Contacts of the strand formed by residues 336 - 354 (chain X) in PDB entry 4HSC
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 PRO 336 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113X ILE* 4.5 17.0 - - + -
116X LEU* 3.6 19.5 - - + -
118X TYR* 5.2 1.5 + - - +
178X LEU* 6.0 3.8 - - + -
179X GLN 3.4 7.2 - - - +
180X LEU* 4.8 1.1 - - + -
193X VAL* 5.8 3.4 - - + -
316X PHE* 5.7 3.1 - - + -
325X LEU* 6.0 1.3 - - + -
330X VAL* 4.1 23.1 - - + -
334X ALA 3.9 0.2 - - - -
335X PRO* 1.3 89.8 - - + +
337X LEU* 1.3 61.8 + - - +
437X PHE* 3.7 8.0 - - - +
438X LEU* 3.0 50.5 + - + -
439X LYS* 5.0 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124X LEU* 4.7 1.8 - - + -
178X LEU* 3.2 13.0 - - - +
179X GLN* 2.7 37.7 + - + +
180X LEU 3.9 2.2 - - - +
181X ALA* 3.7 26.5 - - + +
185X PHE* 3.6 41.7 - - + -
336X PRO* 1.3 75.6 - - - +
338X PHE* 1.3 60.0 + - - +
339X VAL* 4.2 0.9 - - + -
435X SER* 4.3 9.6 - - - -
436X VAL 3.4 4.5 - - - +
437X PHE* 3.6 39.3 - - + -
438X LEU* 4.6 2.9 - - - -
444X ALA* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176X ALA* 3.7 26.7 - - + -
177X ALA 3.6 2.0 - - - -
178X LEU* 3.9 17.0 - - + -
197X ARG* 4.2 1.3 - - - -
200X GLN* 3.6 16.8 - - - -
306X ALA* 3.8 20.2 - - + -
307X ASN 3.6 19.1 - - - -
308X LEU* 4.0 20.2 - - + -
309X PRO* 4.0 15.9 - - + -
315X VAL* 4.0 15.5 - - + -
337X LEU* 1.3 73.8 - - - +
339X VAL* 1.3 75.4 + - - +
340X SER* 3.4 1.3 + - - -
435X SER* 3.2 3.3 - - - -
436X VAL* 2.7 45.2 + - + +
438X LEU* 4.1 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173X THR* 4.8 1.3 - - + -
174X TYR 3.3 26.9 - - - +
175X PRO* 3.7 0.8 - - + -
176X ALA* 2.7 29.0 + - - +
177X ALA* 2.9 28.6 + - + +
179X GLN* 4.2 13.0 - - + +
306X ALA* 4.0 0.7 - - - +
337X LEU* 5.7 0.7 - - + +
338X PHE* 1.3 73.6 - - - +
340X SER* 1.3 61.9 + - - +
341X ASN 3.8 5.2 - - - +
342X VAL* 3.7 23.3 - - + -
433X TYR* 3.8 29.6 - - + -
434X THR 3.6 12.3 - - - +
435X SER* 4.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175X PRO* 5.5 0.4 - - - -
305X SER* 3.2 6.8 - - - -
306X ALA* 2.8 28.6 + - - +
308X LEU* 3.7 28.0 - - - -
338X PHE* 3.4 10.6 + - - -
339X VAL* 1.3 73.9 - - - +
341X ASN* 1.3 61.4 + - - +
434X THR* 2.9 31.3 + - - -
436X VAL* 4.0 15.5 - - - +
443X ILE* 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175X PRO* 5.4 0.4 - - - -
303X THR* 3.3 36.1 + - - +
304X VAL 3.3 8.1 - - - -
305X SER* 3.4 20.5 - - - -
339X VAL* 3.5 2.0 + - - +
340X SER* 1.3 82.8 + - - +
342X VAL* 1.3 72.0 + - - +
343X ALA* 4.0 2.4 - - - +
433X TYR* 3.2 5.9 - - - +
434X THR* 2.9 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165X ILE* 4.0 14.4 - - + -
173X THR* 4.4 4.7 - - + +
174X TYR* 3.8 7.6 - - - -
175X PRO* 3.7 29.4 - - + -
303X THR* 3.2 3.5 - - - -
304X VAL 2.9 31.3 + - - -
339X VAL* 3.7 12.8 - - + -
341X ASN* 1.3 80.7 + - - +
343X ALA* 1.3 68.3 + - - +
344X TYR* 3.4 34.7 - - + +
430X PRO* 4.2 2.5 - - + -
432X SER 3.5 11.4 - - - +
433X TYR* 3.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300X ILE* 4.2 21.8 - - + -
302X TYR 3.8 3.8 - - - -
303X THR* 4.0 16.4 - - + -
341X ASN* 4.0 2.6 - - - +
342X VAL* 1.3 73.2 - - - +
344X TYR* 1.3 61.3 + - - +
430X PRO* 3.6 3.8 - - - +
431X ILE* 2.8 28.8 + - + -
432X SER* 2.9 30.6 + - - +
433X TYR* 4.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 344 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174X TYR* 4.9 2.3 - - - +
175X PRO* 3.4 15.4 - - - +
229X ILE* 3.4 27.8 - - + +
300X ILE* 3.6 1.4 - - - -
301X PHE* 2.7 28.9 + - - +
302X TYR* 2.8 58.3 + + + +
304X VAL* 3.6 19.1 - - + -
342X VAL* 3.4 33.7 - - + +
343X ALA* 1.3 72.6 - - - +
345X GLY* 1.3 52.2 + - - +
428X ALA* 4.0 5.8 - - + -
429X TYR* 3.2 7.2 - - - +
430X PRO* 3.7 36.1 - - + -
431X ILE* 4.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299X GLN 3.3 10.3 - - - -
301X PHE* 3.8 9.6 - - - -
