Contacts of the strand formed by residues 330 - 343 (chain B) in PDB entry 2MPR
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 MET 330 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 5.5 0.9 - - + -
93A GLU* 5.9 2.9 - - - +
326B TRP* 3.1 25.6 + - + -
327B THR* 3.0 35.7 + - - +
329B ILE* 1.3 83.4 - - + +
331B SER* 1.3 67.3 + - - +
359B GLN* 3.5 25.6 - - + +
360B GLN 3.3 9.6 - - - +
361B TRP* 3.3 44.9 - - + +
362B GLN* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B MET* 3.1 31.2 - - - +
324B TYR 3.1 17.5 - - - -
325B LYS* 4.1 1.6 - - - -
326B TRP* 3.7 6.7 - - - -
330B MET* 1.3 77.0 - - - +
332B THR* 1.3 63.7 - - - +
333B LEU* 3.9 2.4 - - - +
359B GLN* 3.4 7.6 + - - -
360B GLN* 2.8 36.8 + - - -
362B GLN* 2.9 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO 4.1 0.7 - - - +
323B MET* 3.6 2.3 - - - +
324B TYR* 3.0 36.9 + - + +
326B TRP* 2.7 29.6 + - + -
331B SER* 1.3 73.2 - - - +
333B LEU* 1.3 64.0 + - - +
334B LEU* 6.0 0.4 - - + -
357B LEU* 4.0 26.5 - - + -
358B ALA 3.3 9.0 - - - +
359B GLN* 2.6 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.1 19.3 - - + -
321B ARG* 4.2 30.7 - - + +
322B PRO 3.7 4.0 - - - +
323B MET* 4.2 20.9 - - + -
331B SER* 3.9 7.9 - - - +
332B THR* 1.3 77.5 - - - +
334B LEU* 1.3 61.2 + - - +
356B THR 3.8 0.4 - - - +
357B LEU* 3.4 7.8 - - - +
358B ALA* 2.7 42.6 + - + +
360B GLN* 3.4 52.5 - - + +
367B ILE* 4.7 8.3 - - + +
374B ARG* 5.6 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.8 0.7 - - - -
320B VAL* 5.9 1.3 - - + -
321B ARG* 3.2 10.1 - - - +
322B PRO* 3.1 49.3 + - + +
332B THR* 6.0 0.4 - - + -
333B LEU* 1.3 76.6 - - - +
335B GLU* 1.3 62.4 + - - +
336B VAL* 4.1 17.5 - - + -
355B ILE* 4.0 21.8 - - + -
356B THR 3.1 18.6 - - - +
357B LEU* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.6 15.8 - - + +
34B LEU* 3.0 36.4 + - + +
114B MET* 3.3 23.7 - - + +
320B VAL 3.4 8.7 - - - +
321B ARG* 2.6 34.7 + - - -
334B LEU* 1.3 76.0 - - - +
336B VAL* 1.3 68.8 + - - +
354B LYS* 2.8 28.9 + - - +
355B ILE* 3.3 4.2 - - - -
356B THR* 2.7 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 4.7 0.2 - - - -
319B GLY* 3.0 3.3 - - - -
320B VAL* 2.9 43.8 + - + +
334B LEU* 4.1 20.2 - - + -
335B GLU* 1.3 81.7 - - - +
337B GLY* 1.3 64.0 + - - +
338B TYR* 6.3 0.7 - - + -
353B TYR* 5.9 2.2 - - + -
354B LYS 3.3 3.6 - - - +
355B ILE* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.6 30.9 - - - -
318B VAL 3.4 7.0 - - - -
335B GLU* 4.2 0.6 - - - +
336B VAL* 1.3 79.1 - - - +
338B TYR* 1.3 60.5 + - - -
339B ASP* 5.3 0.4 - - - -
352B GLN 3.9 0.4 - - - +
353B TYR* 3.1 5.9 - - - +
354B LYS* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.8 0.8 - - - -
316B TRP* 4.9 5.2 - - + -
317B THR* 3.2 8.3 + - - -
318B VAL* 2.7 53.3 + - + +
336B VAL* 6.3 0.4 - - + -
337B GLY* 1.3 75.2 - - - +
339B ASP* 1.3 68.5 + - - +
340B ASN* 3.0 44.7 + - + -
351B ASN* 3.7 18.9 + - + +
352B GLN 3.3 13.0 - - - -
353B TYR* 4.0 17.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 4.0 21.0 + - + +
28B ALA* 4.5 7.4 - - + -
30B SER* 4.7 8.2 + - - +
31B LYS* 5.0 2.6 - - - -
32B TYR* 3.7 18.4 - - - -
315B TRP* 3.0 26.2 + - + +
316B TRP 3.4 2.2 - - - -
317B THR* 2.7 24.7 + - - -
337B GLY 5.3 0.3 - - - -
338B TYR* 1.3 75.9 - - - +
340B ASN* 1.3 61.1 + - - +
341B VAL* 4.3 0.7 - - + -
351B ASN* 3.1 7.4 - - - +
352B GLN* 2.9 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU 3.7 1.2 - - - +
315B TRP* 3.4 2.6 - - - -
316B TRP* 2.9 48.2 + - + +
338B TYR* 3.0 32.3 + - + +
339B ASP* 1.3 75.1 - - - +
341B VAL* 1.3 60.4 + - - +
349B ARG* 2.8 46.7 + - - +
350B ASN 3.3 5.5 + - - -
351B ASN* 3.6 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 4.5 7.6 - - + -
26B THR 3.8 12.6 - - - +
27B GLY* 3.7 23.8 - - - +
28B ALA* 3.8 24.2 - - + +
313B THR* 3.9 18.6 - - - -
314B GLU 3.4 7.6 - - - +
315B TRP* 3.8 19.7 - - + +
340B ASN* 1.3 78.9 + - - +
342B LYS* 1.3 62.0 + - - +
349B ARG* 4.3 1.3 - - - -
350B ASN* 2.8 39.6 + - + +
386B TRP* 3.1 13.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B THR* 3.3 4.9 - - - -
314B GLU* 2.8 64.2 + - + +
340B ASN 4.3 0.4 - - - -
341B VAL* 1.3 71.7 - - - +
343B SER* 1.3 82.5 + - - +
344B GLN* 3.4 12.0 + - - +
347B GLY* 3.7 16.6 - - - +
348B ASP 3.3 12.6 - - - +
349B ARG* 3.5 39.5 - - + +
386B TRP* 4.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLY 4.1 5.3 + - - -
342B LYS* 1.3 74.6 - - - +
344B GLN* 1.3 57.9 + - - +
345B GLN* 3.3 9.9 + - - +
346B THR* 3.2 28.5 + - - -
347B GLY* 2.8 28.4 + - - -
348B ASP 2.9 8.6 + - - -
386B TRP* 3.5 38.5 - - - +
399B ALA* 3.8 11.6 - - - +
----------------------------------------------------------
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