Contacts of the helix formed by residues 403 - 417 (chain A) in PDB entry 2ES0
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 ASP 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A LEU* 1.3 77.7 - - - +
404A SER* 1.3 67.2 + - - +
405A HIS* 3.1 15.0 + - + +
406A SER* 2.5 39.7 + - - -
407A TYR* 3.1 17.2 + - - +
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU 3.7 2.3 + - - -
403A ASP* 1.3 72.4 - - - +
405A HIS* 1.3 59.9 + - - +
407A TYR* 3.3 7.4 + - - +
408A GLU* 2.9 42.1 + - - +
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Residues in contact with HIS 405 (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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403A ASP* 3.1 13.5 + - + +
404A SER* 1.3 83.2 + - - +
406A SER* 1.3 69.3 + - - +
408A GLU* 3.4 4.4 + - - +
409A ILE* 3.0 55.9 + - + +
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Residues in contact with SER 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU* 3.6 18.9 - - - +
403A ASP* 2.5 33.3 + - - -
405A HIS* 1.3 82.8 - - - +
407A TYR* 1.3 57.6 + - - +
409A ILE* 3.9 5.6 - - - +
410A THR* 2.5 40.9 + - - -
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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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388A TRP* 3.7 33.8 - + - -
392A LEU* 4.0 32.8 + - + -
394A PRO* 5.4 5.2 - - - +
402A LEU* 3.8 15.9 - - + +
403A ASP 3.1 13.8 + - - +
404A SER* 3.6 11.2 - - - +
406A SER* 1.3 79.2 + - - +
408A GLU* 1.3 78.8 + - - +
410A THR* 3.3 2.4 + - - -
411A SER* 2.8 38.4 + - - -
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Residues in contact with GLU 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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404A SER* 2.9 27.0 + - - +
405A HIS* 3.9 4.3 - - - +
407A TYR* 1.3 95.8 - - + +
409A ILE* 1.3 59.8 + - + +
411A SER* 3.8 6.7 - - - -
412A GLN* 3.0 29.3 + - - +
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Residues in contact with ILE 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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405A HIS* 3.0 53.7 + - + +
406A SER* 3.9 5.4 - - - +
408A GLU* 1.3 75.2 - - + +
410A THR* 1.3 65.9 + - - +
412A GLN* 3.4 10.2 + - - +
413A ASN* 3.0 40.2 + - - +
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Residues in contact with THR 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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365A PHE* 6.0 2.0 - - + -
388A TRP* 3.9 19.3 - - + -
392A LEU* 3.9 17.0 - - + -
402A LEU* 4.1 9.1 - - + +
406A SER* 2.5 27.3 + - - -
407A TYR* 3.6 5.4 - - - -
409A ILE* 1.3 75.9 - - - +
411A SER* 1.3 58.4 + - - +
413A ASN* 3.3 10.6 + - + +
414A VAL* 3.0 39.7 + - + +
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Residues in contact with SER 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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388A TRP* 3.7 23.1 - - - -
407A TYR* 2.8 29.6 + - - -
408A GLU* 3.8 8.7 - - - -
409A ILE 3.3 0.2 - - - -
410A THR* 1.3 77.6 - - - +
412A GLN* 1.3 57.0 + - - +
414A VAL* 3.5 1.2 + - - +
415A LYS* 2.9 58.1 + - - +
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Residues in contact with GLN 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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408A GLU 3.0 18.3 + - - +
409A ILE* 3.7 9.5 - - - +
411A SER* 1.3 74.2 - - - +
413A ASN* 1.3 60.4 + - - +
415A LYS* 4.5 3.8 - - - -
416A ASP* 2.7 61.0 + - - +
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Residues in contact with ASN 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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384A VAL* 5.9 0.2 - - - -
409A ILE* 3.0 39.0 + - - +
410A THR* 3.5 8.4 - - + +
412A GLN* 1.3 81.0 - - - +
414A VAL* 1.3 59.3 + - + +
416A ASP* 3.7 8.5 - - - +
417A GLY* 3.0 26.5 + - - -
418A GLY 4.6 1.4 + - - -
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Residues in contact with VAL 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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384A VAL* 3.9 30.8 - - + +
385A GLU* 4.1 18.8 - - - +
388A TRP* 3.8 38.4 - - + -
410A THR* 3.0 27.7 + - + +
411A SER* 3.8 4.0 - - - +
413A ASN* 1.3 78.6 - - + +
415A LYS* 1.3 74.8 + - - +
417A GLY* 3.5 9.8 + - - -
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Residues in contact with LYS 415 (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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388A TRP* 3.5 31.5 - - - +
411A SER* 2.9 45.0 + - - +
412A GLN* 3.8 4.7 - - - +
414A VAL* 1.3 86.0 - - - +
416A ASP* 1.3 67.5 + - - +
417A GLY 3.4 0.2 + - - -
419A ARG* 3.3 14.4 + - - -
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Residues in contact with ASP 416 (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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412A GLN* 2.7 49.0 + - - +
413A ASN* 3.7 9.1 - - - +
415A LYS* 1.3 70.9 - - - +
417A GLY* 1.3 65.8 + - - +
418A GLY* 3.3 4.3 - - - +
419A ARG* 2.9 33.1 + - - +
420A TYR* 3.8 37.9 - - + +
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Residues in contact with GLY 417 (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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381A ALA* 6.1 1.2 - - - +
413A ASN 3.0 15.7 + - - -
414A VAL 3.9 8.7 - - - -
415A LYS 3.3 1.4 - - - -
416A ASP* 1.3 76.4 - - - +
418A GLY* 1.3 58.1 + - - +
419A ARG* 3.3 13.5 + - - +
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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