Contacts of the strand formed by residues 294 - 307 (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 TRP 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A SER* 3.5 1.2 - - - -
290A LEU* 2.7 60.1 + - + +
291A GLY 4.1 1.6 - - - +
292A ASP 3.6 1.6 - - - -
293A LYS* 1.3 87.9 - - + +
295A ASP* 1.3 67.0 + - - +
322A PRO* 4.1 26.5 - - + -
323A MET 3.3 19.1 - - - -
324A TYR* 3.5 43.0 - + + -
325A LYS* 4.3 0.9 - - - -
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE 3.5 5.8 - - - +
289A SER* 2.7 27.7 + - - -
290A LEU* 4.6 1.1 - - - -
294A TRP* 1.3 79.3 - - - +
296A LEU* 1.3 63.8 + - - +
322A PRO* 3.4 3.1 - - - +
323A MET* 2.8 36.9 + - + +
325A LYS* 3.0 30.4 + - - -
366A SER* 3.6 6.1 + - - -
367A ILE* 3.0 46.5 + - + +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY 4.0 0.3 - - - +
287A ALA* 3.1 5.2 - - - +
288A ILE* 2.8 43.9 + - + +
290A LEU* 3.6 25.4 - - + -
295A ASP* 1.3 75.8 - - - +
297A MET* 1.3 76.6 + - - +
298A TYR* 4.3 16.1 - - + -
320A VAL* 3.7 19.7 - - + -
321A ARG 3.5 3.1 - - - -
322A PRO* 3.7 29.4 - - + -
367A ILE* 4.3 2.4 - - - +
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Residues in contact with MET 297 (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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113A HIS* 3.8 20.6 - - + -
114A MET* 3.9 19.7 - - + -
286A GLY 3.4 10.1 - - - +
287A ALA* 4.2 9.9 - - + -
296A LEU* 1.3 77.8 - - - +
298A TYR* 1.3 64.1 + - - +
320A VAL* 3.5 0.7 - - - -
321A ARG* 2.7 61.3 + - + +
367A ILE* 4.0 26.5 - - + +
368A TRP* 3.5 49.4 - - + -
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Residues in contact with TYR 298 (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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112A VAL* 5.1 0.2 - - - +
114A MET* 3.8 3.8 - - - +
223A MET* 4.5 8.5 - - + +
227A TYR 3.8 2.4 + - - -
228A ASN* 2.7 40.5 + - - +
284A ASP* 3.6 11.4 - - - -
285A HIS* 3.3 8.5 - - - +
286A GLY* 3.2 56.8 + - - +
287A ALA 4.1 2.0 - - - -
288A ILE* 4.4 20.4 - - + +
296A LEU* 4.3 17.0 - - + -
297A MET* 1.3 78.7 - - - +
299A VAL* 1.3 66.2 + - - +
319A GLY 3.4 12.1 - - - +
320A VAL* 4.0 12.6 - - + -
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 4.1 23.6 - - + +
112A VAL* 3.5 24.9 - - + -
114A MET* 3.3 36.6 - - + -
115A ILE* 4.0 16.2 - - + -
283A LEU* 3.9 18.2 - - + -
284A ASP 3.5 5.2 - - - -
285A HIS* 4.0 1.6 - - + -
298A TYR* 1.3 76.0 - - - +
300A GLY* 1.3 62.8 + - - +
301A MET* 5.1 2.9 - - + +
317A THR* 5.3 1.1 - - + +
318A VAL* 3.4 7.0 - - - +
319A GLY 3.0 26.6 + - - +
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Residues in contact with GLY 300 (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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282A ILE 4.1 0.2 - - - +
283A LEU* 3.5 1.8 - - - +
284A ASP* 2.8 37.8 + - - +
299A VAL* 1.3 76.0 - - - +
301A MET* 1.3 61.1 + - - +
317A THR 3.5 6.3 - - - -
318A VAL* 4.4 9.2 - - - -
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Residues in contact with MET 301 (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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115A ILE* 4.7 5.8 - - + -
117A PHE* 4.0 20.9 - - + -
