Contacts of the strand formed by residues 406 - 414 (chain B) in PDB entry 5EMV
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 PHE 406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347B VAL* 3.7 24.7 - - + -
348B CYS 3.5 9.0 - - - -
349B SER* 5.7 3.6 - - - -
380B P1L 4.1 15.3 - - + -
382B TYR* 4.7 6.7 - + - -
383B LEU* 3.7 24.7 - - + -
386B PHE* 3.7 37.5 - + + -
402B VAL 4.1 2.7 - - - +
403B LEU* 3.1 36.4 + - + +
404B GLU 3.4 1.0 + - - -
405B ASN* 1.3 78.6 - - - +
407B THR* 1.3 65.7 + - - +
408B ILE* 4.2 9.6 - - + -
428B PHE* 3.7 39.7 + + - -
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Residues in contact with THR 407 (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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277B LYS* 2.8 49.6 + - + +
278B PHE* 3.4 13.4 - - + -
347B VAL* 3.8 1.4 - - - +
348B CYS* 2.8 44.9 + - - +
351B GLY 5.1 1.0 + - - +
404B GLU 5.0 3.6 - - - +
405B ASN 4.2 1.3 - - - -
406B PHE* 1.3 84.7 - - - +
408B ILE* 1.3 64.8 + - - +
426B TYR 3.5 15.5 - - - +
427B VAL* 4.3 10.5 - - + -
428B PHE* 4.5 0.4 - - - -
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Residues in contact with ILE 408 (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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278B PHE* 3.6 5.6 - - - -
345B SER* 5.0 0.7 - - - -
346B LYS 3.2 14.8 - - - +
347B VAL* 4.4 11.2 - - + -
348B CYS* 5.4 0.2 - - - -
380B P1L 3.8 48.0 - - + -
383B LEU* 4.7 1.6 - - + -
406B PHE* 4.2 17.9 - - + -
407B THR* 1.3 81.1 - - - +
409B LEU* 1.3 68.2 + - - +
410B GLN* 4.5 4.0 - - + -
426B TYR* 2.7 60.8 + - + -
428B PHE* 4.0 21.7 - - + -
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Residues in contact with LEU 409 (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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278B PHE* 3.8 23.8 - - + -
279B PRO* 5.1 2.9 - - + -
283B GLY 4.0 20.6 - - - +
285B LEU* 4.3 16.2 - - + +
288B LEU* 4.1 14.6 - - + -
344B SER 3.6 1.9 - - - +
345B SER* 3.5 0.7 - - - -
346B LYS* 2.8 57.1 + - + +
348B CYS* 5.1 1.7 - - - -
408B ILE* 1.3 73.8 - - - +
410B GLN* 1.3 61.2 + - - +
411B VAL* 4.1 10.4 + - + +
423B CYS* 3.7 24.5 - - - -
424B THR 3.5 9.4 - - - +
425B ALA* 4.1 16.4 - - + -
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Residues in contact with GLN 410 (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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233B PHE* 3.9 22.0 - - - -
329B VAL* 5.5 0.6 - - - +
331B SER* 4.6 5.7 + - - -
333B TYR* 4.2 10.6 + - - -
343B CYS* 4.2 15.2 - - - -
344B SER 3.2 2.9 - - - +
345B SER* 3.1 28.5 + - - +
380B P1L 4.2 9.2 - - - +
408B ILE* 4.2 4.5 - - + -
409B LEU* 1.3 74.8 - - - +
411B VAL* 1.3 63.6 + - - +
412B VAL* 4.2 3.8 - - + -
422B LEU 3.8 0.9 - - - +
423B CYS* 3.3 5.2 - - - -
424B THR* 2.8 43.2 + - - +
426B TYR* 2.7 42.4 + - + -
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Residues in contact with VAL 411 (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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288B LEU* 3.9 35.0 - - + -
342B THR 3.4 3.3 - - - +
343B CYS* 3.5 0.2 - - - -
344B SER* 2.7 49.6 + - - +
346B LYS* 4.9 9.0 - - - +
409B LEU* 4.3 11.2 - - + +
410B GLN* 1.3 78.3 - - - +
412B VAL* 1.3 62.1 + - - +
413B THR* 3.9 15.0 + - + -
420B LEU* 3.6 22.0 - - + -
422B LEU 3.7 2.7 - - - -
423B CYS* 4.2 9.2 - - - -
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Residues in contact with VAL 412 (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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228B LEU* 3.7 24.2 - - + -
333B TYR* 3.8 30.7 - - + +
341B LEU* 4.1 24.7 - - + -
342B THR 3.4 7.9 - - - +
343B CYS* 4.1 15.3 - - + -
410B GLN* 5.3 4.0 - - + -
411B VAL* 1.3 77.9 - - - +
413B THR* 1.3 63.1 + - - +
420B LEU* 3.5 3.1 - - - +
421B LEU* 2.8 24.7 + - + -
422B LEU* 2.7 30.9 + - + +
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Residues in contact with THR 413 (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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341B LEU* 3.6 5.9 - - - +
342B THR* 3.0 47.2 + - - +
411B VAL* 3.9 20.0 - - + -
412B VAL* 1.3 80.3 - - - +
414B ASN* 1.3 64.6 + - - +
415B ARG* 3.2 0.5 + - - -
418B GLN* 4.3 12.8 + - - +
419B GLU 3.4 16.6 - - - +
420B LEU* 3.9 10.3 - - + -
421B LEU* 4.0 7.2 - - - +
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Residues in contact with ASN 414 (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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227B ARG* 4.2 5.1 - - - +
339B MET* 3.8 31.6 - - - +
340B THR 3.9 5.0 - - - +
341B LEU* 5.1 0.4 - - - -
413B THR* 1.3 69.3 + - - +
415B ARG* 1.3 57.9 + - - +
416B ASP* 2.9 23.6 + - - +
417B THR* 3.1 26.4 + - - +
418B GLN* 2.6 35.3 + - - -
419B GLU* 3.0 31.8 + - + +
421B LEU* 3.8 13.0 - - + +
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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