Contacts of the helix formed by residues 354 - 364 (chain B) in PDB entry 1U3T
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 LYS 354 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350B LEU* 3.8 19.2 - - + +
351B PRO* 2.7 48.3 + - + +
353B GLU* 1.3 78.8 - - - +
355B ILE* 1.3 63.8 + - - +
356B ASN 3.3 3.1 - - - -
357B GLU* 2.9 44.6 + - + +
358B GLY 3.2 4.7 + - - -
372B LEU* 4.7 0.7 - - - -
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 3.7 22.7 - - + -
21B PHE* 3.9 25.4 - - + -
23B ILE* 4.4 13.5 - - + -
45B ILE* 4.1 0.3 - - - +
146B PHE* 3.7 33.7 - - + -
352B PHE* 3.1 18.9 + - + +
353B GLU 3.2 6.0 - - - +
354B LYS* 1.3 74.3 - - - +
356B ASN* 1.3 70.5 + - - +
358B GLY* 2.9 17.8 + - - -
359B PHE* 3.1 28.9 + - + -
372B LEU* 3.7 24.2 - - + -
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Residues in contact with ASN 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PRO* 3.6 16.2 - - + +
21B PHE* 2.7 60.8 + - - +
23B ILE* 6.0 0.8 - - - +
353B GLU 5.0 2.0 + - - -
354B LYS 3.3 0.6 - - - -
355B ILE* 1.3 85.1 - - - +
357B GLU* 1.3 59.5 - - - +
359B PHE* 3.4 8.3 + - - +
360B ASP* 3.1 31.7 + - - +
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Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B LEU* 4.0 25.6 - - + +
354B LYS* 2.9 37.8 + - + +
356B ASN* 1.3 75.6 - - - +
358B GLY* 1.3 59.1 + - - +
360B ASP* 3.2 14.9 + - + +
361B LEU* 3.0 34.3 + - + +
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Residues in contact with GLY 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 3.7 23.1 - - - +
350B LEU* 3.8 13.9 - - - +
354B LYS 3.2 6.2 + - - -
355B ILE* 2.9 9.1 + - - -
357B GLU* 1.3 78.6 - - - +
359B PHE* 1.3 60.2 + - - +
361B LEU* 3.4 7.3 + - - +
362B LEU* 3.3 18.2 + - - +
367B SER* 4.7 0.3 + - - -
370B THR* 4.1 12.4 + - - -
372B LEU* 5.1 0.7 - - - -
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Residues in contact with PHE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 3.3 40.2 - + + -
45B ILE* 3.6 34.5 - - + -
49B ASP* 3.9 5.8 - - + -
50B ASP* 3.8 45.5 - - + -
53B VAL* 4.7 2.5 - - + -
146B PHE* 3.9 12.3 - + - -
355B ILE* 3.1 42.1 + - + -
356B ASN* 3.9 8.5 - - - +
357B GLU 3.2 0.2 - - - -
358B GLY* 1.3 74.5 - - - +
360B ASP* 1.3 65.6 + - - +
362B LEU* 3.2 6.7 + - + +
363B HIS* 3.1 40.9 + - + -
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Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ASN* 3.1 20.4 + - - +
357B GLU* 3.2 15.9 + - + +
359B PHE* 1.3 78.2 - - - +
361B LEU* 1.3 55.0 + - + +
363B HIS* 3.3 13.3 + - - +
364B SER* 2.7 37.7 + - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B HIS* 3.6 48.0 - - + +
350B LEU* 4.1 20.4 - - + -
357B GLU* 3.0 22.8 + - + +
358B GLY* 3.4 8.7 - - - +
360B ASP* 1.3 78.2 - - + +
362B LEU* 1.3 61.4 + - - +
364B SER* 3.3 9.0 + - - +
365B GLY 3.2 16.5 + - - -
366B LYS* 3.5 18.8 + - + -
367B SER* 3.3 16.8 + - - +
370B THR* 3.9 9.0 - - - +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 4.5 24.0 - - + +
47B GLY* 4.5 12.3 - - - +
50B ASP* 4.1 30.7 - - + +
358B GLY 3.3 9.6 + - - +
359B PHE* 3.2 12.9 + - + +
360B ASP 3.2 0.4 - - - -
361B LEU* 1.3 78.7 - - - +
363B HIS* 1.3 66.1 + - + +
365B GLY* 3.2 13.5 + - - -
367B SER* 3.5 11.6 + - - +
368B ILE 4.1 17.0 - - - +
369B ARG* 5.8 0.7 - - - +
2377B NAD 3.5 35.6 + - - +
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Residues in contact with HIS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASP* 2.9 37.8 + - - -
53B VAL* 6.4 1.1 - - + -
359B PHE* 3.1 29.9 + - + +
360B ASP* 3.3 15.3 + - - +
362B LEU* 1.3 82.4 - - + +
364B SER* 1.3 62.4 + - - +
365B GLY* 3.4 0.9 + - - -
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Residues in contact with SER 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ASN* 5.0 0.5 + - - -
360B ASP* 2.7 24.2 + - - +
361B LEU* 3.4 14.5 - - - +
362B LEU 3.2 0.2 - - - -
363B HIS* 1.3 77.9 - - - +
365B GLY* 1.3 59.4 + - - +
366B LYS* 3.9 26.1 - - - +
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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