Contacts of the helix formed by residues 304 - 323 (chain B) in PDB entry 7CAL
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 SER 304 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B VAL* 3.2 18.6 + - - -
301B HIS* 4.2 8.4 + - - -
302B TRP 3.5 2.4 - - - -
303B THR* 1.3 78.6 - - - +
305B ARG* 1.3 67.0 + - - +
307B ARG* 3.9 18.6 - - - +
308B THR* 3.3 30.4 + - - +
346B LEU* 4.3 3.5 - - - +
311C ASP* 5.0 5.2 + - - -
314C ARG* 4.4 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TRP 4.7 4.4 + - - +
303B THR* 3.4 1.2 - - - +
304B SER* 1.3 86.0 - - - +
306B THR* 1.3 64.4 + - - +
308B THR* 3.9 2.3 + - - -
309B PHE* 3.4 22.3 + - - +
341B PHE* 3.5 37.4 + - + -
345B GLY* 4.0 25.9 - - - -
346B LEU* 4.0 23.0 - - + +
314C ARG* 4.8 21.5 - - - +
318C GLU* 3.9 28.9 + - - -
322C ARG* 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU* 4.3 29.3 + - + +
187A LYS* 4.2 26.9 - - + +
193A TYR* 4.4 13.8 - - + -
303B THR* 4.3 8.5 + - - -
305B ARG* 1.3 79.5 + - - +
307B ARG* 1.3 59.4 + - - +
309B PHE* 4.0 10.8 - - + +
310B ARG* 3.3 24.8 + - - +
341B PHE* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 4.3 15.7 - - + +
297A ASN* 2.9 37.4 + - - +
298A LEU* 6.2 0.2 - - - -
300A VAL* 5.0 13.8 - - - +
301A HIS* 3.6 47.5 + - + +
300B VAL* 4.3 17.0 + - - +
303B THR 3.3 17.2 + - - +
304B SER* 3.8 25.2 + - - +
305B ARG 3.3 0.6 - - - -
306B THR* 1.3 77.0 - - - +
308B THR* 1.3 72.5 + - - +
309B PHE 3.2 1.3 - - - -
310B ARG* 3.3 1.7 + - - -
311B ASP* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B SER* 3.3 17.7 + - - +
307B ARG* 1.3 89.5 - - - +
309B PHE* 1.3 64.5 + - - +
310B ARG 3.4 0.2 - - - -
311B ASP* 3.7 13.8 - - - +
312B SER* 3.4 20.6 + - - -
346B LEU* 3.3 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS* 4.0 22.9 - - + -
189A ILE* 4.2 11.9 - - + -
305B ARG 3.4 16.5 + - - +
306B THR* 4.0 9.4 - - + +
307B ARG 3.2 0.4 - - - -
308B THR* 1.3 81.2 + - - +
310B ARG* 1.3 81.6 + - + +
311B ASP 3.2 0.2 - - - -
312B SER* 3.2 7.3 + - - -
313B VAL* 3.2 47.4 + - + +
337B ILE* 4.0 15.7 - - + -
338B CYS* 4.2 12.6 - - + -
341B PHE* 3.8 54.1 - + + -
346B LEU* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU 4.2 1.4 + - - -
186A GLU* 2.4 41.2 + - - +
188A ASP 3.1 22.9 + - - +
189A ILE* 4.1 14.7 + - - +
191A PHE 2.4 28.5 + - - -
192A ASN* 4.0 8.7 + - - +
193A TYR* 4.1 31.4 - - + +
301A HIS* 4.5 8.6 + - + -
306B THR 3.3 18.8 + - - +
307B ARG 3.3 6.7 + - - +
309B PHE* 1.3 94.9 - - + +
311B ASP* 1.3 63.6 + - - +
313B VAL* 4.1 11.8 - - - +
314B ARG* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A HIS* 2.6 27.1 + - - -
304A SER* 5.0 5.2 + - - -
307B ARG* 3.1 16.2 + - - +
308B THR* 3.8 14.1 - - - +
309B PHE 3.2 0.4 - - - -
310B ARG* 1.3 78.7 - - - +
312B SER* 1.3 58.5 + - - +
314B ARG* 2.5 38.9 + - - +
315B ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A THR* 5.4 1.6 - - - +
308B THR 3.4 10.5 + - - -
309B PHE* 3.2 12.6 + - - -
311B ASP* 1.3 76.7 - - - +
313B VAL* 1.3 66.8 + - - +
315B ALA* 3.8 7.5 - - - +
316B ALA* 3.2 23.2 + - - +
337B ILE* 3.7 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 3.7 28.5 - - + +
309B PHE* 3.2 43.8 + - + +
310B ARG* 4.5 13.2 - - - +
311B ASP 3.4 0.2 - - - -
312B SER* 1.3 78.4 + - - +
314B ARG* 1.3 62.9 + - - +
316B ALA* 3.4 2.8 + - - +
317B SER* 3.1 26.0 + - - +
334B LEU* 4.1 20.2 - - + +
337B ILE* 3.9 16.4 - - + -
338B CYS* 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 3.9 20.0 - - - -
