Contacts of the helix formed by residues 301 - 321 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D LEU* 1.3 73.4 - - - +
302D THR* 1.3 60.7 + - - +
303D VAL* 3.4 11.9 + - - +
304D SER* 2.7 37.5 + - - -
305D CYS* 2.9 29.1 + - - +
418D MET* 4.0 6.3 - - - -
419D VAL* 5.0 4.7 - - + +
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Residues in contact with THR 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D ASP* 1.3 75.2 - - - +
303D VAL* 1.3 66.1 + - - +
305D CYS* 3.9 1.0 - - - +
306D LEU* 3.0 34.7 + - - +
418D MET* 4.0 27.3 - - - +
419D VAL 5.4 0.2 + - - -
466D THR* 4.5 13.7 - - - -
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Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D ASP* 3.3 11.5 + - - +
302D THR* 1.3 78.8 - - - +
304D SER* 1.3 60.2 + - - +
306D LEU* 3.4 6.2 + - - +
307D ARG* 3.0 55.7 + - - +
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Residues in contact with SER 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D TYR* 5.9 1.8 - - - -
300D LEU* 3.6 15.9 - - - +
301D ASP* 2.7 42.5 + - - -
303D VAL* 1.3 73.7 - - - +
305D CYS* 1.3 64.3 + - - +
307D ARG* 3.9 16.1 - - - +
308D ILE* 3.2 32.3 + - - +
348D GLY 4.9 0.6 - - - +
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Residues in contact with CYS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D LEU* 4.1 13.5 - - + -
301D ASP 2.9 16.5 + - - +
302D THR 3.9 1.3 - - - +
304D SER* 1.3 78.5 + - - +
306D LEU* 1.3 61.8 + - + +
308D ILE* 3.3 5.0 + - - +
309D VAL* 3.2 25.3 + - - +
414D VAL* 4.0 18.8 - - - -
415D ALA* 4.5 4.3 - - - -
418D MET* 3.8 33.7 - - + -
466D THR* 5.5 0.9 - - - -
470D LEU* 3.8 28.5 - - - -
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D THR* 3.0 26.1 + - - +
303D VAL* 3.9 5.2 - - - +
305D CYS* 1.3 71.5 - - - +
307D ARG* 1.3 60.4 + - - +
309D VAL* 3.7 5.7 - - + +
310D LEU* 2.9 38.0 + - + +
466D THR* 3.9 28.0 - - + +
470D LEU* 4.5 5.4 - - + -
495D LEU* 4.4 27.1 - - + +
498D ILE* 3.8 40.6 - - + +
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Residues in contact with ARG 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D VAL* 3.0 44.4 + - + +
304D SER* 3.9 15.4 - - - +
305D CYS 3.3 0.2 - - - -
306D LEU* 1.3 76.5 - - - +
308D ILE* 1.3 58.6 + - - +
310D LEU* 4.1 4.6 - - - +
311D SER* 3.0 28.4 + - - -
347D ASN 3.6 25.9 + - - -
348D GLY* 3.6 20.5 - - - +
349D GLN* 4.0 14.9 + - + +
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Residues in contact with ILE 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D LEU* 4.1 12.8 - - + -
294D TYR* 4.4 15.7 - - + +
300D LEU* 4.0 30.7 - - + -
304D SER* 3.2 16.4 + - - +
305D CYS 3.6 6.3 - - - +
306D LEU 3.2 0.2 - - - -
307D ARG* 1.3 75.3 - - - +
309D VAL* 1.3 64.4 + - - +
311D SER* 2.7 21.3 + - - -
312D ILE* 3.1 23.7 + - + +
344D VAL* 5.8 2.5 - - + -
348D GLY 3.8 15.0 - - - +
350D CYS* 3.8 22.4 - - - -
414D VAL* 4.1 21.1 - - + -
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Residues in contact with VAL 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D CYS* 3.2 20.4 + - - +
306D LEU* 3.7 10.5 - - + +
308D ILE* 1.3 78.6 - - + +
310D LEU* 1.3 65.6 + - - +
312D ILE* 3.3 9.8 + - + +
313D ALA* 2.9 24.8 + - - +
407D PHE* 4.2 4.5 - - + -
410D VAL* 6.3 0.4 - - + -
411D LEU* 3.5 33.2 - - + -
414D VAL* 3.9 26.9 - - + -
470D LEU* 4.4 7.4 - - + -
495D LEU* 3.8 28.1 - - + +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D LEU* 2.9 22.2 + - + +
307D ARG* 4.2 4.3 - - - +
309D VAL* 1.3 79.6 - - - +
311D SER* 1.3 57.5 + - - +
313D ALA* 3.4 0.7 + - - +
314D SER* 3.0 36.6 + - - +
492D LYS* 3.9 26.0 - - + +
495D LEU* 3.9 22.0 - - + +
496D THR* 3.8 33.4 - - + +
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Residues in contact with SER 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D ASN* 3.4 37.2 - - - +
307D ARG 3.0 16.4 + - - -
308D ILE* 2.7 19.8 + - - -
310D LEU* 1.3 74.4 - - - +
312D ILE* 1.3 65.2 + - - +
314D SER* 3.2 2.8 + - - -
315D GLY 3.0 19.1 + - - -
349D GLN* 3.9 14.1 - - - +
350D CYS* 3.0 26.6 + - - +
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Residues in contact with ILE 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D LEU* 4.0 20.0 - - + -
