Contacts of the strand formed by residues 330 - 343 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A TRP* 3.1 24.7 + - + -
327A THR* 3.0 36.3 + - + +
329A ILE* 1.3 82.4 - - + +
331A SER* 1.3 66.4 + - - +
359A GLN* 3.5 27.8 - - + +
360A GLN 3.2 11.7 - - - +
361A TRP* 3.3 43.1 - - + +
362A GLN* 3.9 0.4 - - - +
92C ILE* 5.6 0.9 - - + -
93C GLU* 6.0 1.6 - - - +
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Residues in contact with SER 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A MET* 3.2 28.3 - - - +
324A TYR 3.0 19.7 - - - -
325A LYS* 4.1 1.6 - - - -
326A TRP* 3.7 6.3 - - - -
330A MET* 1.3 76.6 - - - +
332A THR* 1.3 60.8 + - - +
333A LEU* 3.9 4.9 - - - +
359A GLN* 3.4 7.1 + - - -
360A GLN* 2.8 39.1 + - - +
362A GLN* 3.0 19.1 + - - -
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Residues in contact with THR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A PRO 4.1 0.9 - - - +
323A MET* 3.6 1.9 - - - +
324A TYR* 2.9 36.7 + - + +
326A TRP* 2.7 31.8 + - + -
331A SER* 1.3 72.4 - - - +
333A LEU* 1.3 64.2 + - - +
334A LEU* 6.0 0.4 - - + -
357A LEU* 4.0 26.7 - - + -
358A ALA 3.4 10.3 - - - +
359A GLN* 2.7 18.4 + - - +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.1 19.1 - - + -
321A ARG* 4.1 32.1 - - + +
322A PRO 3.6 3.4 - - - +
323A MET* 4.2 19.7 - - + -
331A SER* 3.9 8.7 - - - +
332A THR* 1.3 78.1 - - - +
334A LEU* 1.3 60.7 + - - +
356A THR 3.8 0.2 - - - +
357A LEU* 3.4 7.1 - - - +
358A ALA* 2.7 42.3 + - + +
360A GLN* 3.5 52.0 - - + +
367A ILE* 4.6 9.2 - - + +
374A ARG* 5.6 1.6 - - + +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.8 0.7 - - - -
320A VAL* 5.8 1.3 - - + -
321A ARG* 3.2 10.3 - - - +
322A PRO* 3.0 48.2 + - + +
332A THR* 6.0 0.4 - - + -
333A LEU* 1.3 76.2 - - - +
335A GLU* 1.3 62.4 + - - +
336A VAL* 4.1 17.3 - - + -
355A ILE* 3.9 22.4 - - + -
356A THR 3.1 19.5 - - - +
357A LEU* 4.3 16.8 - - + -
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.5 16.1 - - + +
34A LEU* 3.0 29.6 + - + +
114A MET* 3.3 24.2 - - + +
320A VAL 3.4 8.3 - - - +
321A ARG* 2.7 41.6 + - - -
334A LEU* 1.3 76.8 - - - +
336A VAL* 1.3 68.5 + - - +
354A LYS* 2.9 26.8 + - - +
355A ILE* 3.3 4.0 - - - -
356A THR* 2.7 38.6 + - - +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLY* 3.1 2.9 - - - -
320A VAL* 2.9 42.0 + - + +
334A LEU* 4.1 20.6 - - + -
335A GLU* 1.3 83.1 - - - +
337A GLY* 1.3 63.9 + - - +
338A TYR* 6.3 0.7 - - + -
353A TYR* 5.9 2.0 - - + -
354A LYS 3.4 2.9 - - - +
355A ILE* 3.7 37.9 - - + -
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Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.6 31.1 - - - -
318A VAL 3.4 7.9 - - - -
335A GLU* 4.2 0.6 - - - +
336A VAL* 1.3 78.1 - - - +
338A TYR* 1.3 60.0 + - - -
339A ASP* 5.3 0.4 - - - +
352A GLN 3.9 0.2 - - - +
353A TYR* 3.1 5.5 - - - +
354A LYS* 3.0 35.0 + - - +
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Residues in contact with TYR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.7 0.8 - - - -
316A TRP* 5.1 5.4 - - + -
317A THR* 3.2 8.0 + - - -
318A VAL* 2.8 52.4 + - + +
336A VAL* 6.3 0.7 - - + -
337A GLY* 1.3 75.2 - - - -
339A ASP* 1.3 67.7 + - - +
340A ASN* 3.0 43.7 + - + -
351A ASN* 3.8 17.8 + - + +
352A GLN 3.3 13.5 - - - -
353A TYR* 4.1 16.6 - + + -
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Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 3.9 21.0 + - + +
28A ALA* 4.5 8.1 - - - -
30A SER* 4.6 7.8 + - - +
31A LYS* 5.0 2.6 - - - -
32A TYR* 3.7 18.2 - - - -
315A TRP* 3.1 24.0 + - + +
316A TRP 3.4 1.8 - - - -
317A THR* 2.7 26.0 + - - -
337A GLY 5.3 0.2 - - - -
338A TYR* 1.3 76.4 - - - +
340A ASN* 1.3 61.6 + - - +
341A VAL* 5.0 0.7 - - + -
350A ASN 4.4 0.2 - - - -
351A ASN* 3.1 7.7 - - - +
352A GLN* 2.9 47.2 + - + +
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Residues in contact with ASN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLU 3.7 1.0 - - - +
315A TRP* 3.4 3.3 - - - -
316A TRP* 2.9 45.7 + - + +
338A TYR* 3.0 33.4 + - + +
339A ASP* 1.3 75.8 - - - +
341A VAL* 1.3 62.3 + - - +
349A ARG* 2.8 47.3 + - - +
350A ASN 3.2 5.4 + - - -
351A ASN* 3.6 17.4 - - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 4.5 7.4 - - + -
26A THR 3.9 13.2 - - - +
27A GLY* 3.7 24.2 - - - +
28A ALA* 3.7 24.5 - - + +
313A THR* 3.9 18.6 - - - -
314A GLU 3.4 8.5 - - - +
315A TRP* 3.8 19.5 - - + +
340A ASN* 1.3 80.2 + - - +
342A LYS* 1.3 62.2 + - - +
349A ARG* 4.2 0.9 - - - -
350A ASN* 2.8 39.7 + - + +
386A TRP* 3.2 12.4 + - + -
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A THR* 3.3 5.4 - - - -
314A GLU* 2.8 58.0 + - + +
341A VAL* 1.3 73.0 - - - +
343A SER* 1.3 86.3 + - - +
344A GLN* 3.4 11.5 + - - +
347A GLY* 3.7 17.0 - - - +
348A ASP 3.2 7.0 - - - +
349A ARG* 3.4 51.3 - - + +
386A TRP* 4.2 1.6 - - - -
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Residues in contact with SER 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLY 4.1 5.2 + - - -
342A LYS* 1.3 74.1 - - - +
344A GLN* 1.3 59.3 + - - +
345A GLN* 3.3 9.2 + - - +
346A THR* 3.2 29.9 + - - -
347A GLY* 2.8 27.4 + - - -
348A ASP 2.8 8.2 + - - -
386A TRP* 3.5 37.4 - - - +
399A ALA* 3.8 10.7 - - - +
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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