Contacts of the helix formed by residues 409 - 417 (chain D) in PDB entry 3U1K
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 409 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406C ILE 5.3 0.2 - - - +
407C LYS* 4.1 8.8 - - - +
408C SER* 3.2 35.1 + - - -
407D LYS* 3.4 3.0 - - + +
408D SER* 1.3 78.3 - - - +
410D GLN* 1.3 66.0 + - - +
411D VAL* 3.3 15.9 + - - +
412D ILE* 3.0 51.5 + - + +
413D THR* 3.0 26.3 + - - -
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Residues in contact with GLN 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C GLU* 5.5 2.1 - - - +
408C SER* 5.1 0.4 - - - -
629C LYS* 6.2 3.4 - - + -
632C GLN* 3.4 37.9 + - + +
633C ALA* 5.7 1.0 - - - +
637C VAL 3.3 18.2 + - - -
638C THR* 3.1 38.6 + - - +
112D ILE* 4.0 17.0 - - + +
407D LYS 5.5 0.2 - - - -
408D SER 3.6 3.6 + - - -
409D ASP* 1.3 74.6 + - - +
411D VAL* 1.3 69.4 + - + +
413D THR* 3.2 8.8 + - - -
414D ALA* 3.1 23.5 + - + +
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Residues in contact with VAL 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C SER* 5.0 15.3 - - - +
112D ILE* 4.1 21.1 - - + +
113D PRO 4.1 15.3 - - - +
114D THR* 4.2 3.4 - - + -
116D TYR* 4.2 14.4 - - - +
117D LEU* 3.6 31.6 - - + -
409D ASP* 3.3 12.9 + - - +
410D GLN* 1.3 82.1 - - + +
412D ILE* 1.3 62.0 + - - +
414D ALA* 3.4 12.0 + - - +
415D ILE* 3.4 13.9 + - - +
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Residues in contact with ILE 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 5.5 4.7 - - + -
407D LYS* 3.7 34.2 - - + +
409D ASP* 3.0 32.7 + - + +
410D GLN 3.3 0.2 - - - -
411D VAL* 1.3 74.8 - - + +
413D THR* 1.3 66.8 + - - +
415D ILE* 3.2 31.3 + - + +
416D ASN* 3.9 3.6 + - - +
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Residues in contact with THR 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629C LYS* 5.2 3.4 - - + +
633C ALA* 3.9 22.4 - - + -
405D GLY 5.6 0.4 - - - +
406D ILE* 4.2 12.6 - - + +
407D LYS* 3.3 34.1 + - - +
409D ASP 3.0 15.0 + - - -
410D GLN* 3.2 13.3 + - - -
412D ILE* 1.3 78.2 - - - +
414D ALA* 1.3 52.3 + - - +
415D ILE 3.1 0.2 + - - -
416D ASN* 3.6 0.3 + - - +
417D GLY* 2.7 40.1 + - - +
418D ILE* 4.1 16.4 - - + -
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Residues in contact with ALA 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632C GLN 5.3 1.3 - - - +
633C ALA* 4.8 17.4 - - - +
107D ALA* 3.4 20.5 - - + +
108D ALA* 4.0 14.6 + - + +
112D ILE* 4.2 23.6 - - + -
410D GLN* 3.1 12.8 + - + +
411D VAL 3.6 9.6 - - - +
412D ILE 3.3 0.2 - - - -
413D THR* 1.3 79.7 - - - +
415D ILE* 1.3 64.4 + - - +
417D GLY* 3.5 9.3 + - - +
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Residues in contact with ILE 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLN* 4.8 6.5 + - - +
107D ALA* 3.8 7.8 - - + +
114D THR* 3.8 27.4 - - + -
117D LEU* 4.3 14.4 - - + -
124D SER* 3.5 34.2 - - - +
126D LYS* 5.8 2.4 - - - +
411D VAL 3.4 15.3 - - - +
412D ILE* 3.3 22.4 - - + +
413D THR 3.1 1.0 - - - -
414D ALA* 1.3 79.7 - - - +
416D ASN* 1.3 68.4 + - + +
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Residues in contact with ASN 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D SER* 3.9 5.6 - - - +
125D ASP* 3.1 54.3 + - - +
126D LYS 4.8 0.2 + - - -
407D LYS* 6.4 2.0 - - - -
412D ILE 3.9 3.6 + - - +
413D THR 3.6 2.0 + - - +
415D ILE* 1.3 85.1 - - - +
417D GLY* 1.3 68.3 + - - +
418D ILE 5.0 1.9 - - - -
419D LYS* 5.5 8.3 + - - +
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Residues in contact with GLY 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633C ALA* 5.1 7.2 - - - -
405D GLY 4.7 4.3 - - - +
413D THR* 2.7 22.6 + - - +
414D ALA* 3.5 9.7 + - - -
415D ILE 3.3 2.6 - - - -
416D ASN* 1.3 88.2 - - - +
418D ILE* 1.3 65.5 + - - +
419D LYS* 4.1 1.6 + - - +
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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