Contacts of the helix formed by residues 308 - 328 (chain A) in PDB entry 6CNB
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 308 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 1.3 81.3 - - - +
309A ILE* 1.3 66.6 + - - +
310A ASN* 3.1 10.6 + - - +
311A ASN* 2.4 31.5 + - - +
312A MET* 2.5 41.5 + - - +
519O GLU* 4.6 3.3 + - - -
530O GLU* 4.0 2.7 - - - -
534O ARG* 3.2 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 1.3 77.2 + - - +
310A ASN* 1.3 65.1 + - - +
312A MET* 3.7 23.5 - - + +
313A MET* 3.7 10.9 + - + +
519O GLU* 3.6 35.9 - - + +
534O ARG* 4.5 4.6 - - - +
537O LEU* 4.4 14.6 - - + -
541O ILE* 4.5 5.8 - - + -
548O ILE* 4.2 20.6 - - + -
564O PHE* 3.2 32.6 - - + -
566O PHE* 3.4 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 3.1 7.2 + - - +
309A ILE* 1.3 83.9 - - + +
311A ASN* 1.3 52.1 + - - +
312A MET 3.1 5.0 + - - -
313A MET 3.5 3.8 + - - -
314A GLU* 2.7 23.9 + - - +
519O GLU* 5.0 5.6 - - - +
559O ALA 4.2 3.1 - - - +
560O SER* 3.7 27.9 + - - +
562O ALA 4.0 8.7 + - - +
563O VAL* 5.8 1.8 - - - -
564O PHE* 3.6 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 3.0 18.2 + - - +
308A SER* 2.4 53.7 + - - +
310A ASN* 1.3 76.7 - - + +
312A MET* 1.3 59.7 + - - +
314A GLU* 2.8 34.9 - - - +
315A HIS* 3.5 16.7 + - + -
530O GLU* 5.5 0.4 + - - -
31X G 4.6 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.9 9.0 - - + -
299A ILE* 5.2 10.4 - - + +
303A LEU* 3.6 34.3 - - + -
307A ILE* 3.8 25.8 - - + -
308A SER 2.5 24.3 + - - +
309A ILE* 3.7 27.8 - - + +
310A ASN 3.1 0.4 - - - -
311A ASN* 1.3 73.9 - - - +
313A MET* 1.3 77.2 + - + +
315A HIS* 3.2 19.9 + - - +
316A TRP* 3.4 7.3 + - + +
537O LEU* 6.0 0.4 - - + -
538O ALA* 3.8 22.9 - - + -
541O ILE* 5.0 8.3 - - + -
548O ILE* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LYS* 3.8 25.8 - - - +
221A ASP* 5.6 2.9 - - - +
223A ASN* 4.4 13.9 - - - +
309A ILE* 3.7 6.0 + - + +
310A ASN 3.5 2.0 + - - -
312A MET* 1.3 86.0 - - + +
314A GLU* 1.3 56.1 + - - +
316A TRP* 2.5 45.8 + - + -
317A ASP* 2.8 13.6 + - + -
548O ILE* 4.1 30.1 - - + -
550O GLU* 5.9 4.3 - - + +
559O ALA* 5.3 2.7 - - + -
564O PHE* 3.3 50.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN 2.7 18.9 + - - +
311A ASN* 2.8 38.8 - - - +
313A MET* 1.3 70.2 - - - +
315A HIS* 1.3 79.0 + - + +
317A ASP* 3.7 3.2 - - - +
318A TYR* 2.9 22.9 + - - +
336A MET* 5.6 1.0 - - - +
559O ALA* 3.5 30.6 - - + +
560O SER* 4.1 19.1 - - - +
564O PHE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 4.5 4.1 + - - +
298A LEU* 3.4 38.4 - - + +
299A ILE* 3.9 20.1 - - + +
