Contacts of the strand formed by residues 364 - 373 (chain C) in PDB entry 2W3S
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 VAL 364 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LEU* 2.7 41.7 + - + +
362C SER* 4.0 3.5 - - - -
363C ALA* 1.3 86.0 - - + +
365C CYS* 1.3 60.0 + - - +
384C PHE* 3.8 27.8 - - + -
385C GLY 3.8 6.5 - - - +
387C MET* 4.2 10.1 - - + -
434C TYR* 5.9 0.2 - - + -
435C ARG* 3.6 37.9 - - + +
438C ALA* 4.2 10.1 - - + -
439C ALA* 4.3 4.7 - - - -
442C MET* 3.6 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 4.3 21.8 - - - -
291C ILE 6.0 0.9 - - - +
292C GLY 5.5 0.7 - - - +
293C ASP* 4.0 17.7 - - - +
296C PRO* 4.4 18.3 - - + +
351C TYR 3.2 14.6 - - - -
352C LYS* 4.5 2.2 - - - -
362C SER* 4.0 14.3 - - - +
364C VAL* 1.3 73.3 - - - +
366C GLY* 1.3 59.0 + - - +
367C CYS* 4.5 7.6 - - - -
383C ALA 3.9 0.3 - - - +
384C PHE* 3.3 8.8 - - - -
385C GLY* 2.8 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C CYS* 3.7 0.5 - - - -
351C TYR* 2.8 45.7 + - - +
365C CYS* 1.3 74.6 - - - +
367C CYS* 1.3 63.9 + - - -
368C LEU* 3.9 5.4 - - - -
383C ALA 3.6 5.2 - - - -
384C PHE* 3.6 20.4 - - - -
442C MET* 3.6 11.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 4.6 0.4 - - - -
296C PRO* 3.6 15.0 - - - +
297C ALA* 3.6 22.2 - - - -
300C ALA* 3.5 23.6 - - + +
348C LEU* 4.7 0.2 - - + -
349C ARG 3.3 5.6 - - - +
350C CYS* 3.4 31.6 - - - -
365C CYS* 4.5 9.9 - - - -
366C GLY* 1.3 78.6 - - - -
368C LEU* 1.3 63.4 + - - +
382C ILE* 3.4 2.3 - - - +
383C ALA 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C LEU* 3.3 2.0 - - - -
349C ARG 2.8 38.2 + - - +
351C TYR* 3.8 33.0 - - + -
366C GLY* 3.8 10.3 - - - +
367C CYS* 1.3 80.4 - - - +
369C ASN* 1.3 60.8 + - - +
370C LEU* 4.9 1.1 - - + -
381C ARG 3.3 3.8 - - - -
382C ILE* 4.1 29.8 - - + -
384C PHE* 5.6 3.4 - - + -
397C PHE* 5.6 0.7 - - + -
442C MET* 4.5 5.6 - - + +
443C ALA* 3.9 21.5 - - + +
446C TYR* 3.2 44.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ALA 3.4 27.9 + - - +
301C MET* 3.7 14.8 + - - +
345C ALA* 3.7 18.8 - - - +
347C GLY* 3.3 10.6 + - - -
348C LEU* 3.2 26.4 + - + +
368C LEU* 1.3 75.9 - - - +
370C LEU* 1.3 65.5 + - - +
371C THR* 5.3 2.5 + - - -
379C THR* 4.1 1.0 - - - +
380C ALA* 3.5 0.9 - - - -
381C ARG* 2.6 41.7 + - + +
446C TYR* 3.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C GLY* 4.2 7.6 - - - -
368C LEU* 4.9 1.6 - - + -
369C ASN* 1.3 89.6 - - - +
371C THR* 1.3 66.3 + - - +
372C LEU* 4.3 7.3 + - + +
377C ILE* 4.1 22.4 - - + -
379C THR 3.2 5.4 - - - +
380C ALA* 3.4 25.1 - - + -
382C ILE* 3.8 21.5 - - + -
401C LEU* 4.5 9.4 - - + -
406C PHE* 3.7 32.5 - - + -
411C ILE* 5.2 2.0 - - + -
446C TYR* 3.1 29.4 + - + +
450C LEU* 5.8 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C ASN* 5.3 2.1 + - - -
370C LEU* 1.3 74.6 + - - +
372C LEU* 1.3 70.0 + - - +
377C ILE* 3.6 1.7 - - - +
378C GLU* 2.7 40.9 + - + +
379C THR* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU* 5.1 8.1 - - + +
371C THR* 1.3 91.0 - - - +
373C LYS* 1.3 59.9 + - - +
374C GLY* 2.9 8.5 + - - +
375C SER* 4.2 16.8 - - - +
376C LYS 3.2 12.3 - - - +
377C ILE* 3.9 11.9 - - + -
378C GLU* 4.5 0.7 - - - -
406C PHE* 3.7 50.7 - - + -
450C LEU* 5.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C LEU* 1.3 66.0 - - - +
374C GLY* 1.3 68.3 + - - +
375C SER 3.7 0.2 - - - -
376C LYS* 2.8 28.5 + - + +
378C GLU* 3.3 41.6 - - + +
----------------------------------------------------------
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