Contacts of the strand formed by residues 386 - 398 (chain A) in PDB entry 2CW9
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 GLY 386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A MSE 3.8 7.9 - - - -
383A VAL* 3.0 39.1 + - - +
384A GLU 3.2 1.0 + - - -
385A GLN* 1.3 80.1 - - - +
387A PRO* 1.3 74.7 - - - +
426A CYS* 3.9 4.5 - - - -
427A ARG 4.0 1.3 - - - -
429A GLN* 5.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.7 21.8 - - + +
302A GLU* 4.5 2.7 - - + +
303A ILE* 3.8 24.0 - - + +
381A LYS 4.0 0.2 - - - +
382A MSE 3.8 23.3 - - + -
386A GLY* 1.3 84.5 - - - +
388A VAL* 1.3 59.2 + - - +
426A CYS* 3.5 2.1 - - - -
427A ARG* 3.1 42.7 + - + +
429A GLN* 3.8 29.4 - - + +
438A TRP* 3.9 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.8 2.3 - - - +
380A GLY* 3.3 5.0 - - - -
381A LYS* 2.7 58.8 + - + +
383A VAL* 3.6 38.1 - - + -
387A PRO* 1.3 77.8 - - - +
389A LEU* 1.3 74.5 + - - +
390A ILE* 4.0 3.4 - - + -
424A ALA* 4.0 25.4 - - + -
425A LEU 3.3 9.9 - - - +
426A CYS* 4.0 7.0 - - + -
441A LEU* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A MSE 4.1 22.0 - - - -
299A VAL* 4.1 17.3 - - + -
300A LEU* 5.4 3.6 - - + -
303A ILE* 4.1 7.6 - - + -
310A PHE* 3.7 27.1 - - + -
312A LYS* 6.4 0.2 - - + -
315A PHE* 3.7 22.7 - - + -
377A LEU* 3.8 21.1 - - + -
379A MSE 3.8 1.1 - - - -
380A GLY* 4.6 0.9 - - - -
388A VAL* 1.3 81.5 - - - +
390A ILE* 1.3 62.6 + - - +
391A ILE* 3.9 2.2 + - - +
423A TRP 3.8 1.0 - - - +
425A LEU* 3.0 32.2 + - - +
438A TRP* 3.5 29.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.7 2.9 - - + -
377A LEU* 3.6 3.1 - - - +
378A ALA* 2.8 31.2 + - + +
379A MSE 2.9 59.9 + - + +
381A LYS* 4.3 21.1 - - + +
388A VAL* 4.0 13.9 - - + -
389A LEU* 1.3 73.9 - - - +
391A ILE* 1.3 63.4 + - - +
422A VAL* 3.6 30.5 - - + -
423A TRP 3.3 6.1 - - - +
424A ALA* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 4.1 26.2 - - + -
316A LEU* 4.1 11.7 - - + -
319A CYS* 3.9 21.5 - - + -
324A ILE* 4.0 27.1 - - + -
375A VAL* 4.9 3.4 - - + -
376A ASP 3.2 14.4 - - - +
377A LEU* 4.2 6.1 - - + -
378A ALA 4.3 0.2 - - - +
389A LEU 4.6 4.3 - - - +
390A ILE* 1.3 78.0 - - - +
392A THR* 1.3 71.1 + - - +
393A PHE* 4.7 3.8 - - + -
422A VAL* 3.4 2.4 - - - +
423A TRP* 2.9 51.8 + - + +
425A LEU* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 4.0 22.3 + - - +
283A VAL* 4.2 10.0 - - + +
284A THR* 4.6 4.8 + - - +
287A LEU* 4.2 7.9 - - + -
374A ASN 3.5 0.4 - - - +
375A VAL* 3.4 3.3 - - - +
376A ASP* 2.9 36.5 + - - +
378A ALA* 4.0 20.6 - - + -
391A ILE* 1.3 81.1 - - - +
393A PHE* 1.3 68.7 + - - +
420A LEU* 4.6 8.2 - - - +
421A TYR 3.1 15.9 - - - +
422A VAL* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 5.7 0.4 - - - -
324A ILE* 3.6 39.7 - - + -
328A LEU* 4.2 6.1 - - + -
372A ILE* 4.3 8.5 - - + -
373A ASP 3.7 7.4 - - - +
374A ASN 3.5 9.6 - - - -
375A VAL* 4.0 16.8 - - + -
391A ILE* 4.7 5.2 - - + -
392A THR* 1.3 82.8 - - - +
394A GLN* 1.3 73.6 + - - +
395A ALA* 3.9 12.6 - - + -
420A LEU* 3.7 4.7 - - - +
421A TYR* 2.9 68.3 + + + +
423A TRP* 3.6 38.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 2.8 41.0 + - - +
279A LEU* 4.4 11.5 - - - +
280A THR* 3.0 19.3 + - - +
372A ILE* 3.6 1.0 - - - -
373A ASP* 2.8 47.1 + - - +
374A ASN* 3.5 12.7 + - + +
393A PHE* 1.3 75.9 - - - +
395A ALA* 1.3 63.9 + - - +
418A ARG* 4.7 20.5 + - + +
419A MSE 3.2 9.0 - - - +
420A LEU* 3.3 27.7 - - + +
448A THR* 5.1 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 4.4 11.0 - - + -
371A ASP 3.3 12.3 - - - +
372A ILE* 4.3 7.6 - - + -
393A PHE* 3.9 20.6 + - + -
394A GLN* 1.3 76.7 - - - +
396A GLN* 1.3 62.7 + - - +
397A LEU* 4.0 6.9 + - + -
417A LEU 3.5 1.4 - - - +
418A ARG* 3.6 2.5 - - - +
419A MSE 2.8 39.7 + - - +
421A TYR* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 2.8 53.9 + - + +
371A ASP* 3.0 27.6 + - + +
395A ALA* 1.3 76.1 - - - +
397A LEU* 1.3 63.8 + - - +
416A VAL* 3.9 21.8 - - + +
417A LEU 3.2 5.6 - - - +
418A ARG* 3.4 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 4.2 16.4 - - + -
332A ILE* 4.4 8.5 - - + -
368A ARG 3.7 4.7 - - - +
369A ILE* 3.3 38.4 - - + -
370A LEU 4.6 0.2 - - - +
395A ALA* 4.7 8.5 - - + +
396A GLN* 1.3 81.8 - - - +
398A VAL* 1.3 64.1 + - - +
399A MSE 4.0 25.1 - - + -
415A LYS 3.9 0.3 - - - +
416A VAL* 3.6 2.9 - - - -
417A LEU* 2.7 45.4 + - + +
419A MSE 4.4 10.1 - - + -
421A TYR* 3.5 28.0 - - + +
1001A 1PE 4.3 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A HIS 5.8 0.4 - - - +
367A SER* 3.1 5.9 - - - -
368A ARG* 3.0 40.8 + - + +
370A LEU* 5.3 9.9 - - + -
397A LEU* 1.3 78.3 - - - +
399A MSE 1.3 62.3 + - - +
400A VAL* 4.8 5.2 - - + -
412A ASP 4.2 1.8 - - - +
413A PRO* 3.7 30.1 - - + +
415A LYS 3.9 17.9 - - - +
416A VAL* 4.4 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