Contacts of the strand formed by residues 294 - 317 (chain A) in PDB entry 1QFG
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 PHE 294 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLU 3.7 0.2 - - - -
290A PHE* 2.8 48.6 + + + +
291A ASN* 3.0 23.7 + - - +
293A THR* 1.3 104.4 - - + +
295A THR* 1.3 55.7 + - - +
361A LEU* 4.0 21.8 - - + -
362A GLN 3.8 2.5 - - - -
363A SER* 2.8 33.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 5.2 5.2 - - + -
288A HIS 3.2 20.9 - - - +
289A GLU* 3.7 20.7 - - + +
290A PHE* 4.9 0.4 - - - -
293A THR 5.6 0.2 - - - -
294A PHE* 1.3 76.5 + - - +
296A VAL* 1.3 70.6 + - - +
297A ARG* 4.3 13.6 + - - +
360A GLN 4.2 0.2 - - - +
361A LEU* 3.6 5.9 - - - +
362A GLN* 2.9 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PHE* 4.5 10.8 - - + -
287A ASP* 3.4 2.1 - - - -
288A HIS* 2.6 58.4 + - + +
290A PHE* 3.7 26.6 - - + -
295A THR* 1.3 77.8 - - - +
297A ARG* 1.3 70.5 + - - +
298A GLN* 4.6 2.0 - - + +
359A THR* 4.7 11.9 - - + -
360A GLN 3.2 14.4 - - - +
361A LEU* 4.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS 3.0 17.0 + - - -
39A THR* 4.4 5.3 - - - +
40A ASP* 4.8 4.6 - - - +
286A PHE* 3.0 17.9 - - - +
287A ASP* 4.0 12.2 - - + +
295A THR* 4.3 10.7 - - - +
296A VAL* 1.3 80.6 - - - +
298A GLN* 1.3 56.7 + - - +
299A ASN* 5.3 10.1 - - - +
359A THR* 3.7 0.2 - - - -
360A GLN* 2.7 84.9 + - + +
362A GLN* 2.4 42.4 + - - +
375A LEU* 4.2 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 2.7 31.4 + - - +
285A SER* 3.9 0.3 - - - -
286A PHE* 3.0 47.6 + - + +
296A VAL* 5.5 1.6 - - + -
297A ARG* 1.3 73.1 - - - +
299A ASN* 1.3 62.6 + - - +
357A VAL* 3.8 12.3 - - + +
358A ASP 3.2 15.3 - - - +
359A THR* 3.3 25.8 + - + +
1009A FTT 3.3 27.5 - - - +
1100A DDQ 3.4 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 3.7 19.7 + - + +
108A GLY* 4.8 4.8 - - - -
109A LEU* 3.5 24.7 - - + +
155A ARG* 5.7 0.2 + - - -
284A TYR 3.7 3.5 - - - +
285A SER* 3.3 27.7 + - - -
286A PHE 4.3 1.1 + - - +
297A ARG* 5.3 12.0 - - - +
298A GLN* 1.3 72.8 - - - +
300A LEU* 1.3 60.7 + - - +
357A VAL* 3.3 2.3 - - - -
358A ASP* 2.9 34.7 + - + +
360A GLN* 5.1 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.5 4.5 - - - +
283A GLY* 3.0 7.9 - - - -
284A TYR* 3.0 81.7 + - + +
298A GLN 4.2 0.4 - - - -
299A ASN* 1.3 76.1 - - - +
301A ARG* 1.3 72.7 + - - +
355A PHE* 3.6 23.8 - - + -
356A SER 3.2 8.5 - - - +
357A VAL* 3.3 26.9 - - + -
1009A FTT 4.3 3.6 - - + -
1011A FTT 4.4 18.2 - - + -
1012A DAO 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 2.6 42.5 + - - +
107A ASN* 4.4 6.2 - - - +
109A LEU* 3.1 38.0 + - + +
110A LYS 3.4 19.6 + - - -
111A LEU* 3.7 17.0 - - - +
232A LEU 5.8 1.3 - - - -
281A MET* 4.0 28.8 - - - -
282A VAL 3.6 13.5 - - - +
283A GLY* 4.5 1.3 - - - -
300A LEU* 1.3 84.1 - - - +
302A PHE* 1.3 72.6 - - - +
