Contacts of the strand formed by residues 330 - 346 (chain N) in PDB entry 4G7Z
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 THR 330 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224N ARG* 2.6 44.4 + - + -
225N LEU 3.3 11.0 - - - -
226N PRO* 3.9 14.6 - - + -
227N LEU* 3.4 4.1 - - - +
249N TYR* 4.8 8.3 - - + +
326N GLU* 3.8 0.9 - - - -
327N GLU 2.8 31.0 + - - +
328N GLY 3.1 2.1 - - - +
329N GLU* 1.3 89.3 - - + +
331N VAL* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223N LEU 3.6 2.4 - - - +
224N ARG* 3.4 6.7 - - - -
225N LEU* 2.8 40.1 + - + +
226N PRO 4.7 0.7 - - - +
227N LEU* 3.6 26.9 - - + -
230N TRP* 4.1 26.7 - - + +
324N ALA* 5.4 1.1 - - + -
325N GLU 3.4 5.6 - - - +
326N GLU* 3.6 34.1 - - + +
330N THR* 1.3 74.5 - - - +
332N TYR* 1.3 59.9 + - - +
333N LEU* 3.8 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 332 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222N GLY* 3.4 20.6 + - - -
223N LEU* 3.6 28.7 - - - -
224N ARG* 3.8 24.1 - - + +
251N PHE* 5.8 0.9 - + - -
254N GLU* 4.3 26.0 - - - -
281N THR 4.6 2.1 + - - -
282N TYR* 4.5 15.3 - + - -
323N GLU 3.6 2.3 - - - +
325N GLU* 2.8 56.8 + - + +
327N GLU* 5.0 0.2 - - - +
331N VAL* 1.3 70.7 - - - +
333N LEU* 1.3 62.5 + - - +
334N THR* 4.4 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221N ALA 3.9 0.3 - - - +
222N GLY* 3.1 25.6 - - - -
223N LEU* 2.9 20.5 + - + +
225N LEU* 3.8 24.2 - - + -
230N TRP* 3.5 53.6 - - + -
242N LEU* 4.5 12.3 - - + -
322N VAL* 5.3 3.4 - - + -
323N GLU 3.6 2.7 - - - -
324N ALA* 4.0 10.1 - - + -
331N VAL* 4.0 16.6 - - + +
332N TYR* 1.3 79.6 - - - +
334N THR* 1.3 62.2 + - - +
335N LEU* 3.8 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 334 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220N ARG* 3.4 38.1 + - + +
221N ALA 4.3 3.6 - - - +
222N GLY* 4.8 1.8 - - - -
321N GLN 3.5 2.4 - - - +
322N VAL* 3.3 5.9 - - - -
323N GLU* 2.8 65.9 + - - +
332N TYR* 4.4 14.4 + - - -
333N LEU* 1.3 71.4 + - - +
335N LEU* 1.3 63.5 + - - +
336N PHE* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220N ARG* 3.4 5.4 - - - +
221N ALA 3.0 42.8 + - - +
223N LEU* 4.8 11.0 - - + -
236N TYR* 4.6 8.3 - - + -
242N LEU* 5.3 8.5 - - + -
283N PHE* 3.7 35.9 - - + -
313N MET* 5.3 2.7 - - + -
319N ALA* 4.3 10.1 - - + -
321N GLN 3.9 2.0 - - - -
322N VAL* 3.4 31.9 - - + -
333N LEU* 4.5 17.9 - - + -
334N THR* 1.3 74.5 - - - +
336N PHE* 1.3 62.8 + - - +
337N LEU* 3.6 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 336 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219N GLU 3.7 2.9 - - - -
220N ARG* 3.4 46.9 - - + -
319N ALA* 3.6 1.0 - - - -
320N ALA* 2.7 39.1 + - + +
321N GLN* 3.3 48.4 + - + +
323N GLU* 3.4 41.5 - - + -
334N THR* 4.3 4.9 - - + -
335N LEU* 1.3 72.5 - - - +
337N LEU* 1.3 58.7 + - - +
338N GLU* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217N LYS 3.7 0.7 - - - +
218N LYS* 3.1 9.4 - - - +
219N GLU 2.7 38.5 + - - +
221N ALA* 4.0 13.9 - - + -
269N PHE* 3.6 17.0 - - + -
283N PHE* 3.4 36.3 - - + -
313N MET* 3.5 21.5 - - + -
317N VAL* 4.3 8.1 - - + -
318N ARG 3.2 13.2 - - - +
319N ALA* 3.8 7.0 - - - -
335N LEU* 3.6 28.0 - - + +
336N PHE* 1.3 74.1 - - - +
338N GLU* 1.3 61.9 + - - +
