Contacts of the strand formed by residues 337 - 350 (chain A) in PDB entry 4EWS
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 337 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLN* 2.9 35.4 + - - +
335A ASN 3.3 1.4 + - - -
336A LYS* 1.3 81.1 - - - +
338A VAL* 1.3 63.7 + - - -
339A VAL* 3.5 0.9 + - - +
370A THR* 4.2 5.2 - - - -
371A VAL 3.5 10.8 - - - -
372A GLN* 4.7 2.9 - - - -
450A THR* 3.3 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 5.6 4.0 - - + -
331A ILE* 3.5 32.1 - - + -
332A SER 3.6 5.6 - - - +
333A CYS* 4.8 8.5 - - - +
337A GLY* 1.3 70.7 - - - -
339A VAL* 1.3 59.3 + - - +
340A VAL* 3.9 9.0 + - + -
369A THR 3.7 1.2 - - - +
370A THR* 3.5 0.9 - - - -
371A VAL* 2.8 41.5 + - + +
373A ALA* 6.2 1.1 - - + +
450A THR* 3.6 22.2 - - + +
455A LEU* 4.0 15.0 - - + -
502A 2OB 3.7 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LYS 3.5 1.4 - - - +
331A ILE* 3.4 2.8 - - - -
332A SER* 2.9 61.9 + - - +
334A GLN* 3.3 29.6 - - + +
336A LYS* 5.2 8.3 - - - +
337A GLY 4.3 0.2 - - - +
338A VAL* 1.3 72.9 - - - +
340A VAL* 1.3 60.8 + - - +
341A ASP* 5.1 2.5 - - + +
368A VAL* 3.8 26.0 - - + -
369A THR 3.5 4.0 - - - +
370A THR* 4.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A PRO* 4.2 7.0 - - + -
330A LYS 3.6 3.1 - - - -
331A ILE* 4.2 21.8 - - + -
338A VAL* 4.0 13.7 - - + +
339A VAL* 1.3 75.3 - - - +
341A ASP* 1.3 61.7 + - - +
342A SER* 4.0 14.3 + - - +
367A ILE 3.7 1.9 - - - +
368A VAL* 3.4 2.8 - - - +
369A THR* 2.9 45.6 + - - +
371A VAL* 4.7 0.9 - - + -
502A 2OB 3.8 33.9 - - + +
503A DLP 4.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A MET 4.7 0.2 - - - +
329A PRO* 3.7 1.3 - - - +
330A LYS* 2.9 70.4 + - + +
339A VAL* 4.2 3.1 - - + -
340A VAL* 1.3 71.0 - - - +
342A SER* 1.3 63.1 + - - +
343A SER 4.4 0.3 + - - -
366A ASP* 4.3 19.2 - - - +
367A ILE 3.6 4.4 - - - +
368A VAL* 3.4 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A CYS* 4.4 6.1 - - - -
329A PRO* 4.1 13.7 - - - -
340A VAL* 4.1 5.5 + - - +
341A ASP* 1.3 75.3 + - - +
343A SER* 1.4 58.3 + - - +
344A VAL* 3.6 6.2 + - - +
366A ASP* 3.5 1.7 - - - -
367A ILE* 2.8 45.3 + - - +
502A 2OB 4.4 10.0 - - - +
503A DLP 3.5 40.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A CYS* 3.7 4.3 - - - +
326A LEU* 2.8 46.7 + - - +
327A LYS* 3.8 35.8 + - - +
328A MET 5.7 0.4 + - - -
330A LYS* 6.2 1.0 - - - +
341A ASP 4.4 0.8 + - - -
342A SER* 1.4 68.7 - - - +
344A VAL* 1.3 53.7 + - - +
364A GLU* 5.6 1.6 + - - +
365A GLU 3.5 5.2 + - - -
366A ASP* 2.7 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 4.3 8.1 - - + -
