Contacts of the strand formed by residues 313 - 325 (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 THR 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY 4.4 8.0 + - - +
303A GLN* 4.0 3.1 + - - +
304A ASN* 3.6 3.3 - - - +
305A ILE* 2.9 47.6 + - - +
311A LEU 4.9 1.1 - - - +
312A GLY* 1.3 79.4 - - - +
314A GLU* 1.3 60.3 + - - +
315A TRP* 4.1 3.2 - - - +
341A VAL* 3.9 15.9 - - + -
342A LYS 3.3 10.8 - - - +
344A GLN* 4.1 2.9 - - - +
386A TRP* 4.0 18.2 - - + -
388A TYR* 3.7 23.3 - - - +
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Residues in contact with GLU 314 (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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302A TYR* 3.0 41.3 + - + +
303A GLN 3.5 3.4 - - - -
304A ASN* 3.7 12.4 - - - +
313A THR* 1.3 72.3 - - - +
315A TRP* 1.3 63.1 + - - +
316A TRP* 3.4 14.7 + - - +
340A ASN 3.7 1.6 - - - +
341A VAL* 3.4 3.5 - - - -
342A LYS* 2.8 57.8 + - + +
349A ARG* 3.1 29.6 + - - -
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Residues in contact with TRP 315 (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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27A GLY 5.3 1.6 - - - +
28A ALA* 3.8 16.0 - - + +
29A GLN* 3.4 38.6 - - + -
30A SER* 3.2 29.8 - - - -
117A PHE* 4.3 6.1 - + - -
301A MET* 3.7 28.2 - - + +
302A TYR* 3.3 6.8 - - - -
303A GLN* 2.7 65.6 + - + +
313A THR* 5.3 4.3 - - - +
314A GLU* 1.3 75.9 - - - +
316A TRP* 1.3 81.9 + - - +
317A THR* 3.7 12.7 - - + -
339A ASP* 3.1 28.9 + - - -
340A ASN 3.4 8.7 - - - -
341A VAL* 3.8 21.1 - - + -
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Residues in contact with TRP 316 (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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301A MET 3.4 8.5 - - - -
302A TYR* 3.4 43.3 - + + -
314A GLU* 3.4 24.4 + - + -
315A TRP* 1.3 81.4 - - - +
317A THR* 1.3 62.2 + - - +
318A VAL* 5.2 3.8 - - + -
338A TYR* 3.9 5.2 - - + +
339A ASP* 3.4 0.7 - - - -
340A ASN* 2.9 50.4 + - + +
349A ARG* 4.2 14.7 - - - +
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Residues in contact with THR 317 (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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30A SER* 5.4 0.2 + - - -
32A TYR* 2.7 29.1 + - - +
115A ILE* 4.8 10.9 - - + +
299A VAL* 5.4 2.2 - - + -
300A GLY* 3.5 0.9 - - - -
301A MET* 2.9 70.3 + - + +
315A TRP* 3.7 11.5 - - + -
316A TRP* 1.3 74.4 - - - +
318A VAL* 1.3 65.4 + - - +
338A TYR 3.2 4.2 + - - -
339A ASP* 2.7 25.8 + - - -
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Residues in contact with VAL 318 (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* 3.0 6.2 + - - -
299A VAL 3.4 12.1 - - - +
300A GLY* 4.4 6.1 - - - -
316A TRP* 5.2 6.5 - - + -
317A THR* 1.3 82.4 - - - +
319A GLY* 1.3 64.3 + - - +
337A GLY* 3.4 0.3 - - - -
338A TYR* 2.8 47.9 + - + +
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Residues in contact with GLY 319 (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* 3.3 17.3 + - - -
114A MET* 4.1 4.5 - - - -
298A TYR* 3.4 4.9 - - - +
299A VAL 3.0 33.9 + - - +
318A VAL* 1.3 79.3 - - - +
320A VAL* 1.3 63.6 + - - +
336A VAL 3.1 12.6 - - - -
