Contacts of the strand formed by residues 51 - 55 (chain D) in PDB entry 2ZSU
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 THR 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D GLU* 3.5 20.6 - - + +
47D ALA* 3.2 4.2 - - - -
48D ILE* 2.6 45.9 + - - +
49D ASP* 4.2 6.7 - - + +
50D GLY* 1.3 80.8 - - - +
52D VAL* 1.3 65.5 + - - +
53D GLN* 3.5 16.0 + - - -
163D THR* 5.6 1.7 - - - +
164D ASP* 5.0 11.7 - - - +
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PHE* 3.5 29.2 - - + -
8D GLU* 2.6 26.7 + - + +
10D TYR* 5.4 0.4 + - - +
16D VAL* 5.1 1.6 - - + -
18D PHE* 4.8 6.1 - - + -
45D LEU* 4.5 8.7 - - + -
46D LEU 3.8 4.7 - - - +
47D ALA* 4.6 1.1 - - - +
51D THR* 1.3 73.5 - - - +
53D GLN* 1.3 68.7 + - - +
54D LEU* 3.5 24.7 - - - +
55D VAL* 4.6 6.3 - - + -
228D GLY* 3.4 32.5 - - - +
229D TYR* 4.3 15.9 - - + -
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Residues in contact with GLN 53 (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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46D LEU* 2.8 32.4 + - + +
48D ILE* 3.3 45.4 - - + +
51D THR* 3.5 22.6 + - - -
52D VAL* 1.3 81.0 + - - +
54D LEU* 1.3 66.9 + - + +
62D TYR* 5.3 1.0 - - - -
63D HIS* 5.6 0.9 + - - -
87D ASP* 5.1 9.1 - - - +
162D SER 5.1 4.0 - - - +
163D THR* 4.1 21.5 - - - +
229D TYR* 2.6 26.3 + - - -
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Residues in contact with LEU 54 (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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44D LYS 4.4 1.8 - - - +
45D LEU* 3.5 1.6 - - - -
46D LEU* 2.9 42.5 + - + +
52D VAL* 3.5 7.3 - - - +
53D GLN* 1.3 81.3 - - - +
55D VAL* 1.3 69.7 + - - +
56D THR* 3.6 19.7 - - + +
59D GLU* 3.9 18.4 - - + +
63D HIS* 4.6 4.7 - - + -
87D ASP* 3.3 42.6 - - + +
120D ILE* 4.1 20.2 - - + -
122D ILE* 3.7 15.0 - - + -
227D ILE 5.6 0.4 - - - -
229D TYR* 4.6 8.1 - - + +
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Residues in contact with VAL 55 (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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18D PHE* 4.3 17.7 - - + -
39D THR* 4.9 1.3 - - + -
42D PHE* 3.5 21.3 - - + +
44D LYS 3.2 4.7 - - - -
45D LEU* 3.9 28.7 - - + -
52D VAL* 4.6 4.9 - - + -
54D LEU* 1.3 80.1 - - - +
56D THR* 1.3 67.7 + - - +
57D GLU 2.9 16.4 + - - +
58D GLY* 4.4 1.3 - - - -
59D GLU* 3.0 16.5 + - - +
227D ILE* 3.8 31.9 - - + +
228D GLY* 4.5 0.7 - - - -
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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