Contacts of the helix formed by residues 354 - 364 (chain D) in PDB entry 1D1T
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350D LEU* 3.6 23.9 - - + +
351D PRO* 3.2 43.3 + - + +
352D PHE 3.1 1.8 - - - -
353D LYS* 1.3 90.7 - - + +
355D ILE* 1.3 61.8 + - - +
356D SER 3.4 2.5 - - - -
357D GLU* 3.2 20.1 + - + +
358D GLY 3.2 8.0 + - - -
372D LEU* 4.5 1.1 - - - -
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Residues in contact with ILE 355 (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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12D ALA* 4.0 15.5 - - + -
21D PHE* 4.0 18.8 - - + -
23D ILE* 4.6 11.4 - - + -
45D ILE* 4.3 0.4 - - + +
146D PHE* 3.7 33.4 - - + -
352D PHE* 3.1 19.5 + - + +
353D LYS 3.2 6.2 - - - +
354D LYS* 1.3 77.0 - - - +
356D SER* 1.3 66.9 + - - +
358D GLY* 2.8 17.5 + - - -
359D PHE* 2.9 32.4 + - + -
372D LEU* 3.6 30.5 - - + -
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Residues in contact with SER 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PRO* 5.2 4.9 - - - +
21D PHE* 4.6 19.5 + - - +
353D LYS 4.9 1.5 + - - -
354D LYS* 3.4 1.2 - - - +
355D ILE* 1.3 86.3 - - - +
357D GLU* 1.3 56.8 + - - +
359D PHE* 3.2 9.2 + - - +
360D GLU* 2.9 26.4 + - - +
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Residues in contact with GLU 357 (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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350D LEU* 4.0 13.0 - - + -
354D LYS* 3.2 18.2 + - + +
355D ILE 3.2 0.6 - - - -
356D SER* 1.3 75.4 - - - +
358D GLY* 1.3 66.7 + - - +
360D GLU* 3.0 38.9 + - - +
361D LEU* 3.0 50.2 + - + +
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Residues in contact with GLY 358 (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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45D ILE* 3.5 24.9 - - - +
350D LEU* 4.0 2.6 - - - +
354D LYS 3.2 7.0 + - - -
355D ILE 2.8 8.7 + - - -
357D GLU* 1.3 80.1 - - - +
359D PHE* 1.3 56.8 + - - +
361D LEU* 3.6 4.6 + - - +
362D LEU* 3.1 25.5 + - - +
370D THR* 3.9 20.4 + - - -
372D LEU* 5.2 0.2 - - - -
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Residues in contact with PHE 359 (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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21D PHE* 3.2 34.3 - + + -
45D ILE* 3.8 30.5 - - + -
49D ASP* 4.0 6.5 - - + -
50D ASP* 3.9 36.1 - - + -
53D ILE* 4.0 18.2 - - + -
146D PHE* 3.7 19.3 - + - -
355D ILE* 2.9 37.4 + - + +
356D SER* 3.7 9.2 - - - +
357D GLU 3.2 0.4 - - - -
358D GLY* 1.3 76.5 - - - +
360D GLU* 1.3 61.0 + - - +
362D LEU* 3.6 7.4 - - + +
363D ASN* 2.8 37.4 + - - +
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Residues in contact with GLU 360 (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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356D SER 2.9 13.7 + - - +
357D GLU* 3.0 33.6 + - - +
359D PHE* 1.3 77.8 - - - +
361D LEU* 1.3 73.2 + - - +
363D ASN* 3.3 5.6 + - - +
364D SER* 2.8 41.7 + - - -
366D GLN* 5.3 1.4 - - - +
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Residues in contact with LEU 361 (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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348D HIS* 4.1 31.9 - - + +
350D LEU* 4.9 3.8 - - + -
357D GLU* 3.0 50.5 + - + +
358D GLY* 3.9 6.7 - - - +
360D GLU* 1.3 93.6 - - - +
362D LEU* 1.3 65.7 + - - +
364D SER* 3.3 11.7 + - - +
366D GLN* 3.0 42.1 + - + +
367D SER* 3.5 19.1 + - - +
370D THR* 4.6 1.8 - - - +
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Residues in contact with LEU 362 (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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45D ILE* 3.7 33.4 - - + +
47D ARG* 3.6 32.6 + - - +
50D ASP* 4.0 27.8 - - + -
358D GLY 3.1 19.0 + - - +
359D PHE* 3.6 10.5 - - + +
360D GLU 3.2 0.2 - - - -
361D LEU* 1.3 80.1 - - - +
363D ASN* 1.3 63.3 + - - +
365D GLY* 3.1 10.4 + - - -
367D SER* 4.3 11.6 - - - +
368D ILE 4.5 12.8 - - - +
369D ARG* 5.4 0.9 - - - +
370D THR* 5.8 0.7 - - - +
4377D NAD 3.8 29.5 + - - +
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Residues in contact with ASN 363 (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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47D ARG* 3.0 29.0 + - - +
50D ASP* 3.1 26.5 + - - +
54D LYS* 3.8 17.7 - - - +
359D PHE* 2.8 30.2 + - - +
360D GLU* 3.8 4.0 - - - +
362D LEU* 1.3 81.6 - - - +
364D SER* 1.3 56.2 + - - +
365D GLY 3.1 4.4 + - - -
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Residues in contact with SER 364 (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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225D ASN* 5.4 0.3 + - - -
360D GLU* 2.8 28.1 + - - -
361D LEU* 3.3 12.8 + - - +
362D LEU 3.3 0.2 - - - -
363D ASN* 1.3 71.1 - - - +
365D GLY* 1.3 56.9 + - - +
366D GLN* 3.0 38.6 + - - +
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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