281A ARG* 3.8 23.8 - - + -
282A ILE 3.4 11.4 - - - +
283A LEU* 3.8 26.0 - - + -
299A VAL* 5.2 1.8 - - + -
300A GLY* 1.3 75.7 - - - +
302A TYR* 1.3 72.2 + - - +
303A GLN* 4.6 3.1 - - + +
315A TRP* 3.7 40.2 - - + +
316A TRP* 3.4 9.0 - - - +
317A THR* 2.9 52.4 + - + +
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Residues in contact with TYR 302 (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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280A TRP* 4.7 9.6 - - + -
281A ARG* 3.4 2.6 - - - -
282A ILE* 2.9 54.5 + - + +
301A MET* 1.3 75.3 - - - +
303A GLN* 1.3 64.0 + - - +
304A ASN* 3.4 32.6 + - + +
314A GLU* 3.0 35.8 + - + -
315A TRP 3.3 4.3 - - - -
316A TRP* 3.4 52.0 - + + -
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Residues in contact with GLN 303 (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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29A GLN* 3.3 33.3 + - - +
117A PHE* 4.0 4.0 - - - -
279A MET* 4.2 15.0 - - + -
280A TRP 3.3 8.7 - - - +
281A ARG* 2.7 46.6 + - + +
301A MET* 4.6 4.3 - - + +
302A TYR* 1.3 78.2 - - - +
304A ASN* 1.3 62.7 + - - +
305A ILE* 4.0 14.1 - - + +
313A THR* 4.0 3.4 + - - +
314A GLU* 3.5 2.1 - - - +
315A TRP* 2.7 66.8 + - + +
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Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN* 3.7 4.5 + - - +
279A MET* 3.2 5.1 - - - -
280A TRP* 2.9 40.6 + - + +
302A TYR* 3.4 30.8 + - + +
303A GLN* 1.3 74.8 - - - +
305A ILE* 1.3 67.8 + - - +
306A ASP* 3.6 21.1 + - - +
313A THR 3.6 8.7 - - - +
314A GLU* 3.7 15.2 - - + +
342A LYS* 5.9 0.2 + - - -
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Residues in contact with ILE 305 (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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29A GLN* 4.0 15.3 - - - +
240A THR* 3.9 24.0 - - - +
241A THR 5.4 0.4 - - - +
278A ASN 3.7 4.3 - - - +
279A MET* 4.0 17.5 - - + +
303A GLN* 4.0 23.6 - - + +
304A ASN* 1.3 74.6 - - - +
306A ASP* 1.3 58.4 + - - +
307A TRP* 3.6 46.9 - - + +
312A GLY* 3.3 7.4 - - - -
313A THR* 2.9 46.3 + - - +
344A GLN* 3.7 3.3 - - - +
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Residues in contact with ASP 306 (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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277A GLY* 3.3 4.2 - - - -
278A ASN* 2.9 55.9 + - - +
304A ASN* 3.6 17.4 + - - +
305A ILE* 1.3 71.7 - - - +
307A TRP* 1.3 65.2 + - - +
308A ASP* 5.2 0.2 - - - +
344A GLN* 2.8 25.4 + - - +
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Residues in contact with TRP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A THR* 2.9 36.0 + - - -
241A THR* 3.9 21.5 - - + -
274A ASN 5.1 1.1 - - - -
275A ASN* 3.1 22.2 + - + -
276A ASN 3.3 16.8 - - - +
277A GLY* 4.2 2.2 - - - -
278A ASN 4.9 0.2 - - - -
305A ILE* 3.6 25.0 + - + +
306A ASP* 1.3 80.9 - - - +
308A ASP* 1.3 57.3 + - - +
309A ASN* 3.4 21.3 - - - +
310A ASN* 2.8 21.8 + - - -
311A LEU* 3.7 16.2 - - + -
312A GLY* 3.6 22.9 - - - +
344A GLN* 3.1 21.2 + - - +
397A ARG* 4.2 26.2 - - - -
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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