4.2 15.7 - - - +
313B ASN* 3.7 39.7 - - + +
314B LEU* 4.3 21.5 - - + +
317B ALA* 4.7 4.7 - - + -
325B GLU* 3.4 23.6 - - + +
326B PHE 3.9 6.7 - - - +
327B GLU 3.3 0.6 - - - -
328B LYS* 1.3 86.3 - - + +
330B LEU* 1.3 58.6 + - + +
332B THR* 4.6 2.9 - - - +
333B ASN* 2.9 49.7 + - + +
337B ILE* 6.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 4.8 7.9 - - + -
326B PHE* 3.8 22.4 - - + +
327B GLU* 3.5 15.4 + - + +
328B LYS 3.3 0.6 - - - -
329B ILE* 1.3 78.3 - - + +
331B LYS* 1.3 67.5 + - + +
333B ASN 3.2 17.6 - - - +
334B HIS* 3.8 16.5 - - - -
337B ILE* 3.8 34.5 - - + -
338B MET* 4.0 20.6 - - + +
347B ILE* 4.0 31.2 - - + -
351B LEU* 6.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLU* 3.3 22.9 + - + +
328B LYS* 3.9 7.4 - - + +
329B ILE 3.2 0.6 - - - -
330B LEU* 1.3 83.0 - - - +
332B THR* 1.3 64.1 + - - +
334B HIS* 4.6 12.3 - - + +
338B MET* 6.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS* 3.0 27.8 + - - +
329B ILE* 4.1 4.3 - - - -
331B LYS* 1.3 81.0 - - - +
333B ASN* 1.3 73.6 + - - +
334B HIS* 3.6 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PRO 4.4 6.2 - - - +
310B ALA* 3.6 24.7 - - + +
313B ASN* 5.3 3.2 + - - +
329B ILE* 2.9 41.6 + - + +
330B LEU 3.2 11.1 - - - +
332B THR* 1.3 84.2 - - - +
334B HIS* 1.3 59.0 + - - +
336B ASN* 3.4 27.3 + - - +
337B ILE* 3.4 18.6 - - + +
----------------------------------------------------------
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