Contacts of the strand formed by residues 344 - 358 (chain B) in PDB entry 2W77
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 THR 344 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASP* 3.5 2.8 - - - +
340B LEU* 2.8 41.0 + - + -
341B ASN* 2.8 38.5 + - - +
342B PRO 3.8 0.4 - - - -
343B ASP* 1.3 81.1 - - - +
345B MET* 1.3 59.4 + - - +
402B LEU* 3.9 23.1 - - + -
403B GLU 3.4 10.5 - - - +
404B HIS* 3.0 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LYS* 4.8 5.6 - - - +
308B ARG* 4.0 13.5 - - - -
337B GLU* 3.8 34.1 - - + +
338B PHE 3.3 17.5 - - - +
339B ASP* 3.6 9.2 - - - +
344B THR* 1.3 76.4 - - - +
346B LEU* 1.3 63.0 + - - +
347B THR* 3.8 15.6 + - - +
401B ASN 3.6 1.6 - - - +
402B LEU* 3.4 7.2 - - - -
403B GLU* 3.0 62.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU 4.0 0.3 - - - +
337B GLU* 3.7 1.4 - - - -
338B PHE* 3.0 50.3 + - + +
340B LEU* 4.1 32.5 - - + +
344B THR 4.4 0.2 - - - -
345B MET* 1.3 71.6 - - - +
347B THR* 1.3 71.7 + - - +
348B VAL* 4.6 13.5 - - + -
400B ALA* 5.1 5.2 - - + -
401B ASN 3.3 15.7 - - - +
402B LEU* 4.2 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LYS* 4.7 7.5 + - - +
335B ILE* 3.6 30.7 - - + -
336B LEU 3.2 15.9 - - - +
337B GLU* 3.7 19.7 + - + +
345B MET* 3.8 14.6 + - - +
346B LEU* 1.3 75.7 - - - +
348B VAL* 1.3 68.0 + - - +
399B PHE* 4.6 7.0 - - + -
400B ALA* 3.3 6.3 - - - +
401B ASN* 2.7 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE* 3.3 4.5 - - - +
336B LEU* 2.9 61.7 + - + -
338B PHE* 4.7 7.3 - - + -
346B LEU* 4.6 17.5 - - + -
347B THR* 1.3 83.5 - - - +
349B GLY* 1.3 59.9 + - - +
399B PHE* 3.4 11.0 - - - +
400B ALA* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLY 3.2 12.8 - - - -
335B ILE* 4.2 1.3 - - - -
348B VAL* 1.3 79.6 - - - +
350B ALA* 1.3 60.9 + - - +
398B VAL* 3.5 6.1 - - - +
399B PHE* 2.9 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TYR* 3.0 8.0 - - - -
334B GLY* 2.9 32.9 + - - +
349B GLY* 1.3 76.0 - - - +
351B ASP* 1.3 61.8 + - - +
397B THR 3.1 12.1 - - - +
398B VAL* 4.8 11.2 - - + -
399B PHE* 4.2 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 3.8 23.0 - - + +
243B TYR* 5.1 1.1 + - - -
270B ARG* 2.6 33.5 + - - -
332B TYR 3.3 12.6 - - - +
333B TYR* 3.7 10.8 - - + -
350B ALA* 1.3 76.3 - - - +
352B TYR* 1.3 64.1 + - - +
395B THR* 5.8 0.9 + - - -
396B ARG* 3.2 9.5 - - - +
397B THR* 2.8 47.9 + - - +
399B PHE* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 6.2 0.2 - - - +
330B SER* 4.1 6.7 - - - -
331B VAL* 3.5 4.3 - - - +
332B TYR* 3.0 66.6 + + + +
351B ASP* 1.3 78.1 - - - +
353B GLN* 1.3 64.5 + - - +
354B ASP* 3.0 43.7 + - + -
394B TYR* 5.6 8.4 - + + +
395B THR 3.6 5.6 - - - -
396B ARG* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU 2.9 25.4 + - - -
238B SER* 3.6 6.6 - - - -
239B ASP* 2.9 38.5 + - - +
242B ILE* 6.0 1.6 - - - +
329B THR* 4.1 6.0 + - - +
330B SER 3.3 11.9 - - - +
331B VAL* 4.2 8.7 - - + +
352B TYR* 1.3 78.9 - - - +
354B ASP* 1.3 66.3 + - - +
355B ASN* 2.9 25.2 + - - +
393B GLN 4.2 0.5 - - - +
394B TYR* 3.3 4.7 - - - +
395B THR* 2.7 55.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS 3.7 1.6 - - - +
329B THR* 3.3 6.8 - - - -
330B SER* 2.9 37.8 + - - +
352B TYR* 3.0 31.0 + - + +
353B GLN* 1.3 75.2 - - - +
355B ASN* 1.3 68.1 + - - +
356B ASP* 3.8 8.1 - - - +
392B GLU* 2.6 29.1 - - - +
393B GLN 4.0 2.0 - - - -
394B TYR* 4.3 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ASP* 6.0 0.2 - - - +
234B GLY* 4.6 6.1 + - - -
237B LEU* 3.6 41.9 - - + +
327B ARG* 4.6 9.6 + - - -
328B LYS 4.0 1.8 - - - -
329B THR* 3.6 15.7 - - - +
353B GLN* 2.9 33.7 + - - +
354B ASP* 1.3 73.9 + - - +
356B ASP* 1.3 61.6 + - - +
357B PRO* 3.8 2.9 - - + +
391B TRP 5.6 0.7 - - - +
392B GLU* 3.3 7.3 - - - +
393B GLN* 2.8 57.6 + - - +
394B TYR 5.8 0.2 - - - -
395B THR* 5.6 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLU 4.3 0.2 - - - +
327B ARG* 3.8 3.0 - - - +
328B LYS* 3.0 46.7 + - + +
354B ASP* 3.8 12.7 - - - +
355B ASN* 1.3 75.6 - - - +
357B PRO* 1.3 62.1 - - - +
358B LYS* 3.5 25.9 + - - +
390B SER* 4.3 0.5 + - - -
392B GLU* 3.7 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ASP* 3.2 28.3 - - - +
325B TYR* 3.9 7.4 - - + +
326B GLU 3.1 13.5 - - - +
327B ARG* 3.7 10.1 - - + -
355B ASN 3.8 1.8 - - - +
356B ASP* 1.3 86.9 - - - +
358B LYS* 1.3 74.0 + - - +
360B SER* 3.4 17.7 - - - +
390B SER* 3.1 30.9 + - - +
391B TRP 3.7 10.5 - - - +
392B GLU* 3.7 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B HIS 4.2 2.5 - - - +
325B TYR* 3.4 8.1 - - - -
326B GLU* 2.8 41.0 + - + +
356B ASP* 3.5 24.9 + - - +
357B PRO* 1.3 83.9 + - - +
359B GLY* 1.3 63.6 + - - +
360B SER 3.2 2.0 - - - -
387B LYS 4.0 10.5 - - - +
388B TRP* 5.0 7.4 - - - +
389B SER 3.5 3.8 - - - +
390B SER* 4.0 15.2 + - - -
----------------------------------------------------------
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