308D ILE* 3.1 32.5 + - + +
309D VAL* 3.3 12.1 + - + +
311D SER* 1.3 76.3 + - - +
313D ALA* 1.3 56.7 + - - +
315D GLY* 3.3 2.1 + - - +
316D LEU* 2.9 28.6 + - + +
337D LEU* 5.1 5.4 - - + -
342D ILE* 4.1 26.2 - - + -
350D CYS* 4.1 15.5 - - + -
351D CYS* 6.5 0.2 - - - +
352D ILE* 3.8 17.8 - - + +
407D PHE* 3.5 26.7 - - + -
410D VAL* 4.2 10.1 - - + -
414D VAL* 5.2 0.2 - - + -
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Residues in contact with ALA 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D VAL 2.9 17.6 + - - +
310D LEU* 3.7 4.7 - - - +
312D ILE* 1.3 78.4 - - - +
314D SER* 1.3 56.4 + - - +
316D LEU* 3.9 5.1 - - - +
317D ALA* 2.8 32.1 + - - +
407D PHE* 4.0 14.5 - - + -
488D ALA* 4.5 4.8 - - - +
491D ILE* 4.1 9.9 - - + -
492D LYS* 4.2 15.9 - - + +
495D LEU* 4.0 17.7 - - + -
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Residues in contact with SER 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D HIS* 3.9 9.7 + - - -
260D GLU* 5.9 0.4 - - - -
261D ASN* 3.6 18.6 - - - -
310D LEU* 3.0 23.9 + - - +
311D SER* 3.2 2.0 + - - -
313D ALA* 1.3 74.1 - - - +
315D GLY* 1.3 59.8 + - - +
317D ALA* 3.8 0.9 - - - +
318D HIS* 2.9 30.1 + - - +
492D LYS* 3.5 35.6 + - - +
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Residues in contact with GLY 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D HIS* 4.3 7.0 - - - -
261D ASN* 3.7 29.9 - - - +
262D ILE* 4.1 2.9 - - - +
311D SER 3.0 11.1 + - - -
312D ILE 3.7 2.7 - - - -
314D SER* 1.3 75.1 - - - +
316D LEU* 1.3 63.4 + - - +
318D HIS* 3.2 4.0 + - - +
319D LEU* 3.0 25.5 + - - +
352D ILE* 3.9 7.9 - - - -
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Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ILE* 2.9 18.1 + - + +
313D ALA* 3.9 4.9 - - - +
315D GLY* 1.3 74.3 - - - +
317D ALA* 1.3 63.6 + - - +
319D LEU* 3.0 18.8 + - + +
320D HIS* 2.9 49.9 + - + +
334D HIS* 4.9 1.8 - - + -
337D LEU* 4.1 27.4 - - + -
352D ILE* 3.6 9.9 - - + +
403D ASP* 3.9 17.7 - - + +
404D ILE* 4.3 19.7 - - + -
407D PHE* 4.2 22.2 - - + -
488D ALA* 4.2 5.2 - - + -
491D ILE* 6.1 0.2 - - + -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D ALA 2.8 19.3 + - - +
314D SER 3.9 3.6 - - - +
316D LEU* 1.3 75.8 - - - +
318D HIS* 1.3 57.4 + - - +
320D HIS* 3.3 1.9 + - - +
321D ILE* 3.0 33.3 + - - +
488D ALA* 3.7 29.7 - - + +
489D LEU* 4.2 13.2 - - + +
492D LYS* 4.5 14.1 - - + +
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Residues in contact with HIS 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D LEU* 4.3 15.8 - - + +
258D ARG 4.0 15.2 + - - -
259D HIS* 3.4 34.0 + + + +
262D ILE* 3.8 20.6 - - + -
314D SER 2.9 19.7 + - - +
315D GLY* 3.6 4.5 - - - +
317D ALA* 1.3 75.2 - - - +
319D LEU* 1.3 64.4 + - - +
321D ILE* 3.6 15.6 - - - +
323D ILE* 5.8 8.1 - - + -
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D LEU* 4.0 24.5 - - + -
262D ILE* 3.5 25.1 - - + -
315D GLY 3.0 17.1 + - - +
316D LEU* 3.0 11.0 + - + +
318D HIS* 1.3 77.8 - - - +
320D HIS* 1.3 58.3 + - + +
321D ILE 3.6 1.2 + - - +
330D PRO 4.3 0.9 - - - +
331D ALA* 3.7 2.4 - - - -
332D ILE* 2.7 57.6 + - + +
334D HIS* 4.4 32.8 - - + +
352D ILE* 4.5 17.7 - - + -
355D LEU* 4.3 12.1 - - + -
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Residues in contact with HIS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D LEU* 2.9 36.6 + - + +
317D ALA* 3.9 6.1 - - - +
319D LEU* 1.3 79.1 - - + +
321D ILE* 1.3 57.6 + - - +
322D GLU 3.7 0.5 + - - -
331D ALA* 3.2 21.6 - - - +
332D ILE 3.2 20.4 - - - +
333D ALA* 4.4 0.2 - - - -
400D LYS* 3.6 63.2 + - + +
403D ASP* 2.9 29.6 + - + -
404D ILE* 4.4 4.9 - - + +
488D ALA* 3.7 18.3 + - + +
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Residues in contact with ILE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ALA 3.0 17.5 + - - +
318D HIS* 3.6 14.3 + - - +
319D LEU 3.5 0.4 - - - +
320D HIS* 1.3 76.3 - - - +
322D GLU* 1.3 66.4 + - - +
323D ILE* 3.5 3.8 + - - +
329D LYS* 4.8 3.3 - - - +
330D PRO 4.0 8.5 - - - +
331D ALA* 4.4 1.1 - - - -
489D LEU* 6.5 1.6 - - + -
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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