Contacts of the helix formed by residues 301 - 321 (chain B) in PDB entry 4BGG
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 301 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 1.3 74.1 - - - +
302B THR* 1.3 65.3 + - - +
303B VAL* 3.4 10.5 + - - +
304B SER* 2.7 44.8 + - - -
305B CYS* 2.9 23.6 + - - +
418B MET* 4.0 6.1 - - - -
419B VAL* 5.0 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP* 1.3 76.1 - - - +
303B VAL* 1.3 67.2 + - + +
305B CYS* 3.9 0.9 - - - +
306B LEU* 3.0 39.0 + - + +
418B MET* 3.2 25.1 - - - +
419B VAL 5.3 0.3 + - - -
464B ASP* 4.9 2.4 + - - -
466B THR* 3.4 28.4 + - + +
498B ILE* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 6.1 7.0 - - + -
303A VAL* 4.4 23.8 - - + -
301B ASP* 3.3 11.5 + - - +
302B THR* 1.3 78.2 - - + +
304B SER* 1.3 60.3 + - - +
306B LEU* 3.5 5.4 + - - +
307B ARG* 3.0 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B TYR* 6.1 0.9 - - - -
299B THR 5.1 0.2 + - - -
300B LEU* 3.7 15.7 - - - +
301B ASP* 2.7 39.1 + - - -
303B VAL* 1.3 76.8 - - - +
305B CYS* 1.3 64.0 + - - +
307B ARG* 3.6 17.3 + - - +
308B ILE* 3.2 32.1 + - - +
348B GLY* 4.9 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 4.1 13.2 - - + +
301B ASP 2.9 16.2 + - - +
302B THR 3.9 3.4 - - - +
304B SER* 1.3 75.9 + - - +
306B LEU* 1.3 65.3 + - + +
308B ILE* 3.3 4.5 + - - +
309B VAL* 3.2 25.4 + - - +
414B VAL* 4.0 19.3 - - - -
415B ALA* 4.5 4.5 - - - -
418B MET* 3.9 32.3 - - + -
470B LEU* 3.9 27.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B THR* 3.0 36.8 + - + +
303B VAL* 3.9 4.9 - - - +
305B CYS* 1.3 76.6 - - + +
307B ARG* 1.3 57.9 + - - +
309B VAL* 3.7 6.1 - - + +
310B LEU* 2.9 37.1 + - + +
466B THR* 4.0 20.0 - - + -
470B LEU* 4.5 5.6 - - + -
495B LEU* 4.4 27.4 - - + +
498B ILE* 3.8 42.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
302A THR* 5.6 4.4 - - - +
303A VAL* 5.3 5.5 - - - +
306A LEU* 5.1 9.5 - - - +
498A ILE* 4.9 18.0 + - - +
303B VAL* 3.0 45.0 + - + +
304B SER* 3.9 16.1 - - - +
305B CYS 3.3 0.2 - - - -
306B LEU* 1.3 75.2 - - - +
308B ILE* 1.3 59.7 + - - +
310B LEU* 4.1 4.5 - - - +
311B SER* 3.0 28.8 + - - -
347B ASN 3.6 25.8 + - - -
348B GLY* 3.6 19.4 - - - +
349B GLN* 4.0 15.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 4.2 13.0 - - + -
294B TYR* 4.4 15.7 - - + -
295B LEU* 5.2 0.4 - - + -
300B LEU* 4.0 30.3 - - + -
304B SER* 3.2 15.9 + - - +
305B CYS 3.6 6.7 - - - +
307B ARG* 1.3 78.2 - - - +
309B VAL* 1.3 62.6 + - - +
311B SER* 2.7 21.7 + - - -
312B ILE* 3.1 23.1 + - + +
344B VAL* 5.9 1.6 - - + -
348B GLY 3.7 15.9 - - - +
350B CYS* 3.8 21.3 - - - -
414B VAL* 4.1 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B CYS* 3.2 21.0 + - - +
306B LEU* 3.7 12.8 - - + +
308B ILE* 1.3 77.6 - - + +
310B LEU* 1.3 61.0 + - - +
312B ILE* 3.4 10.0 + - + +
313B ALA* 2.9 29.6 + - - +
407B PHE* 4.2 4.7 - - + -
410B VAL* 6.3 0.4 - - + -
411B LEU* 3.5 33.4 - - + -
414B VAL* 3.9 27.4 - - + -
470B LEU* 4.5 4.9 - - + -
495B LEU* 3.8 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ARG* 3.9 24.7 - - - +
306B LEU* 2.9 22.3 + - + +
307B ARG* 4.2 4.5 - - - +
309B VAL* 1.3 77.7 - - - +
311B SER* 1.3 57.4 + - - +
313B ALA 3.4 0.5 + - - -
314B SER* 3.0 37.3 + - - +
492B LYS* 3.9 26.5 - - + +
495B LEU* 4.0 21.3 - - + +
496B THR* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ASN* 3.4 37.7 - - - +
307B ARG 3.0 16.5 + - - -
308B ILE 2.7 19.9 + - - -
310B LEU* 1.3 74.7 - - - +
312B ILE* 1.3 64.5 + - - +
314B SER* 3.3 2.2 + - - -
315B GLY 3.0 18.9 + - - -
