Contacts of the strand formed by residues 406 - 414 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A VAL* 3.6 21.5 - - + -
348A CYS 3.5 9.4 - - - -
349A SER* 4.8 2.2 - - - +
380A P1L 4.2 16.6 - - + -
382A TYR* 4.5 10.3 - + - -
383A LEU* 3.5 28.3 - - + -
386A PHE* 3.9 24.9 - + + -
402A VAL 4.4 3.1 - - - +
403A LEU* 3.1 37.0 + - + +
404A GLU 3.4 0.6 + - - -
405A ASN* 1.3 78.4 - - - +
407A THR* 1.3 65.9 + - - +
408A ILE* 4.0 17.5 - - + -
426A TYR 4.5 0.5 - - - +
427A VAL* 4.6 0.3 - - - +
428A PHE* 3.6 41.0 + + - -
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Residues in contact with THR 407 (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 LYS* 2.7 48.1 + - + +
278A PHE* 3.4 12.4 - - + -
347A VAL* 4.3 1.2 - - - +
348A CYS* 2.7 49.0 + - - +
351A GLY* 5.4 0.5 + - - -
404A GLU 5.1 2.7 - - - +
405A ASN 5.0 3.5 + - - -
406A PHE* 1.3 84.0 - - - +
408A ILE* 1.3 65.2 + - - +
426A TYR 3.5 13.0 - - - +
427A VAL* 4.3 13.7 - - + -
428A PHE* 4.7 0.4 - - - -
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Residues in contact with ILE 408 (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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278A PHE* 3.6 4.5 - - - -
345A SER* 4.9 0.4 - - - -
346A LYS 3.4 13.9 - - - +
347A VAL* 4.1 16.4 - - + -
380A P1L 3.6 58.6 - - + -
383A LEU* 4.6 0.9 - - + -
406A PHE* 4.0 14.8 - - + -
407A THR* 1.3 80.7 - - - +
409A LEU* 1.3 68.0 + - - +
410A GLN* 4.5 6.1 - - + -
425A ALA* 3.5 1.6 - - - -
426A TYR* 2.7 57.8 + - + -
428A PHE* 3.9 13.2 - - + -
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Residues in contact with LEU 409 (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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278A PHE* 3.6 30.5 - - + -
279A PRO* 5.9 1.3 - - + -
283A GLY 4.3 18.4 - - - +
285A LEU* 4.3 15.3 - - + +
288A LEU* 4.3 15.0 - - + -
344A SER 3.6 1.0 - - - +
345A SER* 3.5 1.4 - - - -
346A LYS* 2.8 54.9 + - + +
348A CYS* 5.4 0.2 - - - -
408A ILE* 1.3 73.8 - - - +
410A GLN* 1.3 60.4 + - - +
411A VAL* 4.1 10.4 + - + +
423A CYS* 3.6 25.1 - - - -
424A THR 3.6 14.4 - - - +
425A ALA* 4.2 11.9 - - + -
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Residues in contact with GLN 410 (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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233A PHE* 4.0 22.0 - - - -
329A VAL* 5.7 0.6 - - - +
331A SER* 4.8 3.6 + - - -
333A TYR* 4.1 16.9 + - - -
343A CYS* 6.2 2.2 - - - +
344A SER 3.2 3.4 - - - +
345A SER* 3.2 28.7 + - - +
380A P1L 4.3 10.5 - - - +
408A ILE* 4.1 4.2 - - + -
409A LEU* 1.3 74.7 - - - +
411A VAL* 1.3 64.7 + - - +
412A VAL* 5.2 6.1 - - + -
422A LEU 3.8 1.0 - - - +
423A CYS* 3.3 5.7 - - - -
424A THR* 2.8 46.3 + - - +
426A TYR* 2.8 37.6 + - + +
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Residues in contact with VAL 411 (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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288A LEU* 4.0 34.1 - - + -
342A THR 3.5 3.3 - - - +
343A CYS* 3.6 0.3 - - - -
344A SER* 2.8 49.1 + - - +
346A LYS* 4.8 10.8 - - - +
409A LEU* 4.4 11.2 - - + +
410A GLN* 1.3 78.3 - - - +
412A VAL* 1.3 62.9 + - - +
413A THR* 3.8 15.2 - - + +
420A LEU* 3.6 23.3 - - + -
422A LEU 3.6 2.2 - - - -
423A CYS* 4.1 9.4 - - - +
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Residues in contact with VAL 412 (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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228A LEU* 3.6 24.2 - - + -
333A TYR* 3.7 29.8 - - + +
341A LEU* 4.1 16.8 - - + -
342A THR 3.4 7.4 - - - +
343A CYS* 4.1 20.2 - - + -
410A GLN* 5.2 6.7 - - + -
411A VAL* 1.3 78.8 - - - +
413A THR* 1.3 63.4 + - - +
420A LEU* 3.6 2.8 - - - +
421A LEU* 2.8 24.2 + - + +
422A LEU* 2.7 32.3 + - + +
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Residues in contact with THR 413 (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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341A LEU* 3.6 5.9 - - - +
342A THR* 2.9 52.6 + - - +
411A VAL* 3.8 21.5 - - + +
412A VAL* 1.3 79.9 - - - +
414A ASN* 1.3 65.3 + - - +
415A ARG* 3.2 1.0 + - - -
418A GLN* 4.6 14.3 + - - +
419A GLU 3.2 15.7 - - - +
420A LEU* 4.1 9.0 - - + -
421A LEU* 4.1 5.6 - - - +
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Residues in contact with ASN 414 (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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227A ARG* 3.5 13.3 - - - +
339A MET* 3.3 37.5 - - - +
340A THR 3.9 6.2 + - - +
413A THR* 1.3 68.6 - - - +
415A ARG* 1.3 56.8 + - - +
416A ASP* 3.1 21.7 + - - +
417A THR* 3.3 28.7 + - - +
418A GLN* 2.6 36.2 + - - -
419A GLU* 2.9 15.5 + - + +
421A LEU* 3.7 18.1 - - + +
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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