Contacts of the strand formed by residues 353 - 360 (chain D) in PDB entry 1TYE
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 SER 353 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D GLN* 2.9 33.6 + - - +
110D TYR* 3.0 22.0 + - - -
352D ARG* 1.3 75.6 - - - +
354D LYS* 1.3 61.4 + - - +
355D VAL* 6.0 0.2 - - - +
388D GLY 3.5 7.1 + - - -
389D LEU* 2.9 46.3 + - - +
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Residues in contact with LYS 354 (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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106D GLN* 6.0 0.2 - - - -
353D SER* 1.3 79.0 - - - +
355D VAL* 1.3 63.8 + - - +
356D GLU* 3.0 54.5 + - + +
385D SER* 5.7 1.8 - - - -
386D CYS 3.4 13.9 - - - +
387D MET* 4.1 19.1 - - + -
389D LEU* 4.5 0.9 - - - -
419D VAL* 4.5 22.0 - - - +
421D PHE* 4.3 14.0 - - - -
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Residues in contact with VAL 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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104D VAL* 3.8 36.3 - - + +
106D GLN* 5.9 3.8 - - + +
353D SER* 6.0 0.4 - - - +
354D LYS* 1.3 73.6 - - - +
356D GLU* 1.3 60.8 + - - +
357D LEU* 4.1 1.8 - - + -
385D SER* 3.1 4.9 - - - -
386D CYS* 2.9 35.1 + - + +
389D LEU* 3.9 27.6 - - + -
395D VAL* 4.7 6.5 - - + -
397D PHE* 3.8 29.2 - - + -
418D PRO* 3.9 14.8 - - + -
421D PHE* 4.9 8.5 - - + -
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Residues in contact with GLU 356 (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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354D LYS* 3.0 44.2 + - + +
355D VAL* 1.3 74.6 - - - +
357D LEU* 1.3 69.4 + - - +
384D LYS* 4.0 4.9 - - + +
385D SER* 3.9 20.7 + - - -
418D PRO* 3.9 5.8 - - - +
419D VAL* 2.7 46.6 + - + +
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Residues in contact with LEU 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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102D ILE* 4.5 8.5 - - + -
104D VAL* 4.5 6.3 - - + -
355D VAL* 4.5 2.0 - - + -
356D GLU* 1.3 82.8 - - - +
358D GLU* 1.3 60.2 + - - +
359D VAL* 5.6 0.4 - - - -
370D PHE* 3.9 27.8 - - + -
384D LYS* 3.3 35.7 + - + +
397D PHE* 3.7 50.7 - - + -
399D ILE* 5.1 0.2 - - + -
416D ILE* 4.2 22.2 - - + -
417D LYS 3.9 2.9 - - - -
418D PRO* 4.1 26.9 - - + -
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Residues in contact with GLU 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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357D LEU* 1.3 77.3 - - - +
359D VAL* 1.3 63.2 + - - +
360D ARG* 2.9 37.8 + - + +
384D LYS* 5.5 1.8 - - - +
416D ILE* 3.7 5.6 - - - -
417D LYS* 3.1 49.2 + - + +
419D VAL* 3.3 32.0 - - + +
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Residues in contact with VAL 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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357D LEU 5.6 0.7 - - - -
358D GLU* 1.3 73.5 - - - +
360D ARG* 1.3 61.6 + - - +
361D ASP 4.0 0.9 + - - -
362D LEU* 3.8 34.6 + - + -
368D LEU* 3.9 18.4 - - + -
370D PHE* 4.0 28.5 - - + -
384D LYS* 4.1 17.6 - - + +
414D PHE* 4.7 3.4 - - + -
415D THR 3.9 7.9 - - - +
416D ILE* 5.1 4.9 - - + +
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Residues in contact with ARG 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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358D GLU* 2.9 40.3 + - + +
359D VAL* 1.3 76.1 - - - +
361D ASP* 1.3 84.9 + - - +
414D PHE* 3.4 1.6 - - - +
415D THR* 3.1 40.0 + - - +
417D LYS* 4.1 28.0 - - - +
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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