307A ILE* 5.3 12.5 - - + +
311A ASN* 3.5 19.3 + - + -
312A MET* 3.2 9.1 + - - +
313A MET 2.8 3.2 + - - -
314A GLU* 1.3 89.0 + - + +
316A TRP* 1.3 52.1 + - - +
318A TYR* 2.6 35.7 + + + +
319A LEU* 2.8 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 4.6 3.8 - - - -
88A LEU* 3.2 52.3 - - + +
89A PRO 4.4 5.6 - - - -
90A VAL* 4.7 7.9 - - - +
177A LYS* 3.9 20.2 - - - -
223A ASN* 2.9 31.0 - - - -
224A PRO* 3.3 36.6 - - + -
225A LEU* 4.0 10.3 - - + -
299A ILE* 3.6 20.6 - - + +
312A MET* 3.4 6.5 + - + +
313A MET* 2.5 33.6 + - + +
315A HIS* 1.3 74.3 - - - +
317A ASP* 1.3 67.1 + - + -
319A LEU* 2.8 34.4 + - + +
320A GLN* 3.0 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY 4.9 3.3 - - - +
173A SER* 4.3 15.7 - - - +
177A LYS* 5.1 10.2 - - - +
313A MET* 2.8 15.8 + - + +
314A GLU* 3.7 13.5 - - - +
316A TRP* 1.3 80.1 - - + +
318A TYR* 1.3 64.0 + - - +
319A LEU 3.0 0.5 + - - -
320A GLN* 3.1 26.5 + - - +
321A LEU* 2.9 27.2 + - - +
558O SER* 5.8 0.5 - - - -
559O ALA* 4.0 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 3.0 37.2 + - - +
295A THR* 4.0 19.1 - - - -
314A GLU 2.9 15.0 + - - +
315A HIS* 2.6 19.5 + + + +
317A ASP* 1.3 73.3 - - - +
319A LEU* 1.3 50.9 + - - -
321A LEU* 4.3 13.7 - - + -
322A THR* 2.4 53.0 + - - +
336A MET* 3.5 38.6 - - + -
338A PRO* 5.0 6.8 - - + +
339A GLY* 4.2 22.4 + - - -
340A SER 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.6 35.2 - - + -
87A ALA 4.2 9.0 - - - +
90A VAL* 4.1 13.7 - - + -
292A ILE* 4.1 25.1 - - + +
295A THR* 3.7 26.5 - - + +
296A SER* 5.0 5.6 - - - +
299A ILE* 4.6 14.6 - - + -
315A HIS 2.8 6.7 + - - +
316A TRP* 2.8 24.7 + - + +
318A TYR* 1.3 77.2 - - - +
320A GLN* 1.3 62.7 + - - +
322A THR* 3.0 5.2 + - - -
323A VAL* 2.9 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.3 26.4 - - + +
91A PHE* 3.3 25.6 + - - +
173A SER 5.8 0.2 + - - -
176A LEU* 3.2 39.2 + - + +
177A LYS* 3.8 22.4 - - - +
224A PRO* 3.8 11.5 - - - +
316A TRP* 3.0 17.6 + - + +
317A ASP* 3.2 29.1 + - - +
319A LEU* 1.3 75.8 - - - +
321A LEU* 1.3 67.5 + - - +
323A VAL* 3.4 1.7 - - - +
324A ALA* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY* 4.0 18.6 - - - +
176A LEU* 4.3 9.2 - - + -
317A ASP* 2.9 22.9 + - - +
318A TYR* 4.0 13.7 - - + +
320A GLN* 1.3 78.2 - - - +
322A THR* 1.3 68.2 + - - +
324A ALA* 3.5 2.6 - - + +
325A MET* 2.9 18.9 + - + +
331A SER* 3.4 29.4 - - - +
334A PRO* 3.7 28.5 - - + -
336A MET* 5.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 4.4 20.2 - - - +
291A GLU* 3.4 23.8 - - - +
292A ILE* 3.5 18.6 - - + -
295A THR* 5.7 0.4 - - - -
