Contacts of the strand formed by residues 406 - 413 (chain A) in PDB entry 1EX0
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 MET 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A LYS* 2.6 40.5 + - - +
343A ASP* 5.0 1.8 - - - +
399A PRO* 3.9 13.6 - - + +
400A GLN* 3.6 26.7 - - - -
401A GLU* 3.7 32.2 + - + +
405A GLY* 1.3 69.0 - - - -
407A TYR* 1.3 60.2 + - - +
12B ARG* 3.9 27.6 - - - +
16B PRO* 4.9 13.5 - - + -
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Residues in contact with TYR 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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264A ALA* 6.2 2.9 - - + -
269A LYS* 4.1 21.1 - - + +
398A THR 4.6 0.2 - - - +
399A PRO* 3.6 13.2 - - - +
400A GLN 3.1 27.2 + - - +
402A ASN* 3.7 13.8 + - - +
404A ASP* 3.6 31.8 + - + -
405A GLY* 3.2 28.4 + - - -
406A MET* 1.3 78.2 - - - +
408A ARG* 1.3 86.4 + - + +
409A CYS* 3.7 2.4 + - - -
1340A PGO 3.4 33.9 - - + +
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Residues in contact with ARG 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ARG* 2.9 56.5 + - - +
261A VAL* 5.6 0.6 - - - +
263A SER* 3.2 21.1 - - - +
264A ALA* 3.5 32.5 - - + +
269A LYS* 5.9 0.2 - - - +
396A ASP 3.3 15.7 - - - +
397A SER* 3.8 17.3 - - - +
399A PRO* 4.1 8.3 - - + +
402A ASN* 3.2 10.5 + - - +
404A ASP* 5.7 0.4 + - - -
407A TYR* 1.3 93.7 - - + +
409A CYS* 1.3 61.1 + - - +
410A GLY 3.9 11.4 - - - -
427A ASP* 3.9 0.2 - - - +
1340A PGO 3.1 29.5 + - - -
404B ASP* 4.0 6.5 + - - +
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Residues in contact with CYS 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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394A ALA 4.3 0.3 - - - +
395A VAL* 3.5 4.2 - - - +
396A ASP* 2.8 40.4 + - + +
398A THR 5.9 0.2 - - - -
400A GLN* 3.2 45.5 - - - +
402A ASN* 3.7 22.7 - - - -
407A TYR 3.9 0.4 - - - -
408A ARG* 1.3 79.4 - - - +
410A GLY* 1.3 61.1 + - - +
427A ASP* 3.3 18.8 - - + -
430A PHE* 4.2 4.5 - - - -
431A VAL* 4.6 10.7 - - + +
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Residues in contact with GLY 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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260A ARG* 2.9 21.8 + - - -
263A SER* 4.8 0.5 + - - -
394A ALA 3.6 4.7 - - - -
395A VAL* 4.4 4.3 - - - -
408A ARG* 3.9 5.9 - - - -
409A CYS* 1.3 76.1 - - - +
411A PRO* 1.3 76.8 - - - +
412A ALA* 3.4 4.0 - - - -
426A PHE* 3.3 17.2 + - - -
427A ASP* 2.8 11.5 + - - -
431A VAL* 5.7 0.4 - - - -
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Residues in contact with PRO 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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256A ILE* 3.8 34.8 - - + +
259A SER* 4.1 9.4 - - - -
260A ARG* 3.9 24.0 - - - +
380A MET* 5.2 2.2 - - + -
382A ARG* 3.1 13.9 + - - +
393A GLN* 3.8 21.5 - - + -
394A ALA 3.3 6.3 - - - +
395A VAL* 3.8 12.1 - - + -
410A GLY* 1.3 80.1 - - - +
412A ALA* 1.4 59.9 + - - +
426A PHE* 2.8 30.6 + - + -
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Residues in contact with ALA 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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393A GLN* 3.8 2.9 - - - -
394A ALA* 2.7 43.5 + - - +
410A GLY* 3.4 1.0 - - - -
411A PRO* 1.4 73.8 - - - +
413A SER* 1.3 63.5 + - - +
414A VAL 3.1 0.3 + - - -
417A ILE* 3.8 20.9 - - + -
425A GLN 4.6 0.7 - - - -
426A PHE 3.3 21.3 - - - +
428A ALA* 4.0 18.2 - - + -
431A VAL* 4.3 8.5 - - + -
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Residues in contact with SER 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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382A ARG* 4.0 3.4 - - - +
385A LEU* 4.2 9.2 - - - -
389A PHE* 2.7 38.3 + - - +
390A GLY 4.6 0.2 + - - -
392A TRP 4.5 0.5 + - - -
393A GLN* 3.2 17.6 + - - -
412A ALA* 1.3 69.6 - - - +
414A VAL* 1.3 63.3 + - - +
415A GLN* 3.4 4.7 + - - +
416A ALA* 3.2 28.5 + - - +
417A ILE* 2.8 24.4 + - - +
424A PHE 5.7 1.0 + - - -
425A GLN 4.8 2.2 + - - -
428A ALA* 5.8 0.8 - - - +
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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