Contacts of the helix formed by residues 89 - 96 (chain B) in PDB entry 1NZ0
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 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B GLN* 3.5 23.3 + - - +
29B ASN 2.8 41.0 + - - -
30B GLU* 3.7 20.0 - - - +
31B TYR* 2.9 18.0 + - - +
32B PHE 3.7 18.4 - - - -
33B VAL* 3.9 14.0 - - + +
54B PHE* 4.7 1.2 - - - -
87B ILE* 4.1 0.4 - - + +
88B PRO* 1.3 79.9 - - - +
90B LYS* 1.4 68.0 + - - +
91B LYS 3.2 1.8 - - - +
92B LEU* 3.0 13.0 + - - +
93B SER* 3.0 11.7 + - - -
5002B SO4 2.9 42.4 + - - +
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LYS* 4.9 23.1 - - + +
89B ARG* 1.4 73.1 - - - +
91B LYS* 1.3 63.8 + - - +
93B SER* 3.1 9.7 + - - -
94B GLU* 2.9 36.8 + - + +
5002B SO4 2.9 30.8 + - - +
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU* 3.6 45.5 - - + +
31B TYR* 4.2 3.1 - - + -
89B ARG* 3.2 3.0 - - - +
90B LYS* 1.3 79.9 - - - +
92B LEU* 1.3 63.0 + - - +
94B GLU* 3.3 25.5 + - - +
95B GLU* 3.2 48.2 + - + +
5002B SO4 5.2 0.6 + - - -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU 4.5 1.0 + - - -
31B TYR* 3.7 49.6 - - + +
32B PHE* 3.7 37.7 - - + -
54B PHE* 4.6 2.7 - - + -
63B LEU* 4.0 11.4 - - + -
88B PRO* 3.9 11.9 - - + -
89B ARG 3.0 9.8 + - - +
91B LYS* 1.3 74.8 - - - +
93B SER* 1.3 67.6 + - - +
95B GLU* 3.2 2.6 + - + +
96B PHE* 2.9 36.8 + - + +
99B VAL* 4.2 11.4 - - + -
104B VAL* 4.2 15.0 - - + -
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LYS 4.4 2.6 + - - -
54B PHE* 3.4 36.5 + - - -
59B ARG* 2.7 42.9 + - - +
89B ARG 3.0 9.1 + - - -
90B LYS* 3.1 12.8 + - - -
92B LEU* 1.3 79.3 - - - +
94B GLU* 1.3 62.7 + - - +
95B GLU 3.3 0.2 + - - -
96B PHE* 3.4 5.7 + - - +
97B GLU 4.9 0.2 + - - -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS* 2.9 29.4 + - + +
91B LYS* 3.5 26.2 - - - +
92B LEU 3.3 0.2 - - - -
93B SER* 1.3 79.7 - - - +
95B GLU* 1.3 59.0 + - + +
96B PHE 3.9 0.3 + - - -
97B GLU* 5.1 1.2 + - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU* 4.8 4.0 - - - +
31B TYR* 2.5 38.0 + - + +
91B LYS* 3.2 39.9 + - + +
92B LEU 3.7 2.9 - - - +
94B GLU* 1.3 77.6 - - + +
96B PHE* 1.3 55.1 + - - +
97B GLU 3.2 3.4 - - - -
98B ARG* 2.9 11.6 + - + -
99B VAL* 2.8 38.9 + - + +
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PHE* 3.9 17.7 - + + -
59B ARG* 3.8 39.7 - - + +
62B LYS* 3.7 35.8 + - + -
63B LEU* 3.6 35.7 - - + -
66B TRP* 3.8 28.6 - + - -
92B LEU* 2.9 31.0 + - + +
93B SER 3.4 12.0 + - - +
94B GLU 3.5 0.2 - - - -
95B GLU* 1.3 77.1 - - - +
97B GLU* 1.3 64.6 + - - +
98B ARG 3.3 0.7 + - - -
99B VAL* 4.0 16.4 + - + +
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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