Contacts of the strand formed by residues 347 - 358 (chain E) in PDB entry 6Q2J
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 VAL 347 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ARG* 3.3 46.2 - - - +
232E GLU* 3.5 28.5 - - + +
233E GLN 3.6 16.8 - - - +
234E ARG* 4.3 2.7 - - - +
235E GLU* 4.8 5.6 - - + +
301E ALA* 5.5 1.3 - - + +
339E SER* 4.6 0.2 - - - -
340E VAL* 2.9 43.9 + - + +
342E ALA* 4.4 7.0 - - + -
345E SER* 4.0 5.6 - - - +
346E PHE* 1.3 71.2 - - - +
348E ARG* 1.3 68.0 + - - +
349E ALA* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 348 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C CYS 5.6 3.2 + - - -
294C ARG* 4.1 19.4 + - - +
301C GLU* 4.6 14.5 + - - -
231E ARG* 3.1 35.9 + - - +
235E GLU* 4.5 13.4 + - - +
303E VAL* 3.8 14.9 - - + +
337E GLU* 2.9 44.0 + - + +
338E THR 3.3 16.0 + - - +
339E SER* 4.9 5.4 - - - -
346E PHE* 3.5 8.9 + - + +
347E VAL* 1.3 79.9 - - - +
349E ALA* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E PHE* 3.9 22.9 - - + -
300E ASP 3.3 13.2 - - - +
301E ALA* 3.8 12.3 - - + -
302E ASP 3.6 8.1 - - - -
303E VAL* 5.5 0.4 - - - -
337E GLU* 3.2 5.0 - - - +
338E THR* 2.9 36.3 + - + +
340E VAL* 4.7 11.4 - - + -
347E VAL* 3.8 0.8 + - + -
348E ARG* 1.3 75.1 - - - +
350E THR* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 350 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E VAL 4.0 0.3 - - - +
299E PHE* 3.8 2.4 - - - -
300E ASP* 2.9 56.5 + - - +
302E ASP 3.3 20.9 + - - +
303E VAL* 4.4 7.2 - - - +
305E PRO 5.8 2.2 - - - +
314E TYR* 4.7 6.3 + - + +
335E PRO* 5.6 2.5 - - + -
336E ASN 3.3 12.1 - - - +
337E GLU* 4.1 15.9 - - + +
349E ALA* 1.3 75.3 - - - +
351E VAL* 1.3 64.5 + - - +
352E HIS* 3.5 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E ARG* 3.4 43.5 - - + +
298E VAL 3.4 7.9 - - - +
299E PHE* 4.0 20.0 - - + -
335E PRO 3.5 0.7 - - - -
336E ASN* 2.9 43.1 + - + +
338E THR* 3.9 26.2 - - + -
349E ALA 4.2 0.4 + - - -
350E THR* 1.3 76.8 - - - +
352E HIS* 1.3 66.6 + - - +
353E ASP* 4.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E PRO* 5.8 0.9 - - + -
297E ARG* 3.2 6.4 - - - +
298E VAL* 2.9 51.3 + - + +
300E ASP* 3.9 16.7 + - + +
314E TYR* 3.3 41.0 - + - -
333E HIS* 3.6 13.1 - + + -
334E TRP 3.9 3.6 - - - -
335E PRO* 3.5 21.2 - - + +
350E THR* 3.5 25.9 + - + -
351E VAL* 1.3 73.9 - - - +
353E ASP* 1.3 62.7 + - - +
354E TYR* 3.8 24.9 + + + -
376E VAL* 6.3 1.6 - - + -
378E ASP* 5.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 353 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E THR* 5.0 3.8 - - + -
296E LEU 3.6 3.1 - - - +
297E ARG* 3.3 31.0 + - - +
332E GLU 4.1 1.2 - - - +
333E HIS* 3.4 7.1 + - - -
334E TRP* 2.9 62.2 + - + +
336E ASN* 5.7 3.6 - - - +
351E VAL* 4.4 6.8 - - - +
352E HIS* 1.3 74.9 - - - +
354E TYR* 1.3 61.6 + - - +
355E ARG* 4.4 20.1 + - - +
702E NAG 5.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E THR* 3.3 4.4 - - - +
296E LEU 2.9 36.5 + - - +
298E VAL* 3.7 32.3 - - + -
314E TYR* 5.1 6.9 + - - +
315E THR 5.4 0.5 + - - -
316E SER* 3.5 26.2 + - - -
331E VAL* 4.5 12.8 - - + -
332E GLU 3.7 2.2 - - - -
333E HIS* 3.2 46.1 + + + -
352E HIS* 3.8 15.0 - - + +
353E ASP* 1.3 75.8 - - - +
355E ARG* 1.3 62.4 + - - +
374E VAL* 4.8 1.1 - - + -
376E VAL* 3.3 30.9 - - + +
391E LEU* 3.8 24.0 - - + -
393E PHE* 4.6 6.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 355 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E VAL* 4.1 30.1 - - + +
294E ALA 3.3 13.2 - - - +
295E THR* 3.8 27.5 + - - +
331E VAL* 3.4 7.1 - - - +
332E GLU* 2.9 48.8 + - + +
334E TRP* 3.3 46.6 - - + +
353E ASP* 4.4 15.2 + - - +
354E TYR* 1.3 75.9 - - - +
356E LEU* 1.3 63.6 + - - +
357E VAL* 4.5 8.7 - - + -
393E PHE* 4.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E THR 3.4 0.9 - - - +
292E VAL* 3.7 2.1 - - - -
293E VAL* 3.0 40.4 + - + -
294E ALA 3.2 6.3 + - - +
318E LEU* 5.3 0.4 - - + -
329E PHE* 4.5 16.2 - - + -
330E ARG 3.6 5.2 - - - +
331E VAL* 3.8 27.8 - - + -
355E ARG* 1.3 75.8 - - - +
357E VAL* 1.3 63.0 + - - +
372E LEU* 3.8 25.6 - - + -
374E VAL* 5.0 1.1 - - + -
393E PHE* 3.5 50.3 - - + -
395E VAL* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E ASP* 3.8 6.7 - - + -
291E THR 3.3 20.9 - - - +
292E VAL* 4.9 4.9 - - + +
329E PHE* 3.5 6.0 - - - -
330E ARG* 2.9 64.4 + - + +
332E GLU* 3.4 30.5 - - + +
355E ARG* 4.5 11.4 - - + -
356E LEU* 1.3 79.5 - - - +
358E LEU* 1.3 75.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E VAL* 4.6 11.9 - - + -
286E LYS* 5.8 0.2 - - + -
287E ARG* 3.9 23.1 - - - +
288E LYS 3.3 26.9 - - - +
289E GLU 2.8 14.1 - - - +
290E ASP* 3.4 0.2 - - - -
291E THR* 3.3 25.4 + - + +
293E VAL* 4.4 9.6 - - + +
328E THR 3.3 8.7 - - - +
329E PHE* 3.6 28.8 - - + -
330E ARG* 3.5 3.3 + - - -
357E VAL* 1.3 87.5 - - - +
359E ASN* 1.3 58.5 + - - +
360E ARG 4.3 4.5 - - - +
362E LEU* 3.8 27.6 - - + -
----------------------------------------------------------
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