Contacts of the strand formed by residues 41 - 48 (chain J) in PDB entry 1OZT
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 GLY 41 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39J THR 3.3 0.6 + - - -
40J GLU* 1.3 77.6 - - - +
42J LEU* 1.3 67.3 + - - -
43J HIS* 3.4 9.7 - - - -
88J THR* 3.3 7.1 - - - -
89J ALA 2.7 42.0 + - - -
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Residues in contact with LEU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J GLY* 1.3 71.9 - - - -
43J HIS* 1.3 69.0 + - - +
86J ASN* 3.9 23.1 - - + +
87J VAL 3.5 1.8 - - - +
88J THR* 3.1 33.2 - - + +
122J LYS* 4.5 0.5 - - - -
123J ALA* 3.4 37.4 + - + +
124J ASP 5.6 0.7 - - - +
125J ASP* 6.5 0.4 - - - -
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Residues in contact with HIS 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J LEU* 3.6 19.3 - - + +
39J THR* 2.8 46.4 + - + -
41J GLY 3.4 23.4 + - - -
42J LEU* 1.3 76.5 + - - +
44J GLY* 1.3 65.2 + - - +
86J ASN* 3.0 6.6 + - - -
87J VAL* 2.8 49.4 + - + +
89J ALA* 4.4 2.5 - - + -
119J VAL* 4.0 6.5 - - + -
120J HIS 2.9 16.2 + - - +
121J GLU 2.8 29.1 + - - -
122J LYS 3.8 2.0 - - - -
144J LEU* 4.3 12.4 - - + +
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Residues in contact with GLY 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J HIS* 1.3 72.2 - - - +
45J PHE* 1.3 59.4 + - - -
46J ARG* 4.9 4.0 - - - -
85J GLY 3.6 3.4 - - - -
86J ASN* 3.3 13.0 + - - -
119J VAL* 3.3 5.4 - - - +
120J HIS* 2.7 42.1 + - - -
122J LYS 2.9 20.1 + - - -
124J ASP* 4.1 8.7 - - - -
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Residues in contact with PHE 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LEU* 5.6 1.3 - - + -
18J ILE* 4.1 19.7 - - + -
31J VAL* 4.1 8.7 - - + -
35J ILE* 4.1 15.5 - - + -
43J HIS 4.1 1.6 - - - +
44J GLY* 1.3 74.3 - - - +
46J ARG* 1.3 62.1 + - - +
84J LEU* 3.1 56.4 + - + +
85J GLY 2.9 18.7 + - - +
87J VAL* 3.5 33.2 - - + -
97J VAL* 4.2 2.7 - - + -
99J ILE* 3.9 21.1 - - + -
117J LEU* 3.9 32.5 - - + -
118J VAL 3.5 9.9 - - - -
119J VAL* 4.6 10.3 - - + -
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Residues in contact with ARG 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J GLY* 4.1 3.7 - - - -
45J PHE* 1.3 83.7 - - - +
47J VAL* 1.3 66.3 + - - +
48J HIS* 3.6 15.9 + - + +
63J HIS* 4.1 15.0 + - + +
82J GLY 3.2 10.3 - - - +
83J ASP* 3.1 28.3 + - - +
84J LEU* 4.9 0.9 - - - -
85J GLY 5.1 1.3 - - - +
117J LEU* 3.4 5.8 - - - +
118J VAL* 2.7 41.8 + - - -
120J HIS* 3.2 38.4 + - - +
122J LYS 5.8 0.4 + - - -
123J ALA 5.3 1.8 + - - -
124J ASP* 3.1 36.5 + - - +
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Residues in contact with VAL 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J PHE* 5.4 0.4 - - + -
46J ARG* 1.3 76.0 - - - +
48J HIS* 1.3 62.8 + - - +
63J HIS* 3.5 4.0 - - - +
64J PHE* 2.7 36.0 + - + +
82J GLY* 2.9 22.9 + - - +
84J LEU* 4.1 15.9 - - + -
104J ILE* 4.9 2.2 - - + -
112J ILE* 3.9 38.8 - - + -
115J ARG* 4.0 9.4 - - + -
116J THR 3.2 9.6 - - - +
117J LEU* 4.1 15.7 - - + -
149J ILE* 4.3 12.8 - - + -
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Residues in contact with HIS 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J ARG* 3.6 14.0 - - + +
47J VAL* 1.3 80.1 - - - +
49J GLU* 1.3 65.6 + - - +
50J PHE 3.2 2.1 + - - -
60J ALA* 3.5 22.0 - - + +
61J GLY 2.9 18.0 + - - -
62J PRO 3.0 13.9 + - - +
63J HIS* 3.9 12.3 - - + -
64J PHE* 3.9 2.2 - - - -
115J ARG* 3.4 7.3 - - - +
116J THR 2.6 28.7 + - - +
118J VAL* 3.1 25.8 - - + +
120J HIS* 3.1 32.5 + + - -
143J ARG* 3.5 24.3 + - - -
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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
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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