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Residues in contact with VAL 320 (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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114A MET* 3.9 3.9 - - - +
296A LEU* 3.7 25.8 - - + -
297A MET 3.5 5.6 - - - +
298A TYR* 4.0 10.3 - - + -
319A GLY* 1.3 77.0 - - - +
321A ARG* 1.3 60.4 + - - +
322A PRO* 3.8 13.6 - - + +
334A LEU* 3.8 1.9 - - + +
335A GLU* 3.4 3.6 - - - +
336A VAL* 2.9 41.7 + - + +
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Residues in contact with ARG 321 (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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33A ARG* 4.1 8.5 - - - +
34A LEU* 3.6 28.8 - - - +
113A HIS* 3.3 31.3 + - - -
114A MET* 3.8 26.3 - - + +
296A LEU* 3.8 2.5 - - - -
297A MET* 2.7 46.1 + - + +
320A VAL* 1.3 76.6 - - - +
322A PRO* 1.3 62.3 - - - +
333A LEU* 4.1 24.9 - - + +
334A LEU 3.2 8.1 - - - +
335A GLU* 2.7 45.0 + - - +
367A ILE* 3.4 11.1 + - + +
370A ARG* 4.1 9.9 - - - +
374A ARG* 4.4 8.3 - - - +
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Residues in contact with PRO 322 (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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294A TRP* 4.1 20.9 - - + -
295A ASP 3.4 7.4 - - - +
296A LEU* 3.7 13.5 - - + -
320A VAL* 3.8 16.8 - - + +
321A ARG* 1.3 90.0 - - - +
323A MET* 1.3 60.8 + - - +
324A TYR 4.3 0.2 - - - -
332A THR 4.1 0.7 - - - +
333A LEU* 3.6 4.3 - - - +
334A LEU* 3.0 53.4 + - + +
367A ILE* 4.9 0.2 - - - -
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Residues in contact with MET 323 (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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293A LYS 3.3 1.0 - - - +
294A TRP* 3.3 11.7 - - - -
295A ASP* 2.8 40.9 + - + +
322A PRO* 1.3 74.9 - - - +
324A TYR* 1.3 63.3 + - - +
325A LYS* 4.0 13.5 + - + +
331A SER* 3.2 35.0 - - - +
332A THR 3.6 3.6 - - - -
333A LEU* 4.2 12.6 - - + -
360A GLN* 4.2 7.2 - - - +
362A GLN* 3.6 24.9 - - - +
365A ASP 4.6 2.7 - - - +
366A SER 3.9 11.2 - - - +
367A ILE* 3.5 44.0 - - + -
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Residues in contact with TYR 324 (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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293A LYS* 3.3 41.6 + - + +
294A TRP* 3.5 45.5 - + + -
322A PRO 4.3 0.2 - - - -
323A MET* 1.3 72.6 - - - +
325A LYS* 1.3 65.8 + - - +
326A TRP* 3.4 55.2 + + - -
331A SER* 3.0 6.8 - - - -
332A THR* 2.9 39.5 + - + +
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Residues in contact with LYS 325 (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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289A SER* 4.6 2.2 + - - -
291A GLY 5.2 2.0 + - - -
292A ASP 3.6 22.0 + - - +
293A LYS* 2.8 39.8 + - + +
294A TRP 4.3 7.1 + - - -
295A ASP* 3.0 39.6 + - - -
323A MET* 4.5 15.0 - - + +
324A TYR* 1.3 75.1 - - - +
326A TRP* 1.3 65.5 + - - +
327A THR 3.3 12.7 - - - +
328A PRO* 5.8 0.2 - - + -
330A MET 4.0 4.3 - - - -
331A SER* 4.1 1.8 - - - -
362A GLN* 6.2 0.4 - - - +
365A ASP* 2.8 43.2 + - + +
366A SER* 4.7 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