Contacts of the strand formed by residues 313 - 327 (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 THR 313 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLY 4.5 8.3 + - - +
303B GLN* 3.8 3.8 + - - +
304B ASN* 3.6 3.3 - - - +
305B ILE* 2.9 46.9 + - - +
311B LEU 4.9 0.7 - - - +
312B GLY* 1.3 79.7 - - - +
314B GLU* 1.3 60.4 + - - +
315B TRP* 4.0 3.6 - - - +
341B VAL* 3.9 15.4 - - + +
342B LYS 3.3 11.7 - - - +
343B SER* 4.6 0.4 - - - -
344B GLN* 4.1 3.1 - - - +
386B TRP* 4.0 17.3 - - + -
388B TYR* 3.6 24.2 - - + +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B TYR* 3.1 39.3 + - + +
303B GLN 3.5 2.7 - - - -
304B ASN* 3.7 12.5 - - - +
313B THR* 1.3 73.6 - - - +
315B TRP* 1.3 61.2 + - - +
316B TRP* 3.5 14.3 + - - +
340B ASN 3.7 1.7 - - - +
341B VAL* 3.4 2.6 - - - -
342B LYS* 2.8 61.1 + - + +
344B GLN* 5.8 0.2 - - - +
349B ARG* 3.2 29.1 + - - -
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Residues in contact with TRP 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLY 5.3 1.6 - - - +
28B ALA* 3.7 20.1 - - + +
29B GLN* 3.4 33.0 - - + -
30B SER* 3.1 30.1 - - - -
117B PHE* 4.2 5.8 - + - -
301B MET* 3.7 26.2 - - + +
302B TYR* 3.3 7.1 - - - -
303B GLN* 2.7 68.2 + - + +
313B THR* 5.3 3.8 - - - +
314B GLU* 1.3 76.0 - - - +
316B TRP* 1.3 80.9 + - - +
317B THR* 3.7 12.7 - - + -
339B ASP* 3.0 28.5 + - - -
340B ASN 3.4 9.2 - - - -
341B VAL* 3.8 21.3 - - + -
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Residues in contact with TRP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B MET 3.4 8.5 - - - -
302B TYR* 3.4 43.7 - + + -
314B GLU* 3.5 20.9 + - + -
315B TRP* 1.3 78.5 - - - +
317B THR* 1.3 62.3 + - - +
318B VAL* 5.2 7.4 - - + -
338B TYR* 3.8 5.5 - - + +
339B ASP* 3.4 3.5 - - - -
340B ASN* 2.9 52.3 + - + +
349B ARG* 4.2 17.2 - - - +
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B SER* 5.3 0.2 + - - -
32B TYR* 2.7 27.4 + - - +
115B ILE* 4.8 10.6 - - + +
299B VAL* 4.7 2.5 - - + -
300B GLY* 3.5 1.3 - - - -
301B MET* 2.9 71.6 + - + +
315B TRP* 3.7 11.6 - - + -
316B TRP* 1.3 74.5 - - - +
318B VAL* 1.3 66.3 + - - +
338B TYR 3.2 3.8 + - - -
339B ASP* 2.7 25.5 + - - -
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.0 5.6 + - - -
299B VAL 3.4 13.7 - - - +
300B GLY* 4.5 6.3 - - - -
316B TRP* 5.2 7.4 - - + -
317B THR* 1.3 81.6 - - - +
319B GLY* 1.3 63.6 + - - +
337B GLY* 3.4 0.7 - - - -
338B TYR* 2.7 50.6 + - + +
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.3 17.7 + - - -
114B MET* 4.2 5.6 - - - -
298B TYR* 3.4 3.8 - - - +
299B VAL* 3.0 32.3 + - - +
318B VAL* 1.3 80.3 - - - +
320B VAL* 1.3 64.1 + - - +
336B VAL 3.0 12.8 - - - -
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B MET* 4.0 3.3 - - - +
296B LEU* 3.8 25.6 - - + -
297B MET 3.6 5.8 - - - +
298B TYR* 4.0 10.1 - - + -
319B GLY* 1.3 77.6 - - - +
321B ARG* 1.3 60.4 + - - +
322B PRO* 3.9 13.5 - - + -
334B LEU* 3.8 1.9 - - + +
335B GLU* 3.4 3.8 - - - +