303A ALA* 4.4 4.4 - - + +
354A ASN* 3.8 1.5 + - - +
355A PHE* 3.4 4.9 - - - -
356A SER* 2.7 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LYS 4.1 0.2 - - - +
281A MET* 3.2 6.1 - - - +
282A VAL* 2.7 43.6 + - + +
300A LEU* 4.8 0.4 - - - +
301A ARG* 1.3 77.4 - - - +
303A ALA* 1.3 76.9 + - - +
304A GLU* 4.4 0.7 - - + -
353A GLN* 3.8 16.4 - - + -
354A ASN 3.4 12.8 - - - -
355A PHE* 3.9 14.8 - - + -
382A ARG* 4.8 0.2 - - - -
1011A FTT 3.5 69.1 - - + -
1012A DAO 4.5 1.8 - - - -
1013A FTT 3.6 44.4 - - + -
1014A MYR 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 5.8 2.0 - - + -
280A LYS 3.3 11.0 - - - +
281A MET* 4.2 15.9 - - + -
301A ARG* 5.1 5.8 - - + +
302A PHE* 1.3 84.7 - - - +
304A GLU* 1.3 60.6 + - - +
305A ASN* 4.0 20.2 - - - +
352A LEU 3.7 0.4 - - - +
353A GLN* 3.0 6.9 - - - +
354A ASN* 2.7 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN* 4.2 1.0 - - - +
279A GLU* 4.1 0.2 - - - -
280A LYS* 2.9 34.4 + - + +
302A PHE* 4.3 2.4 - - + -
303A ALA* 1.3 73.8 - - - +
305A ASN* 1.3 69.8 + - - +
306A LYS* 4.2 19.6 + - - +
351A LYS* 4.2 18.0 + - + +
352A LEU 3.1 6.3 - - - +
353A GLN* 2.5 30.3 + - - +
1013A FTT 4.0 4.4 + - - +
1014A MYR 4.0 30.5 - - + +
2001A PO4 2.7 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 5.7 2.0 - - - +
112A GLN 5.6 1.2 + - - -
117A ASN* 3.0 16.8 + - - +
118A ASP 6.2 1.1 - - - -
119A ALA* 4.1 16.6 - - + +
277A ARG* 5.7 1.6 - - + -
278A ASN* 3.1 9.4 - - - +
279A GLU* 3.2 29.7 - - + +
280A LYS 3.4 7.1 + - - +
281A MET* 4.4 4.7 - - - +
303A ALA* 4.0 18.1 - - - +
304A GLU* 1.3 83.6 - - - +
306A LYS* 1.3 64.8 + - - +
351A LYS* 3.6 1.0 - - - +
352A LEU* 2.9 47.9 + - + +
354A ASN* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 3.5 4.7 - - - -
277A ARG* 3.2 6.6 - - - +
278A ASN* 2.6 59.7 + - + +
280A LYS* 4.3 16.1 - - - +
304A GLU* 4.2 17.0 + - + -
305A ASN* 1.3 79.9 - - - +
307A THR* 1.3 63.3 + - - +
350A GLU 3.4 14.1 - - - +
351A LYS* 3.7 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 4.9 0.2 + - - -
116A TYR* 3.4 35.6 + - + +
117A ASN* 3.6 15.9 - - - +
275A TYR* 3.9 14.9 - - - -
276A SER 2.6 21.4 + - - -
277A ARG* 4.3 8.2 - - - +
306A LYS* 1.3 79.1 - - - +
308A SER* 1.4 65.1 + - - +
309A GLN* 5.4 0.3 + - - -
348A ASP* 4.1 2.9 - - - +
349A ASP* 3.5 2.9 + - - +
350A GLU* 2.9 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A THR* 6.4 0.7 - - - -
275A TYR* 3.6 0.7 - - - -
276A SER* 2.8 43.9 + - - +
307A THR* 1.4 78.4 + - - +
309A GLN* 1.3 65.8 + - - +
348A ASP* 3.2 14.6 - - - -
349A ASP* 3.7 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 3.5 31.1 + - - +
244A TYR* 5.4 0.7 - - - -
274A THR* 2.9 17.3 - - - +
275A TYR* 3.0 47.6 + - + -
307A THR* 5.4 0.4 + - - -
308A SER* 1.3 78.5 - - - +
310A ASN* 1.3 66.7 + - - +
311A SER* 2.9 26.4 + - - +
