Contacts of the strand formed by residues 345 - 352 (chain B) in PDB entry 2W8B
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 PHE 345 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 4.1 0.5 - - - +
340B SER* 2.8 48.0 + - - -
342B ASP* 4.5 8.5 - - - -
343B GLY 3.4 1.0 - - - -
344B LYS* 1.3 86.7 - - + +
346B MET* 1.3 68.2 + - - +
347B VAL* 4.4 1.8 - - + -
360B LYS* 3.7 36.1 - - + -
361B GLN 3.1 19.1 - - - +
362B ASP* 4.1 3.4 - - + -
363B LEU* 3.5 11.8 - - - +
382B LEU* 3.8 26.2 - - + -
386B GLY* 3.4 32.5 - - - -
406B THR* 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA* 4.8 0.9 - - - -
314B VAL* 4.0 9.2 - - + -
327B ILE* 3.6 23.6 - - + -
328B THR* 3.6 30.7 - - + -
337B ALA* 3.9 19.7 - - - -
338B ASP 3.2 17.9 - - - +
339B VAL* 4.0 14.1 - - + -
345B PHE* 1.3 77.8 - - - +
347B VAL* 1.3 69.7 + - - +
348B MET* 4.1 6.9 - - - +
360B LYS* 3.3 6.2 - - - +
361B GLN* 2.8 57.5 + - + +
363B LEU* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASP 4.3 0.2 - - - +
337B ALA* 3.2 4.7 - - - +
338B ASP* 2.8 46.7 + - + +
345B PHE* 4.4 5.4 - - + -
346B MET* 1.3 78.0 - - - +
348B MET* 1.3 63.1 + - - +
358B ILE* 4.2 5.8 - - + -
359B ALA 3.1 12.1 - - - +
360B LYS* 4.3 11.9 - - + -
371B LEU* 4.3 6.3 - - + -
380B PRO* 3.8 25.1 - - + +
382B LEU* 4.0 24.9 - - + +
389B VAL* 4.0 25.1 - - + -
406B THR* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B VAL* 4.6 2.0 - - + -
328B THR* 3.6 22.7 - - + -
330B GLU* 5.8 2.0 - - + +
334B ASN* 3.3 26.0 - - - +
335B GLN 3.6 13.2 - - - +
336B ASP 4.0 6.3 - - - -
337B ALA* 4.2 9.4 - - + -
346B MET* 4.1 13.2 - - + +
347B VAL* 1.3 79.3 - - - +
349B VAL* 1.3 68.7 + - - +
350B SER* 4.9 0.7 - - - +
358B ILE* 3.3 7.1 - - - +
359B ALA* 2.9 51.4 + - + +
361B GLN* 3.5 30.3 - - + +
368B VAL* 4.5 12.1 - - + -
380B PRO* 4.2 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLN 4.0 0.3 - - - +
334B ASN* 3.4 3.3 - - - -
335B GLN* 2.8 48.7 + - + +
336B ASP* 3.8 13.9 - - - +
348B MET* 1.3 73.1 - - - +
350B SER* 1.3 62.3 + - - +
351B SER* 4.2 4.6 + - - +
356B GLN* 4.1 19.3 - - + +
357B HIS 3.4 7.0 - - - +
358B ILE* 4.0 4.5 - - + -
377B ASP 3.5 18.4 - - - +
378B GLU* 3.8 13.7 - - - -
380B PRO* 3.6 27.4 - - + -
114C THR* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU 4.2 6.2 - - - -
331B GLY* 4.9 0.5 - - - -
333B GLN 3.4 6.0 + - - +
334B ASN* 3.1 19.4 + - - +
348B MET* 3.9 1.7 + - - -
349B VAL* 1.3 73.8 - - - +
351B SER* 1.3 61.4 + - - +
352B ASN* 3.5 14.5 + - - -
355B GLN 4.0 0.3 - - - -
356B GLN* 3.3 1.5 - - - +
357B HIS* 2.9 37.4 + - - -
359B ALA* 4.3 19.3 - - - -
368B VAL* 6.0 1.1 - - - +
370B VAL* 5.8 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B SER* 3.7 3.1 + - - -
333B GLN* 3.0 51.5 + - - +
335B GLN* 4.3 6.2 + - - -
349B VAL* 4.5 4.3 + - - +
350B SER* 1.3 71.3 + - - +
352B ASN* 1.3 75.3 + - - +
354B GLY* 6.5 0.4 - - - -
355B GLN 3.0 11.0 - - - -
356B GLN* 3.5 21.3 + - - +
113C GLY* 5.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLY* 3.1 12.9 - - - -
332B SER* 2.5 44.5 + - - +
350B SER* 3.5 18.8 + - - -
351B SER* 1.3 84.0 + - - +
353B GLY* 1.3 61.2 + - - +
354B GLY 3.1 2.9 - - - +
355B GLN* 2.8 30.3 + - - +
----------------------------------------------------------
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