Contacts of the strand formed by residues 32 - 37 (chain Y) in PDB entry 1RZR
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 ASP 32 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30Y ASP 4.5 4.6 - - - +
31Y SER* 1.3 73.1 - - - +
33Y ILE* 1.3 60.4 + - - +
34Y ASN* 4.2 9.7 - - - +
45Y LYS* 4.8 3.6 + - - +
65Y ALA* 3.0 2.6 - - - -
66Y GLU* 2.7 55.5 + - + +
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Residues in contact with ILE 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Y ALA* 4.1 29.2 - - - +
29Y PHE* 4.2 4.9 - - + -
31Y SER 3.3 14.7 + - - +
32Y ASP* 1.3 80.1 - - - +
34Y ASN* 1.3 65.2 + - - +
43Y ASN* 3.1 15.6 + - - +
44Y LEU* 2.9 37.7 + - + +
45Y LYS* 4.3 10.0 - - + +
63Y ILE* 3.9 12.3 - - + -
64Y SER 3.0 17.0 - - - +
65Y ALA* 3.3 20.6 - - + -
73Y ALA* 4.1 16.8 - - + -
77Y LEU* 4.1 8.3 - - + -
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Residues in contact with ASN 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Y ASP* 4.2 8.5 - - - +
33Y ILE* 1.3 86.0 + - - +
35Y LEU* 1.3 60.6 + - - +
36Y GLU* 4.1 1.3 - - + +
41Y THR* 3.7 25.5 - - + +
42Y VAL* 3.1 15.3 + - - +
43Y ASN* 4.3 3.8 - - - +
44Y LEU* 3.8 4.9 - - - +
62Y THR 3.8 0.7 - - - +
63Y ILE* 3.6 6.9 - - - +
64Y SER* 2.9 41.0 + - - +
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Residues in contact with LEU 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Y ILE* 5.2 1.3 - - + -
22Y LEU* 5.3 7.9 - - + -
34Y ASN* 1.3 72.3 - - - +
36Y GLU* 1.3 65.0 + - - +
40Y LYS 3.8 0.5 - - - +
41Y THR* 3.2 5.3 - - - -
42Y VAL* 2.7 41.2 + - + +
44Y LEU* 3.5 32.1 - - + +
50Y VAL* 3.9 13.5 - - + -
53Y LEU* 3.7 14.9 - - + +
55Y ILE* 3.5 31.9 - - + -
61Y ILE* 4.7 13.7 - - + -
62Y THR 3.5 9.2 - - - +
63Y ILE* 3.7 20.4 - - + -
81Y MET* 6.5 0.4 - - + -
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Residues in contact with GLU 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y ASN* 4.1 1.0 - - + -
35Y LEU* 1.3 72.1 - - - +
37Y PHE* 1.3 70.4 + - - +
38Y ASN 4.5 0.7 + - - -
39Y GLY* 3.6 29.7 + - - -
40Y LYS 3.3 5.4 - - - -
41Y THR* 3.4 16.7 + - + +
61Y ILE* 3.6 2.3 - - - +
62Y THR* 2.8 55.4 + - + +
64Y SER* 6.0 1.6 - - - +
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Residues in contact with PHE 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y LEU 5.3 0.2 - - - -
36Y GLU* 1.3 80.9 + - - +
38Y ASN* 1.3 94.2 + - + +
39Y GLY 3.1 0.9 - - - -
40Y LYS* 2.7 28.5 + - - +
53Y LEU* 4.1 36.1 - - + -
55Y ILE* 4.3 17.5 - - + -
56Y GLN* 3.5 25.1 - - - -
59Y ALA* 3.1 26.7 - - + -
60Y THR 3.2 22.9 - - - -
61Y ILE* 3.3 20.0 - - + -
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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