Contacts of the strand formed by residues 363 - 379 (chain A) in PDB entry 1IVV
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 ASN 363 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A HIS 3.5 3.4 - - - -
356A SER* 3.0 35.6 - - - +
357A ASP 3.7 3.5 + - - +
361A GLY 3.8 8.1 + - - +
362A ILE* 1.3 78.1 - - - +
364A TYR* 1.3 59.1 + - - +
365A THR* 4.3 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 4.3 11.5 - - + +
354A LYS* 3.1 4.3 - - - +
355A HIS 2.8 40.5 + - - +
356A SER* 5.1 0.2 + - - -
362A ILE* 4.4 5.6 - - + -
363A ASN* 1.3 72.7 - - - +
365A THR* 1.3 66.8 + - - +
366A ARG* 3.3 57.4 + - + +
622A VAL 4.5 11.3 + - - -
623A LEU* 4.6 9.1 + - - +
625A VAL* 4.9 0.2 - - - +
204B TYR* 3.8 39.7 + + + +
205B THR* 3.7 18.6 - - - -
601B ILE* 3.5 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 3.9 20.6 - - + -
353A ALA 3.5 5.2 - - - +
354A LYS* 3.0 28.5 + - + +
363A ASN* 4.3 1.6 + - - +
364A TYR* 1.3 78.3 + - - +
366A ARG* 1.3 87.5 + - - +
627A ALA* 4.7 4.2 - - - +
315B CYS* 4.2 20.0 - - + +
316B ASP* 3.5 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 3.6 5.7 - - - +
352A LEU* 2.7 39.2 + - + -
353A ALA* 2.8 15.8 + - + +
364A TYR* 3.3 56.4 + - + +
365A THR* 1.3 94.9 + - - +
367A ARG* 1.3 56.7 + - - +
625A VAL* 3.2 35.8 + - + -
626A PRO* 3.2 19.4 + - - +
627A ALA* 3.7 31.8 - - - +
205B THR* 4.9 3.8 + - - +
213B LEU* 5.4 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASP* 2.8 41.2 + - - +
350A GLY* 3.0 27.3 + - - +
351A ILE* 3.9 6.4 - - + +
352A LEU* 3.5 9.8 - - - +
365A THR* 5.8 0.2 - - + -
366A ARG* 1.3 76.0 - - - +
368A ASN* 1.3 65.2 + - - +
369A ARG* 5.2 0.3 - - - +
392A LEU* 3.8 10.7 - - - +
625A VAL* 5.3 2.6 - - - +
627A ALA 5.4 5.9 + - - +
628A ASN* 5.7 10.9 + - + +
217B GLN* 5.4 2.8 - - - +
314B GLY 4.0 14.4 - - - +
315B CYS* 3.1 25.6 + - - +
316B ASP 3.0 29.9 + - - -
318B LEU* 3.7 27.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASP* 3.9 6.8 - - - +
349A TRP* 3.0 42.6 + - + +
350A GLY 2.7 8.3 + - - +
351A ILE 4.2 2.3 - - - +
352A LEU* 3.5 31.0 - - + +
367A ARG* 1.3 76.2 - - - +
369A ARG* 1.3 83.7 + - - +
391A TYR* 3.8 17.7 - - - +
392A LEU* 3.3 31.1 - - - +
393A ASP* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 3.3 11.5 + - - -
240A TRP* 3.5 20.6 - - + +
241A GLU* 5.1 0.9 - - - -
346A GLU* 3.1 30.0 + - - +
347A GLU 3.2 19.3 - - - +
348A ASP* 4.3 2.0 - - - +
349A TRP* 3.8 5.4 - - - +
367A ARG 5.2 0.7 - - - +
368A ASN* 1.3 93.0 + - - +
370A ARG* 1.3 62.2 + - - +
391A TYR* 3.7 2.1 - - - -
392A LEU* 3.5 28.8 + - + +
628A ASN* 5.0 7.9 - - - +
217B GLN* 3.8 34.2 + - - +
218B LYS 2.9 29.9 + - - -
219B PRO* 4.6 1.0 - - - +
220B ILE* 3.7 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TRP* 3.9 3.8 - - - -
346A GLU* 3.1 4.7 - - - +
347A GLU* 2.7 77.9 + - + +
349A TRP* 3.3 44.3 - - + -
369A ARG* 1.3 74.8 - - - +
371A MET* 1.4 63.3 + - - +
372A VAL* 3.7 3.5 + - - +
389A TYR* 3.4 52.4 + - + -
390A LEU 3.2 7.9 - - - +
391A TYR* 3.0 41.8 + - + -
397A GLU* 4.0 3.4 + - - -
399A GLU* 4.6 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.5 52.3 - - + -
238A ILE* 3.9 14.6 - - + -
240A TRP* 3.5 36.7 - - + -
344A MET* 4.1 2.0 - - + -
345A HIS 3.6 21.3 - - - +
