Contacts of the strand formed by residues 387 - 397 (chain D) in PDB entry 5MG3
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 VAL 387 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370D VAL* 4.6 0.7 - - - -
371D GLU* 2.6 41.2 + - + +
372D TYR 4.8 0.7 - - - +
373D LYS* 3.5 36.6 - - + -
385D VAL* 4.1 2.9 - - + +
386D LEU* 1.4 74.2 - - - +
388D LYS* 1.4 59.0 + - - +
389D GLN* 2.9 23.4 + - - +
390D GLU* 4.0 14.0 + - + -
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Residues in contact with LYS 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D ALA* 4.4 16.1 - - + +
276D THR* 3.5 27.0 + - - +
277D ALA* 3.3 8.1 - - - +
278D THR* 3.0 41.2 + - + +
370D VAL* 3.8 15.9 - - + -
386D LEU* 4.4 10.6 + - + +
387D VAL* 1.4 72.3 - - - +
389D GLN* 1.3 67.4 + - + +
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Residues in contact with GLN 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D THR* 3.7 23.1 - - + +
279D LEU 5.4 0.2 - - - +
280D GLU* 4.2 13.3 - - + +
282D ARG* 2.7 66.3 + - - +
368D LEU* 3.6 17.1 - - + +
369D PHE 3.8 9.2 + - - +
387D VAL* 2.9 28.9 + - - +
388D LYS* 1.3 80.9 - - + +
390D GLU* 1.3 66.5 + - - +
391D GLU 3.8 0.9 - - - -
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Residues in contact with GLU 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D ARG* 4.3 10.4 + - - -
313D VAL* 6.1 1.2 - - - +
368D LEU* 4.4 3.5 - - - +
369D PHE 3.3 1.2 + - - -
371D GLU* 3.1 42.9 - - + +
387D VAL* 4.0 14.5 + - + +
389D GLN* 1.3 97.8 + - - +
391D GLU* 1.3 62.3 + - - +
392D VAL* 3.7 3.5 + - - +
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Residues in contact with GLU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ILE* 5.3 0.2 - - - +
236D ASN* 5.8 0.7 + - - -
237D ARG* 2.5 46.5 + - - -
293D ALA* 4.4 18.8 - - + +
368D LEU* 3.4 6.8 - - - -
369D PHE* 2.8 32.0 + - - +
370D VAL 3.3 15.4 - - - +
371D GLU* 4.0 12.3 - - + +
372D TYR* 5.7 1.4 - - - -
389D GLN 3.8 0.2 - - - -
390D GLU* 1.3 77.1 - - - +
392D VAL* 1.3 62.2 + - - +
393D ILE* 3.0 32.7 + - + +
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Residues in contact with VAL 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D VAL* 5.1 4.5 - - + -
286D THR* 5.5 4.7 - - + -
291D ALA 5.3 2.2 - - - +
292D ALA* 4.0 7.4 - - + +
293D ALA* 3.4 16.6 + - - +
310D GLY* 5.8 1.7 - - - -
313D VAL* 5.0 16.8 - - + -
366D ALA* 3.9 13.7 - - + -
367D THR 3.9 2.2 - - - +
368D LEU* 3.7 21.3 - - + -
390D GLU 3.7 4.7 + - - +
391D GLU* 1.3 68.4 - - - +
393D ILE* 1.4 61.5 + - - +
394D ASN 3.4 26.2 - - - +
395D ILE* 3.9 20.4 - - + -
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Residues in contact with ILE 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ILE* 5.0 5.6 - - + -
236D ASN* 5.1 4.7 - - - +
292D ALA* 3.5 0.5 - - - +
293D ALA* 3.2 11.6 + - + +
294D ALA* 3.0 50.6 + - + +
367D THR* 3.2 35.7 + - + +
369D PHE* 3.9 35.7 - - + -
391D GLU* 3.0 29.8 + - + +
392D VAL* 1.4 72.6 - - - +
394D ASN* 1.3 67.3 + - - +
423D LEU* 4.6 15.9 - - + -
424D LEU* 4.3 9.0 - - + -
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Residues in contact with ASN 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D ALA* 3.8 5.2 - - - +
294D ALA* 3.8 12.7 - - - +
295D SER* 4.1 22.2 - - - +
365D MET 4.4 0.2 - - - +
367D THR* 3.3 33.6 + - - -
392D VAL* 3.4 9.5 - - - +
393D ILE* 1.3 85.0 + - + +
395D ILE* 1.4 60.3 + - - +
408D ILE* 3.5 33.7 - - + +
409D THR* 3.7 17.8 + - - -
420D LEU* 5.5 1.2 - - - +
424D LEU* 3.7 21.4 - - + +
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Residues in contact with ILE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D VAL* 3.2 35.0 - - + -
286D THR* 3.3 32.5 - - + +
290D GLN* 4.6 18.8 - - + +
291D ALA 4.6 3.8 - - - +
292D ALA* 3.9 17.7 - - + +
364D PRO* 3.9 15.3 - - + -
365D MET 3.8 16.4 - - - +
366D ALA* 4.4 3.6 - - - -
392D VAL* 3.9 10.1 - - + -
394D ASN* 1.4 73.8 - - - +
396D ALA* 1.3 67.3 + - - +
397D ASN* 5.6 1.3 - - - +
409D THR* 3.2 21.4 + - + +
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Residues in contact with ALA 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D PRO* 3.6 1.6 - - - +
365D MET* 2.8 39.0 + - - +
395D ILE* 1.3 79.3 - - - +
397D ASN* 1.3 63.0 - - - +
406D PHE* 5.3 4.0 - - + -
407D ARG* 3.4 24.9 - - + +
408D ILE* 3.9 9.9 - - + -
409D THR* 3.8 24.0 - - + +
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Residues in contact with ASN 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D GLY* 3.3 22.3 + - - -
363D LYS 3.4 11.2 - - - +
364D PRO* 3.4 24.3 - - - +
395D ILE* 5.6 1.0 - - - +
396D ALA* 1.3 77.8 + - - +
398D ILE* 1.3 68.6 + - - +
399D GLN* 3.6 8.2 + - + +
406D PHE* 5.9 1.6 - - - -
407D ARG* 4.8 14.0 - - - +
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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