344X TYR* 1.3 75.3 - - - +
346X ARG* 1.3 67.7 + - - +
428X ALA* 3.6 13.2 - - - +
429X TYR* 2.8 40.3 + - - +
431X ILE* 3.8 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 346 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297X TYR 3.6 0.9 - - - +
298X LYS* 3.7 0.9 - - - -
299X GLN* 2.7 43.0 + - - +
301X PHE* 3.4 24.7 - - + -
345X GLY* 1.3 79.8 - - - +
347X THR* 1.3 60.8 + - - +
348X VAL* 5.3 0.4 - - - -
393X VAL* 4.0 11.5 - - + +
394X LEU 3.3 23.2 + - - -
395X GLY* 4.3 3.8 - - - -
419X ASN* 3.3 43.4 + - + +
426X ASN* 4.6 10.2 + - - +
427X PRO* 3.1 37.9 + - - +
429X TYR* 3.4 25.4 + - - -
431X ILE* 3.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296X ALA* 5.5 0.2 - - + -
297X TYR 3.3 9.9 - - - +
298X LYS* 4.4 16.1 - - + +
346X ARG* 1.3 74.0 + - - +
348X VAL* 1.3 67.7 + - - +
349X PHE* 3.5 36.1 - - + -
392X VAL 3.9 0.3 - - - +
393X VAL* 3.6 2.1 - - - +
394X LEU* 3.2 47.0 + - + +
431X ILE* 3.4 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 348 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296X ALA* 3.5 2.1 - - - -
297X TYR* 2.8 47.9 + - + +
299X GLN* 5.4 2.9 - - + +
346X ARG 5.3 1.1 - - - -
347X THR* 1.3 79.2 - - - +
349X PHE* 1.3 74.1 + - - +
350X VAL* 4.2 12.8 - - + -
391X ALA* 4.7 1.6 - - + -
392X VAL 3.3 9.9 - - - +
393X VAL* 4.2 12.1 - - + -
415X VAL* 4.4 13.0 - - + -
416X ILE* 4.3 21.1 - - + +
419X ASN* 3.8 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 349 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269X VAL* 3.5 38.4 - - + -
273X ILE* 3.6 25.8 - - + -
274X LEU* 4.2 15.5 - - + -
277X THR* 3.7 8.7 - - - -
278X LEU* 3.9 18.7 - - + +
295X ALA 3.4 4.7 - - - +
296X ALA* 4.1 12.1 - - + -
347X THR* 3.5 17.7 - - + -
348X VAL* 1.3 79.7 - - - +
350X VAL* 1.3 62.7 + - - +
390X THR 3.8 0.3 - - - +
391X ALA* 3.3 5.2 - - - -
392X VAL* 2.9 52.7 + - + +
394X LEU* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278X LEU* 4.6 1.1 - - - -
293X MET 3.8 0.5 - - - +
294X ILE* 3.1 8.1 - - - +
295X ALA* 2.8 41.4 + - + +
297X TYR* 4.1 9.9 - - + -
348X VAL* 4.2 9.0 - - + -
349X PHE* 1.3 79.2 - - - +
351X LYS* 1.3 66.0 + - - +
352X LEU* 4.0 19.8 - - + +
369X LEU* 4.3 10.8 - - + -
390X THR 3.3 9.2 - - - +
391X ALA* 4.6 1.8 - - + -
409X PHE* 4.3 9.0 - - + -
412X ILE* 3.7 33.4 - - + -
416X ILE* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278X LEU* 3.1 38.4 + - + +
279X GLY* 2.7 29.5 + - - +
280X ILE* 5.2 0.2 - - + -
292X VAL* 3.7 25.1 - - + -
293X MET 3.4 2.9 - - - +
294X ILE* 4.2 9.2 - - + -
350X VAL* 1.3 76.2 - - - +
352X LEU* 1.3 70.9 + - - +
353X GLU* 2.7 31.5 + - + +
388X SER 3.8 0.8 - - - +
389X PHE* 3.4 7.6 - - - +
390X THR* 2.8 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292X VAL* 3.2 5.7 - - - +
293X MET* 2.7 53.3 + - + +
350X VAL* 4.0 14.4 - - + +
351X LYS* 1.3 80.1 - - - +
353X GLU* 1.3 60.2 + - - +
365X PHE* 3.3 53.9 - - + +
368X ALA* 4.1 6.1 - - + -
369X LEU* 3.9 24.9 - - + -
388X SER 3.8 3.6 - - - -
389X PHE* 3.8 16.8 - - + -
409X PHE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279X GLY 4.3 1.2 - - - +
281X ASP* 5.4 2.9 + - - +
290X LYS* 3.0 43.1 - - + +
291X LYS 3.5 3.8 - - - -
292X VAL* 4.0 14.3 - - + +
351X LYS* 2.7 43.5 + - + +
352X LEU* 1.3 75.8 - - - +
354X THR* 1.3 64.4 + - - +
365X PHE* 3.9 2.6 - - - -
387X SER* 3.4 3.8 - - - -
388X SER* 2.9 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 354 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290X LYS* 3.5 4.7 - - - +
291X LYS* 2.8 39.7 + - + +
353X GLU* 1.3 74.6 - - - +
355X SER* 1.3 59.0 + - - +
356X SER* 3.1 27.6 + - - +
361X VAL* 3.6 21.3 - - + -
365X PHE* 3.5 17.5 - - + -
383X ILE* 4.2 1.3 + - + -
386X ASN 2.8 22.0 + - - -
387X SER* 3.2 20.0 + - - +
----------------------------------------------------------
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