346A GLU* 4.3 1.8 - - - +
370A ARG* 1.4 71.0 - - - +
372A VAL* 1.3 59.7 + - - +
373A ILE* 3.6 31.2 + - + +
388A TRP 3.4 1.6 - - - +
389A TYR* 3.3 8.1 - - - -
390A LEU* 2.8 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A CYS 3.4 1.2 - - - +
344A MET* 3.3 2.9 - - - -
345A HIS* 2.6 61.6 + - + +
347A GLU* 3.5 39.3 - - + +
370A ARG* 3.8 12.6 - - - +
371A MET* 1.3 78.0 - - - +
373A ILE* 1.3 70.4 + - - +
374A SER* 4.4 4.0 - - - +
387A TYR* 4.0 18.8 - - + -
388A TRP 3.5 3.1 - - - +
389A TYR* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ILE* 3.3 33.2 - - + -
245A LEU* 4.8 5.2 - - + -
247A VAL* 3.9 26.2 - - + -
255A VAL* 4.0 16.1 - - + +
257A LEU* 4.0 16.8 - - + -
342A ILE* 4.2 10.1 - - + -
343A CYS 3.2 2.0 - - - -
344A MET* 3.7 10.1 - - + -
371A MET* 3.6 17.5 - - + +
372A VAL* 1.3 85.1 - - - +
374A SER* 1.3 63.9 + - - +
386A PHE 3.9 0.5 - - - +
387A TYR* 3.7 0.5 - - - -
388A TRP* 3.0 39.4 + - + +
390A LEU* 5.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 4.9 1.8 - - - -
311A LEU* 4.2 2.2 - - - +
317A CYS* 4.6 4.7 - - - -
342A ILE* 3.4 7.8 - - - +
343A CYS* 2.9 51.1 + - - +
345A HIS* 5.0 1.4 - - - -
372A VAL* 4.4 4.5 - - - +
373A ILE* 1.3 77.4 - - - +
375A PHE* 1.3 66.7 + - - +
386A PHE 3.2 15.3 - - - -
387A TYR* 3.4 34.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 4.5 3.8 - + + -
253A GLU 4.1 0.9 - - - -
254A GLY* 3.6 21.3 - - - -
255A VAL* 3.3 41.5 - - + -
304A VAL* 4.1 17.0 - - + -
308A ALA* 4.1 13.0 - - + -
311A LEU* 4.3 6.1 - - - -
341A GLY 3.2 23.1 - - - +
342A ILE* 4.6 0.7 - - + -
374A SER* 1.3 76.6 - - - +
376A PHE* 1.3 71.6 - - - +
377A THR* 4.2 20.6 - - + -
384A TYR 4.0 0.2 - - - +
385A GLY* 3.4 2.1 - - - -
386A PHE* 2.9 69.4 + + + +
387A TYR* 5.1 0.7 - - - -
388A TRP* 6.3 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA* 3.2 8.8 - - - +
309A ASN* 2.8 37.4 + - - +
311A LEU* 3.8 21.7 - - + +
316A ASP* 5.4 0.9 - - + -
341A GLY 4.7 0.4 + - - -
375A PHE* 1.3 75.6 - - - +
377A THR* 1.3 65.9 + - - +
383A ASP* 3.5 17.7 - - + -
384A TYR 3.3 32.1 - - - -
385A GLY* 3.6 22.0 - - - -
387A TYR* 3.6 22.4 - + - -
401A LYS* 4.3 7.2 - - + -
403A THR* 3.7 17.3 - - - -
604A VAL* 5.4 0.2 - - + -
351B ILE* 4.2 13.7 - - + -
354B LYS* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 2.7 45.1 + - + -
307A TYR* 3.2 19.0 - - - +
309A ASN* 3.8 1.8 - - - -
375A PHE* 4.2 7.9 - - + -
376A PHE* 1.3 75.6 - - - +
378A THR* 1.3 65.5 + - - +
379A ILE* 4.3 5.4 + - + +
383A ASP* 3.2 5.4 - - - +
384A TYR* 2.9 58.3 + - + +
386A PHE* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 3.1 32.8 + - - +
309A ASN* 3.0 19.9 + - - -
377A THR* 1.3 74.3 + - - +
379A ILE* 1.3 63.9 + - - +
380A GLY 3.6 19.1 + - - +
382A DAH 3.4 5.4 - - - +
383A ASP* 3.0 22.3 + - - +
356B SER* 3.3 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TYR* 4.1 23.6 - - + -
298A ASP* 3.3 36.3 - - + +
302A TYR* 4.2 28.9 - - + -
304A VAL* 4.5 8.1 - - - -
307A TYR* 3.7 28.7 - - + -
377A THR* 4.3 12.3 + - + +
378A THR* 1.3 74.1 - - - +
380A GLY* 1.3 62.1 + - - +
381A ASN* 3.2 8.8 + - - +
382A DAH 2.8 19.8 + - + +
384A TYR* 4.3 17.0 - - + -
----------------------------------------------------------
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