301A HIS* 3.8 29.2 + - - -
302A TRP 5.0 3.8 + - - -
304A SER* 4.4 9.3 + - - -
305A ARG* 4.8 20.2 - - - +
310B ARG 3.4 16.2 + - - +
311B ASP* 2.5 36.7 + - - +
312B SER 3.3 0.2 - - - -
313B VAL* 1.3 81.9 - - - +
315B ALA* 1.3 56.0 + - - +
317B SER* 3.3 5.5 + - - +
318B GLU* 3.0 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LYS* 4.6 7.9 - - + +
351A THR* 3.7 22.6 + - - +
311B ASP 2.9 17.2 + - - +
312B SER* 3.6 8.3 + - - +
313B VAL 3.3 0.4 - - - -
314B ARG* 1.3 76.9 - - - +
316B ALA* 1.3 57.7 + - - +
318B GLU* 3.9 12.7 + - - +
319B PHE* 3.4 22.2 + - - +
322B ARG* 5.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A THR* 4.2 18.1 - - + +
355A LEU* 6.4 0.2 - - + -
312B SER 3.2 17.2 + - - +
313B VAL 3.7 3.1 - - - +
314B ARG 3.2 0.6 - - - -
315B ALA* 1.3 76.3 - - - +
317B SER* 1.3 60.5 + - - +
319B PHE* 4.0 4.9 - - - -
320B ALA* 3.7 20.3 + - - +
330B GLN* 5.1 0.5 + - - +
333B MET* 4.0 21.0 - - + +
334B LEU* 4.7 7.7 - - + +
337B ILE* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B VAL* 3.1 18.5 + - - +
314B ARG* 3.3 6.5 + - - -
316B ALA* 1.3 76.7 - - - +
318B GLU* 1.3 63.0 + - - +
319B PHE 3.3 0.9 - - - -
320B ALA 4.0 2.3 - - - +
321B SER* 3.3 23.6 + - - -
330B GLN* 4.6 11.4 + - - +
334B LEU* 3.8 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG* 3.9 32.4 + - - -
345A GLY* 5.3 2.1 - - - -
346A LEU 5.7 0.7 + - - -
314B ARG* 3.0 44.9 + - + +
315B ALA* 4.1 10.6 - - - +
316B ALA 3.5 0.2 - - - -
317B SER* 1.3 78.8 - - - +
319B PHE* 1.3 60.3 + - - +
321B SER* 4.1 3.2 - - - -
322B ARG* 3.3 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLN* 3.8 33.7 - - + -
351A THR* 4.9 8.3 - - + -
352A LEU* 3.6 29.2 - - + -
363A ILE* 3.9 36.1 - - + -
367A LEU* 4.8 1.8 - - + -
315B ALA 3.4 16.7 + - - +
316B ALA* 4.3 5.4 - - - +
317B SER 3.3 0.6 - - - -
318B GLU* 1.3 81.7 - - - +
320B ALA* 1.3 62.9 + - - +
321B SER 3.2 1.8 + - - -
322B ARG* 3.8 10.9 + - - +
323B ASN* 3.3 51.1 + - - +
325B LEU* 4.5 6.1 - - + -
333B MET* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA 3.7 15.3 + - - +
317B SER 3.8 1.3 + - - +
318B GLU 3.4 0.2 - - - -
319B PHE* 1.3 77.8 - - - +
321B SER* 1.3 56.6 + - - +
323B ASN 4.5 0.9 - - - -
324B GLN* 4.1 0.7 + - - -
325B LEU* 3.5 48.1 + - + +
330B GLN* 3.4 42.8 + - + +
333B MET* 4.1 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B SER 3.3 18.0 + - - -
318B GLU* 3.6 3.8 + - - -
319B PHE 3.2 0.6 - - - -
320B ALA* 1.3 78.9 - - - +
322B ARG* 1.3 63.5 + - - +
323B ASN 3.3 1.3 - - - -
324B GLN* 3.7 6.6 + - - +
330B GLN* 5.4 2.5 - - - -
118D HIS* 3.0 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG* 5.1 2.6 - - - +
341A PHE 5.6 0.2 + - - -
342A LYS 4.8 5.5 + - - -
343A THR* 3.0 24.7 + - - +
344A GLU 3.7 8.9 + - - -
345A GLY* 3.4 23.0 - - - +
348A GLN* 3.6 24.2 + - - +
315B ALA 5.6 0.8 + - - -
318B GLU* 3.3 35.7 + - + +
319B PHE* 3.8 18.7 + - - +
321B SER* 1.3 79.2 - - - +
323B ASN* 1.3 70.2 + - - +
324B GLN* 3.6 8.0 + - - +
117D SER 6.0 0.7 - - - +
118D HIS* 4.1 25.2 - - + +
120D TYR* 3.5 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLN* 5.6 0.2 + - - -
366A TYR* 4.6 2.4 - - - -
367A LEU* 3.4 44.4 - - + +
319B PHE* 3.3 46.7 + - - +
321B SER 3.3 0.4 - - - -
322B ARG* 1.3 89.9 + - - +
324B GLN* 1.3 71.6 + - - +
325B LEU* 3.3 7.4 + - + -
----------------------------------------------------------
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