Contacts of the strand formed by residues 369 - 373 (chain C) 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 ARG 369 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLY* 5.0 0.7 - - - -
45C ILE 3.4 23.5 + - - +
46C CYS* 3.5 24.3 - - - +
47C ARG 4.1 1.0 - - - +
68C GLU* 3.0 39.0 + - - -
171C LEU* 3.3 24.5 - - + +
175C GLY* 3.4 21.2 - - - -
202C GLY* 4.7 9.6 - - - -
203C VAL* 4.2 2.7 - - - +
345C LEU* 2.9 20.6 + - + +
346C ILE* 3.5 7.1 - - + -
347C THR* 2.8 29.7 + - - -
348C HIS 3.2 5.4 + - - -
362C LEU* 4.9 2.8 - - - +
368C ILE* 1.3 93.8 + - + +
370C THR* 1.3 62.7 + - - +
371C VAL* 4.1 0.9 - - + -
3377C NAD 3.2 30.3 + - - -
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Residues in contact with THR 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLY* 3.1 3.3 - - - -
45C ILE* 2.9 53.7 + - + +
348C HIS* 3.1 25.5 - - + +
350C LEU* 4.2 20.0 - - + -
358C GLY* 4.4 12.3 + - - -
361C LEU* 4.6 2.2 - - + +
362C LEU* 5.3 2.9 + - - +
367C SER* 3.9 19.9 + - - -
368C ILE 4.2 1.6 + - - -
369C ARG* 1.3 76.9 + - - +
371C VAL* 1.3 64.5 + - - +
372C LEU* 3.7 4.9 + - + -
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Residues in contact with VAL 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 3.7 28.5 - - + -
43C THR 3.8 3.4 - - - +
44C GLY* 4.7 2.7 - - - -
167C GLU* 3.2 34.3 - - + +
170C CYS* 3.8 18.2 - - - -
171C LEU* 5.1 4.0 - - + -
346C ILE* 3.9 26.0 - - + -
348C HIS 2.7 11.7 + - - +
349C VAL* 3.3 10.5 - - + +
350C LEU 2.9 26.1 + - - +
369C ARG* 5.4 0.2 - - + -
370C THR* 1.3 76.1 - - - +
372C LEU* 1.3 64.6 + - - +
373C THR* 3.6 1.6 + - - +
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 3.1 5.2 - - - +
43C THR* 2.7 49.9 + - + +
45C ILE* 4.0 25.8 - - + -
146C PHE* 4.4 11.4 - - + -
350C LEU* 3.3 16.4 - - + +
351C PRO 3.9 19.1 - - - +
352C PHE* 4.0 19.3 - - + -
354C LYS 4.5 1.3 - - - +
355C ILE* 3.7 46.2 - - + +
370C THR* 4.7 4.3 - - + -
371C VAL* 1.3 73.2 - - - +
373C THR* 1.3 60.6 + - - +
374C PHE* 4.2 1.5 - - + -
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Residues in contact with THR 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU 3.9 8.8 + - - -
42C ALA* 4.4 5.5 - - - +
167C GLU* 5.6 4.1 - - - +
349C VAL* 4.7 16.8 - - + -
350C LEU 2.8 23.8 + - - +
351C PRO* 3.6 11.5 - - + +
352C PHE* 2.9 24.9 + - - +
371C VAL* 3.6 1.3 + - - -
372C LEU* 1.3 75.6 - - - +
374C PHE* 1.3 73.3 + - - +
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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
------------------------------------------------------------
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