318A TYR* 2.4 50.0 + - - +
319A LEU* 3.0 7.7 + - - -
321A LEU* 1.3 73.8 - - - +
323A VAL* 1.3 56.5 + - - +
325A MET* 2.4 35.3 + - - +
326A TYR* 2.8 7.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 5.8 0.7 - - + -
90A VAL* 3.6 26.7 - - + -
91A PHE 4.4 7.0 - - - +
92A HIS* 6.1 0.2 - - - -
258A TRP* 4.5 17.5 - - + +
261A LEU* 3.9 32.3 - - + -
292A ILE* 3.8 12.8 - - + -
319A LEU* 2.9 16.8 + - + +
320A GLN 3.4 10.3 - - - +
322A THR* 1.3 76.2 - - - +
324A ALA* 1.3 65.5 + - - +
326A TYR* 2.9 31.1 + - + +
327A ILE* 3.0 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 3.7 36.6 - - + +
176A LEU* 4.0 15.9 - - + -
320A GLN 2.9 20.5 + - - +
321A LEU* 3.5 6.7 - - + +
323A VAL* 1.3 79.1 - - - +
325A MET* 1.3 57.7 + - - +
326A TYR 3.1 0.3 + - - -
327A ILE* 3.2 2.6 + - - +
328A ASN* 2.9 31.5 + - - +
330A ASP* 4.7 7.9 - - - +
331A SER* 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 4.2 22.3 - - - +
321A LEU* 2.9 14.1 + - + +
322A THR* 2.4 26.0 + - - +
324A ALA* 1.3 68.9 - - - +
326A TYR* 1.3 56.5 + - - +
328A ASN 2.6 22.4 - - - +
329A SER* 3.1 34.5 - - - +
330A ASP* 4.8 1.3 + - - +
331A SER* 3.8 13.0 + - - +
332A VAL* 5.8 3.4 - - - +
348A LYS 5.0 2.9 - - - +
350A ILE* 3.6 22.4 - - + +
351A ARG* 3.3 39.7 - - + +
352A GLY 4.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.5 19.5 - - + -
262A PRO 4.1 3.3 + - - -
264A PRO* 3.3 30.5 - - - +
285A LEU* 3.6 31.2 - - + +
288A LYS* 3.9 30.2 - - + +
289A LEU* 3.8 23.6 - - + +
292A ILE* 4.4 7.4 - - + -
322A THR 2.8 5.4 + - - +
323A VAL* 2.9 30.7 + - + +
325A MET* 1.3 80.2 - - - +
327A ILE* 1.3 77.6 + - + +
352A GLY 5.0 0.9 + - - -
353A PHE* 3.1 27.9 + + - +
1134B SER* 3.6 11.6 + - - -
1135B MET* 5.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A HIS* 3.3 33.0 - - + +
93A ILE* 3.5 28.7 - - + -
94A GLY 4.0 2.2 - - - +
258A TRP* 4.3 14.1 - - + +
323A VAL* 3.0 7.4 + - + +
324A ALA 3.8 1.6 - - - +
326A TYR* 1.3 100.3 - - + +
328A ASN* 1.3 59.2 + - - +
353A PHE* 4.0 18.8 - - + -
354A CYS* 3.0 26.5 + - - +
1397A PHE* 4.3 15.8 - - + -
1135B MET* 4.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.5 13.8 - - + +
324A ALA 2.9 13.1 + - - +
325A MET* 2.6 29.6 - - - +
326A TYR 3.4 1.2 + - - -
327A ILE* 1.3 81.0 - - - +
329A SER* 1.3 83.5 + - - +
330A ASP* 3.4 33.3 + - - +
351A ARG* 4.0 7.1 - - - +
352A GLY 4.9 0.7 + - - -
353A PHE* 4.9 0.6 - - - +
354A CYS* 3.8 18.7 - - - +
355A GLN* 3.4 13.0 + - - -
1393A THR* 5.8 3.4 - - - +
----------------------------------------------------------
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