324A HIS 3.6 9.4 - - - +
325A CYS* 4.2 4.0 - - - -
326A LEU* 3.4 10.5 - - - +
342A SER* 4.4 8.7 - - - +
343A SER* 1.3 75.9 - - - +
345A MET* 1.3 59.4 + - - +
346A VAL* 4.1 4.9 - - + -
363A PHE 3.8 0.3 - - - +
364A GLU* 3.5 0.5 - - - -
365A GLU* 2.8 49.8 + - + +
367A ILE* 3.5 32.3 - - + -
502A 2OB 4.1 14.4 - - + -
503A DLP 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A THR 3.2 12.0 - - - +
323A VAL* 3.3 0.9 - - - -
324A HIS* 3.0 48.2 + - + +
326A LEU* 3.8 24.9 - - + -
344A VAL* 1.3 73.1 - - - +
346A VAL* 1.3 60.3 + - - +
347A LYS* 3.9 30.3 - - + -
362A THR* 3.9 20.9 - - + +
363A PHE 3.4 19.7 - - - +
364A GLU* 4.2 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 4.0 6.3 - - + -
322A THR 3.4 2.7 - - - -
323A VAL* 4.0 7.2 - - + -
344A VAL* 4.4 9.2 - - + -
345A MET* 1.3 73.1 - - - +
347A LYS* 1.3 61.8 + - - +
348A PHE* 3.5 28.6 + - + -
361A TYR 3.9 0.7 - - - +
362A THR* 3.6 1.7 - - - -
363A PHE* 2.8 45.6 + - + +
365A GLU* 5.3 2.0 - - + +
413A ILE* 4.0 22.2 - - + -
502A 2OB 3.9 50.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN 3.8 0.9 - - - +
321A VAL* 3.2 9.2 - - - +
322A THR* 2.9 53.8 + - + +
324A HIS* 4.9 10.3 - - + -
345A MET* 3.9 31.0 - - + +
346A VAL* 1.3 76.9 - - - +
348A PHE* 1.3 62.2 + - - +
349A LEU 4.3 0.2 - - - -
361A TYR 3.6 3.6 - - - -
362A THR* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 4.5 3.4 - + - -
320A GLN 3.6 1.3 - - - -
321A VAL* 3.6 21.8 - - + -
346A VAL* 3.5 29.6 - - + -
347A LYS* 1.3 72.4 - - - +
349A LEU* 1.3 61.8 + - - +
350A PHE* 3.5 31.0 - + + -
359A VAL 4.2 1.1 - - - -
360A ALA* 3.3 6.4 - - - +
361A TYR 2.9 34.5 + - - +
363A PHE* 4.3 11.2 - + - -
409A LEU* 3.8 29.8 - - + -
412A MET* 3.7 40.8 - - + -
413A ILE* 3.9 14.1 - - + -
502A 2OB 4.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ALA* 3.5 1.9 - - - -
320A GLN* 2.8 71.2 + - + +
348A PHE* 1.3 73.8 - - - +
350A PHE* 1.3 65.1 + - - +
351A PRO* 3.4 31.1 - - + +
358A SER* 5.6 4.5 - - - -
359A VAL 3.6 1.8 - - - +
360A ALA* 4.1 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 3.9 16.4 - + - -
311A VAL* 3.7 32.5 - - + +
312A VAL* 3.4 28.3 - - + -
315A PHE 6.1 0.2 - - - -
319A ALA* 3.8 14.6 - - + +
320A GLN 5.0 1.6 - - - -
348A PHE* 3.5 42.8 - + + -
349A LEU* 1.3 78.7 - - - +
351A PRO* 1.4 67.4 - - - +
352A ARG* 3.6 11.1 + - - +
358A SER* 3.3 4.6 - - - -
359A VAL* 2.9 46.9 + - + +
409A LEU* 3.9 23.1 - - + -
412A MET* 4.5 1.1 - - + -
----------------------------------------------------------
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