346A VAL* 3.8 19.3 - - + +
347A VAL* 3.2 4.3 - - - +
348A ASP* 2.8 43.5 + - + +
1108A GOL 5.3 1.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
272A ASN 4.1 2.3 - - - +
273A ASN* 3.2 5.5 - - - -
274A THR* 2.7 48.7 + - + +
309A GLN* 1.3 79.8 + - - +
311A SER* 1.3 61.7 + - - +
346A VAL 3.4 4.3 - - - -
347A VAL* 3.4 27.7 - - - +
423A PHE* 3.6 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASN* 3.2 10.9 + - - +
274A THR 4.0 2.8 + - - -
275A TYR* 4.0 7.8 - - - +
309A GLN* 2.9 32.1 + - - +
310A ASN* 1.3 80.3 + - - +
312A VAL* 1.3 63.9 + - - +
313A TYR* 3.7 8.5 + - - -
345A TYR* 3.0 4.2 - - - -
346A VAL* 2.6 42.4 + - - -
423A PHE* 3.4 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 3.4 24.3 - - - +
269A GLY* 3.3 7.1 + - - -
270A ALA* 3.5 15.7 - - + +
273A ASN* 2.5 30.6 + - - +
311A SER* 1.3 73.7 - - - +
313A TYR* 1.3 62.7 + - - +
343A ARG* 3.6 19.7 - - + +
344A LYS 3.2 14.6 - - - +
345A TYR* 3.6 12.1 - - + -
397A VAL* 3.7 18.8 - - + -
421A PHE* 4.2 20.6 - - + -
423A PHE* 4.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR 5.5 1.8 - - - +
245A GLY* 4.8 5.8 - - - -
246A TRP* 3.8 36.8 - + + +
268A GLU* 3.5 7.4 - - - +
311A SER* 3.8 9.9 - - - +
312A VAL* 1.3 76.7 - - - +
314A GLY* 1.3 80.6 + - - +
315A TYR* 4.0 12.0 - + - -
343A ARG* 3.2 8.1 - - - -
344A LYS* 2.8 54.6 + - + +
345A TYR* 3.5 37.2 - - - -
346A VAL* 4.5 4.3 - - + -
391A PHE* 5.0 4.8 - + - -
392A GLY 4.9 1.7 + - - -
1108A GOL 3.3 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.5 34.6 + - - +
268A GLU* 2.8 23.4 + - - +
313A TYR* 1.3 92.4 - - - +
315A TYR* 1.3 57.0 - - - -
316A GLY 3.8 1.6 - - - -
341A LEU* 4.5 5.6 - - - -
342A ALA 3.8 5.8 - - - -
343A ARG* 4.3 4.7 - - - -
707A TYR 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.7 31.4 - + - -
313A TYR* 4.0 12.8 - + - -
314A GLY* 1.3 71.9 - - - -
316A GLY* 1.3 62.6 + - - +
322A ALA* 3.9 28.7 - - + +
323A ASN* 3.0 34.2 + - - -
342A ALA* 2.7 21.9 + - + +
344A LYS* 3.4 42.5 + - + -
707A TYR* 3.7 30.7 + + - +
1108A GOL 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PRO* 4.0 12.2 - - - +
314A GLY 3.8 0.8 - - - -
315A TYR* 1.3 78.5 - - - +
317A VAL* 1.3 62.2 + - - -
320A ASP* 4.6 3.8 - - - -
323A ASN* 4.2 0.4 - - - -
341A LEU* 2.9 14.7 - - - +
342A ALA* 2.7 32.6 + - - +
706A THR 5.3 0.2 - - - -
707A TYR* 3.5 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PRO* 4.1 6.1 - - + +
250A GLU* 3.5 47.3 - - + +
256A LEU* 5.1 0.2 - - + -
316A GLY* 1.3 74.1 - - - -
318A CYS* 1.3 57.5 + - - +
319A SER* 3.0 16.8 - - - +
320A ASP* 2.9 23.1 + - + +
323A ASN* 2.9 16.4 + - - -
337A LYS 3.8 7.0 - - - +
338A GLY* 4.0 15.5 - - - +
340A TYR 2.8 21.3 - - - +
402A LEU* 3.9 18.8 - - + -
----------------------------------------------------------
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