336B VAL* 2.9 40.0 + - + +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 4.1 8.1 - - - +
34B LEU* 3.6 29.4 - - - +
113B HIS* 3.3 32.5 + - - -
114B MET* 3.8 25.6 - - + +
296B LEU* 3.9 1.1 - - - -
297B MET* 2.8 47.3 + - + +
320B VAL* 1.3 75.8 - - - +
322B PRO* 1.3 61.4 - - - +
333B LEU* 4.2 23.9 - - + +
334B LEU 3.2 8.7 - - - +
335B GLU* 2.6 43.3 + - + +
367B ILE* 3.5 12.2 + - + +
370B ARG* 4.1 9.7 - - - +
374B ARG* 4.5 8.5 - - - +
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Residues in contact with PRO 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B TRP* 4.1 22.0 - - + -
295B ASP 3.4 7.9 - - - +
296B LEU* 3.7 13.7 - - + -
320B VAL* 3.8 16.6 - - + +
321B ARG* 1.3 90.7 - - - +
323B MET* 1.3 61.2 + - - +
324B TYR 4.3 0.2 - - - -
332B THR 4.1 0.9 - - - +
333B LEU* 3.7 4.2 - - - +
334B LEU* 3.1 54.0 + - + +
367B ILE* 4.8 0.2 - - - -
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Residues in contact with MET 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LYS 3.2 0.9 - - - +
294B TRP* 3.2 12.7 - - - -
295B ASP* 2.7 42.7 + - + +
322B PRO* 1.3 74.7 - - - +
324B TYR* 1.3 62.5 + - - +
325B LYS* 4.4 13.5 - - + +
331B SER* 3.1 34.8 - - - +
332B THR 3.6 3.1 - - - -
333B LEU* 4.2 12.8 - - + -
360B GLN* 4.1 6.1 - - - +
362B GLN* 3.6 25.6 - - - +
365B ASP 4.6 2.9 - - - -
366B SER 3.9 11.0 - - - +
367B ILE* 3.5 44.6 - - + -
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Residues in contact with TYR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LYS* 3.3 39.7 + - + +
294B TRP* 3.5 44.8 - + + -
322B PRO 4.3 0.4 - - - -
323B MET* 1.3 72.1 - - - +
325B LYS* 1.3 68.1 + - - +
326B TRP* 3.4 57.0 + + - -
331B SER* 3.1 5.9 - - - -
332B THR* 3.0 39.6 + - - +
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B SER* 4.7 2.6 + - - -
291B GLY 5.2 2.4 + - - -
292B ASP 3.6 23.6 + - - +
293B LYS* 2.8 38.7 + - + +
294B TRP 4.3 3.3 + - - -
295B ASP* 3.0 44.3 + - - +
323B MET* 4.4 16.2 - - + +
324B TYR* 1.3 75.4 - - - +
326B TRP* 1.3 65.1 + - - +
327B THR* 3.3 12.3 - - - +
328B PRO* 5.8 0.2 - - + -
330B MET 4.0 4.7 - - - -
331B SER* 4.1 1.3 - - - -
362B GLN* 6.0 0.2 - - - +
365B ASP* 2.9 42.1 + - + +
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Residues in contact with TRP 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LYS* 3.7 13.4 + - - +
324B TYR* 3.6 34.6 - + - -
325B LYS* 1.3 75.3 - - - +
327B THR* 1.3 73.1 + - + +
330B MET* 3.1 16.7 + - + +
331B SER* 3.7 17.3 - - - -
332B THR* 2.7 33.8 + - + -
359B GLN* 3.8 13.2 - - - +
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Residues in contact with THR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLU* 5.3 12.7 + - - +
325B LYS* 4.0 11.1 - - - +
326B TRP* 1.3 89.8 + - + +
328B PRO* 1.3 77.9 - - - +
329B ILE* 3.3 10.0 + - - +
330B MET* 3.0 41.0 + - + +
362B GLN* 4.8 1.2 + - - -
365B ASP* 5.4 0.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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