Contacts of the strand formed by residues 420 - 431 (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 LEU 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A LEU* 4.9 10.1 - - + +
292A GLY 3.6 27.6 - - - +
293A PRO* 3.9 19.4 - - + +
296A ALA* 4.4 5.1 - - + +
297A PHE* 3.6 32.5 - - + -
411A VAL* 3.6 26.0 - - + -
412A VAL 3.6 14.6 - - - +
413A THR* 4.1 6.1 - - + -
418A GLN 3.8 2.0 + - - -
419A GLU* 1.3 74.6 - - - +
421A LEU* 1.3 63.8 + - - +
422A LEU 3.8 15.3 - - - +
423A CYS* 4.3 7.2 - - + -
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Residues in contact with LEU 421 (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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225A THR* 3.8 13.6 + - - +
227A ARG* 4.0 47.8 - - + +
228A LEU* 3.9 20.7 - - + +
296A ALA* 3.5 15.7 - - - +
339A MET* 3.8 20.6 - - + -
341A LEU* 3.6 31.4 - - + -
412A VAL* 2.8 15.0 + - + +
413A THR 4.1 0.7 - - - -
414A ASN* 3.7 24.5 - - + +
419A GLU* 3.4 2.0 + - + +
420A LEU* 1.3 79.6 - - - +
422A LEU* 1.3 65.3 + - - +
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Residues in contact with LEU 422 (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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223A LEU* 3.7 23.1 - - + -
224A GLY* 3.8 18.6 - - - -
225A THR* 4.1 6.1 - - + +
228A LEU* 4.4 10.8 - - + +
230A LEU* 4.6 8.5 - - + +
296A ALA* 3.7 5.8 - - - +
298A PHE* 3.6 30.7 - - + -
333A TYR* 4.2 24.9 - - + -
410A GLN 3.8 1.3 - - - +
411A VAL* 3.6 1.4 - - - -
412A VAL* 2.7 48.4 + - + +
420A LEU* 3.7 4.6 - - - +
421A LEU* 1.3 85.3 - - - +
423A CYS* 1.3 59.8 + - - +
424A THR* 4.2 7.2 - - - +
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Residues in contact with CYS 423 (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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285A LEU* 4.2 6.5 - - - -
288A LEU* 4.5 4.9 - - + -
296A ALA 2.9 11.1 + - - +
297A PHE* 3.4 39.5 - - + -
298A PHE 2.9 25.8 + - - +
409A LEU* 3.6 26.2 - - - -
410A GLN 3.3 6.3 - - - +
411A VAL* 4.1 11.0 - - + -
420A LEU* 4.3 11.4 - - + +
422A LEU* 1.3 73.9 - - - +
424A THR* 1.3 65.3 + - - +
425A ALA 5.3 0.2 - - - -
444A LEU* 5.3 1.2 - - - +
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Residues in contact with THR 424 (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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223A LEU* 3.6 26.2 - - + +
298A PHE* 3.3 9.7 - - - +
300A VAL* 3.7 24.7 - - + -
409A LEU* 3.6 5.0 - - - -
410A GLN* 2.8 43.4 + - - -
422A LEU* 4.2 7.3 - - - +
423A CYS* 1.3 77.0 + - - +
425A ALA* 1.3 64.5 + - - +
426A TYR* 3.6 35.7 + - + +
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Residues in contact with ALA 425 (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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274A ILE* 4.2 9.2 - - + -
278A PHE* 3.5 28.9 - - + -
285A LEU* 5.0 1.6 - - + -
298A PHE 2.9 9.9 + - - +
299A LEU* 3.4 17.0 - - + +
300A VAL* 2.8 32.1 + - - -
408A ILE 3.5 4.3 - - - -
409A LEU* 4.2 7.6 - - + +
423A CYS* 4.3 0.6 - - - -
424A THR* 1.3 75.5 - - - +
426A TYR* 1.3 57.4 + - - +
444A LEU* 4.6 4.9 - - + +
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Residues in contact with TYR 426 (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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223A LEU* 5.1 0.3 - - - +
230A LEU* 4.9 10.2 - - - +
233A PHE* 4.6 19.6 - + - -
254A ILE* 5.0 2.2 - - + -
278A PHE* 4.6 0.3 - - - -
300A VAL* 3.3 19.5 - - + +
302A PHE* 3.3 34.3 - + + -
380A P1L 6.0 2.0 - - + -
407A THR* 3.5 10.4 - - - -
408A ILE* 2.7 51.4 + - + +
410A GLN* 2.8 41.1 + - + -
424A THR* 3.6 32.7 + - + +
425A ALA* 1.3 74.0 - - - +
427A VAL* 1.3 64.5 + - - +
428A PHE* 3.7 22.2 - + + -
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Residues in contact with VAL 427 (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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274A ILE* 5.7 2.0 - - + -
277A LYS* 4.1 28.0 - - + -
278A PHE* 5.5 3.8 - - + -
299A LEU* 4.2 23.3 - - + -
300A VAL 3.0 4.2 + - - +
301A LYS* 3.7 35.4 - - + -
302A PHE* 2.8 27.3 + - - +
406A PHE 4.6 3.1 - - - +
407A THR* 4.3 8.7 - - + -
425A ALA 4.3 0.2 - - - -
426A TYR* 1.3 79.1 - - - +
428A PHE* 1.3 67.3 + - - +
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Residues in contact with PHE 428 (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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252A VAL* 4.5 1.6 - - + -
301A LYS* 5.1 1.5 - - - +
302A PHE* 3.5 33.9 - + + -
304A ALA* 5.0 2.2 - - + -
380A P1L 3.4 44.6 - - + -
400A ASN 5.1 0.7 - - - +
403A LEU* 3.4 41.0 + - + +
404A GLU* 4.8 0.9 + - - -
406A PHE* 3.6 36.3 + + + +
408A ILE* 3.9 23.8 - - + -
426A TYR* 3.7 35.0 - + + -
427A VAL* 1.3 77.1 - - - +
429A GLU* 1.3 69.6 + - - +
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Residues in contact with GLU 429 (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 LYS* 2.9 34.8 + - - -
302A PHE 2.7 9.8 + - - +
303A TRP* 3.3 27.3 + - + +
304A ALA* 2.9 25.7 + - - +
400A ASN* 3.4 31.6 + - + +
403A LEU* 3.9 5.9 - - - +
428A PHE* 1.3 81.3 - - - +
430A VAL* 1.3 66.2 + - - +
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Residues in contact with VAL 430 (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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303A TRP* 4.1 10.9 - - - -
304A ALA* 3.6 6.5 - - + +
306A LEU* 3.8 22.0 - - + +
307A ASN* 5.9 0.9 - - - +
396A ARG* 3.8 29.8 - - + +
399A MET* 3.6 33.2 - - + -
400A ASN* 2.8 19.6 + - - +
403A LEU* 3.6 23.8 - - + -
429A GLU* 1.3 75.6 - - - +
431A SER* 1.3 74.3 + - - +
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Residues in contact with SER 431 (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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303A TRP* 3.7 25.6 - - - -
304A ALA 2.8 14.3 + - - +
305A ASP* 4.5 3.7 - - - -
306A LEU 4.8 0.2 + - - -
307A ASN* 4.4 7.3 - - - +
396A ARG* 4.3 2.2 - - - -
430A VAL* 1.3 87.1 - - - +
432A THR* 1.3 70.4 + - - +
435A ARG* 3.6 14.6 + - - +
436A GLY 3.0 27.0 + - - -
438A GLN* 5.6 0.7 - - - +
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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