349B GLN* 3.9 14.1 - - - +
350B CYS* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ASN* 5.6 0.2 - - - -
291B LEU* 4.0 19.3 - - + -
308B ILE* 3.1 32.7 + - + +
309B VAL* 3.7 11.9 - - + +
311B SER* 1.3 75.1 - - - +
313B ALA* 1.3 62.1 + - - +
315B GLY* 3.3 2.5 + - - +
316B LEU* 2.9 22.5 + - + +
337B LEU* 5.1 6.1 - - + -
342B ILE* 4.1 34.3 - - + -
350B CYS* 4.2 6.7 - - + -
351B CYS* 6.5 0.2 - - - +
352B ILE* 3.8 17.7 - - + +
407B PHE* 3.5 26.0 - - + -
410B VAL* 4.2 9.4 - - + -
414B VAL* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B VAL 2.9 16.7 + - - +
310B LEU 3.7 4.0 - - - +
312B ILE* 1.3 78.8 - - - +
314B SER* 1.3 57.3 + - - +
316B LEU* 3.8 4.9 - - - +
317B ALA* 2.9 31.6 + - - +
407B PHE* 3.9 15.2 - - + -
488B ALA* 4.5 5.1 - - - +
491B ILE* 4.1 9.2 - - + -
492B LYS* 4.2 15.9 - - + +
495B LEU* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B HIS* 3.9 10.2 + - - -
261B ASN* 3.6 17.9 - - - -
310B LEU* 3.0 23.3 + - - +
311B SER* 3.6 1.5 - - - -
312B ILE 3.3 0.4 - - - -
313B ALA* 1.3 72.1 - - - +
315B GLY* 1.3 66.3 + - - +
317B ALA* 3.4 1.8 + - - +
318B HIS* 3.0 24.9 + - - +
492B LYS* 3.5 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B HIS* 4.3 7.0 - - - -
261B ASN* 3.8 28.8 - - - +
262B ILE* 4.1 3.9 - - - +
311B SER 3.0 11.7 + - - -
312B ILE 3.7 2.2 - - - -
314B SER* 1.3 75.9 - - - +
316B LEU* 1.3 61.4 + - - +
318B HIS* 3.3 3.3 + - - +
319B LEU* 3.0 26.0 + - - +
352B ILE* 3.8 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ILE* 2.9 18.3 + - + +
313B ALA* 3.8 5.2 - - - +
315B GLY* 1.3 74.7 - - - +
317B ALA* 1.3 63.9 + - - +
319B LEU* 3.0 18.8 + - + +
320B HIS* 3.0 49.3 + - + +
334B HIS* 4.9 1.8 - - + -
337B LEU* 4.1 27.6 - - + -
352B ILE* 3.6 9.2 - - + +
403B ASP* 3.9 17.5 - - + +
404B ILE* 4.3 19.3 - - + -
407B PHE* 4.2 22.4 - - + -
488B ALA* 4.3 5.8 - - + -
491B ILE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ALA 2.9 18.2 + - - +
314B SER 4.0 3.4 - - - +
316B LEU* 1.3 75.8 - - - +
318B HIS* 1.3 61.8 + - - +
320B HIS* 3.3 2.4 + - - +
321B ILE* 3.0 28.9 + - - +
488B ALA* 3.8 28.4 - - + +
489B LEU* 4.3 13.0 - - + +
492B LYS* 4.5 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 4.3 7.6 - - + +
258B ARG 4.0 15.0 + - - -
259B HIS* 3.4 37.4 + + + +
262B ILE* 3.9 18.6 - - + -
314B SER 3.0 18.7 + - - +
315B GLY 3.6 4.3 - - - +
317B ALA* 1.3 75.5 - - - +
319B LEU* 1.3 61.1 + - - +
321B ILE* 3.7 15.1 - - + +
329B LYS* 2.9 45.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 4.0 23.8 - - + -
262B ILE* 3.6 23.8 - - + -
315B GLY 3.0 18.0 + - - +
316B LEU* 3.0 20.4 + - + +
318B HIS* 1.3 77.9 - - - +
320B HIS* 1.3 55.1 + - + +
329B LYS* 3.4 10.3 - - - +
332B ILE* 2.7 58.3 + - + +
334B HIS* 4.4 17.9 - - + +
352B ILE* 4.5 13.5 - - + -
355B LEU* 4.4 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.0 33.5 + - + +
317B ALA* 3.3 6.0 + - - +
319B LEU* 1.3 77.2 - - + +
321B ILE* 1.3 59.4 + - - +
322B GLU 3.7 0.3 + - - -
331B ALA* 3.1 21.2 - - - +
332B ILE 3.2 21.3 - - - +
400B LYS* 3.6 63.0 + - + +
403B ASP* 2.9 30.3 + - + -
404B ILE* 4.4 4.7 - - + +
488B ALA* 3.7 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA 3.0 19.8 + - - +
318B HIS* 3.7 18.6 - - + +
319B LEU 3.4 0.2 - - - -
320B HIS* 1.3 77.4 - - - +
322B GLU* 1.3 74.7 + - - +
323B ILE* 3.5 6.1 + - + +
329B LYS* 3.4 23.2 - - + +
330B PRO 4.0 0.2 - - - +
331B ALA* 4.3 1.6 - - - -
489B LEU* 5.7 10.3 - - + -
----------------------------------------------------------
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