339N TRP* 4.0 8.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 338 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216N VAL* 5.9 1.3 - - + -
217N LYS 3.5 4.3 - - - -
218N LYS* 3.2 42.4 - - + +
316N GLN 4.0 0.7 - - - +
317N VAL* 3.4 2.0 - - - -
318N ARG* 2.8 53.7 + - + +
320N ALA* 4.5 22.9 - - + +
336N PHE 4.9 0.7 - - - +
337N LEU* 1.3 76.3 - - - +
339N TRP* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 339 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216N VAL* 3.7 2.7 - - - +
217N LYS* 2.9 69.5 + - + +
219N GLU* 4.4 15.3 - - + +
262N LYS* 4.3 24.5 - - - -
264N LEU* 3.5 31.9 - - + -
269N PHE* 4.0 24.7 - + - -
316N GLN* 3.5 7.6 - - + +
317N VAL* 3.6 29.6 - - + -
337N LEU* 4.0 13.1 + - + -
338N GLU* 1.3 79.0 - - - +
340N THR* 1.3 68.6 + - - +
341N GLU* 3.3 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 340 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214N GLU* 3.6 29.3 + - + +
215N TYR 3.3 9.6 - - - +
216N VAL* 4.2 20.4 - - + -
316N GLN* 2.7 51.5 + - - +
339N TRP* 1.3 85.3 - - - +
341N GLU* 1.3 58.4 + - - +
342N PRO* 3.5 1.6 - - - +
384N VAL* 5.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213N VAL 3.8 0.9 - - - +
214N GLU* 3.6 0.6 - - - -
215N TYR* 3.0 33.7 + - - +
217N LYS* 3.8 17.5 - - - -
262N LYS* 4.9 9.2 - - - +
264N LEU* 5.5 8.3 - - + -
339N TRP* 3.3 36.0 - - + -
340N THR* 1.3 71.9 - - - +
342N PRO* 1.3 76.2 - - + +
343N LYS* 3.7 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 342 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212N ARG* 3.5 33.9 - - + +
213N VAL 3.6 6.1 - - - +
214N GLU* 3.8 16.6 - - + +
265N GLU* 4.1 13.0 - - + +
316N GLN* 3.9 8.3 - - - +
340N THR 3.5 8.7 - - - +
341N GLU* 1.3 94.9 - - + +
343N LYS* 1.3 72.0 + - - +
344N ASP* 4.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 343 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213N VAL 3.0 30.6 + - - +
215N TYR* 3.8 23.6 - - + -
217N LYS* 6.1 2.7 - - - +
341N GLU* 3.7 28.1 + - - +
342N PRO* 1.3 82.0 + - - +
344N ASP* 1.3 61.7 + - - +
345N TYR* 3.2 32.1 - - + +
380N GLU* 4.6 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 344 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210N ARG* 3.9 26.4 + - - -
211N VAL 3.9 2.0 - - - -
212N ARG* 3.3 48.6 + - - +
342N PRO* 4.3 1.9 - - - +
343N LYS* 1.3 72.8 - - - +
345N TYR* 1.3 63.5 + - - +
346N ARG 4.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 345 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210N ARG* 3.4 6.6 - - - +
211N VAL* 3.0 45.2 + - + +
213N VAL* 3.6 28.9 - - + -
215N TYR* 3.0 25.3 + - - -
343N LYS* 3.2 41.5 - - + +
344N ASP* 1.3 75.5 - - - +
346N ARG* 1.3 62.1 + - - +
377N VAL* 3.5 44.4 - - + -
378N ILE 4.4 6.3 + - - -
380N GLU* 4.2 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 346 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174N GLY* 6.3 0.2 - - - -
209N ARG* 3.5 28.9 + - - +
210N ARG* 4.4 16.9 - - - +
344N ASP 4.3 1.2 + - - -
345N TYR* 1.3 71.0 - - - +
347N VAL* 1.3 67.2 + - - +
348N GLN* 3.9 30.2 + - + +
351N MET* 4.3 8.0 - - - +
377N VAL* 4.8 8.2 - - - +
389N GLU* 3.4 25.6 + - - -
----------------------------------------------------------
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