Contacts of the helix formed by residues 88 - 97 (chain E) in PDB entry 1NQ3
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 88 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E VAL* 3.7 43.2 - - + +
83E LEU* 4.5 3.8 - - + +
85E ASP* 2.9 33.4 + - - +
87E ASN* 1.3 79.3 - - - +
89E PHE* 1.3 65.1 + - - +
90E SER 3.3 1.6 - - - -
91E ALA* 3.2 9.1 + - - +
92E VAL* 2.9 25.2 + - + +
120E ARG* 4.6 12.1 + - - +
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Residues in contact with PHE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E VAL* 5.6 4.5 - - + -
83E LEU* 3.9 20.7 - - + +
86E ILE* 3.0 25.2 + - + +
87E ASN 3.2 0.8 - - - -
88E ASP* 1.3 77.9 - - - +
90E SER* 1.3 57.0 + - - +
92E VAL* 3.2 4.1 + - + +
93E ASN* 2.7 52.2 + - + +
107E ARG* 3.5 31.9 - - - -
109E ALA* 3.6 31.4 - - + -
116F PRO* 5.9 8.3 - - + -
117F LYS* 5.8 6.5 - - - -
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Residues in contact with SER 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ASN 4.4 6.1 + - - -
88E ASP 3.3 0.4 - - - -
89E PHE* 1.3 85.0 - - - +
91E ALA* 1.3 65.2 + - - +
93E ASN* 3.1 7.1 + - - +
94E ASP* 3.0 32.7 + - - +
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Residues in contact with ALA 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 5.1 4.7 - - + -
52E VAL* 4.0 24.4 - - + +
87E ASN 5.2 0.6 + - - +
88E ASP* 3.2 13.7 + - - +
90E SER* 1.3 77.5 - - - +
92E VAL* 1.3 65.6 + - + +
94E ASP* 3.3 17.3 + - - +
95E VAL* 3.4 16.8 + - - +
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Residues in contact with VAL 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 3.6 31.0 - - + +
52E VAL* 5.9 1.1 - - - +
55E ALA* 4.2 19.5 - - + -
59E LEU* 6.4 0.9 - - + -
81E VAL* 4.2 24.0 - - + -
83E LEU* 3.7 15.5 - - + -
88E ASP 2.9 20.8 + - - +
89E PHE* 3.7 4.9 - - + +
91E ALA* 1.3 75.2 - - - +
93E ASN* 1.3 58.6 + - - +
95E VAL* 3.0 9.2 + - - +
96E TYR* 2.8 31.1 + - + +
121E VAL* 4.5 5.6 - - + -
123E ILE* 5.2 6.3 - - + -
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Residues in contact with ASN 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E PHE* 2.7 36.3 + - + +
90E SER* 3.1 10.0 + - - +
92E VAL* 1.3 74.2 - - - +
94E ASP* 1.3 62.5 + - - +
96E TYR* 3.2 5.1 + - - +
97E LYS* 2.9 33.7 + - - +
107E ARG* 2.9 40.3 + - - +
18F ILE 5.8 0.2 + - - -
19F GLY* 5.2 2.6 - - - -
20F PRO* 3.6 19.6 - - - +
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Residues in contact with ASP 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E SER* 3.0 25.6 + - - +
91E ALA* 3.7 11.0 - - - +
92E VAL 3.2 0.4 - - - -
93E ASN* 1.3 82.5 + - - +
95E VAL* 1.3 61.1 + - + +
97E LYS* 3.2 44.9 + - - +
98E GLN* 3.5 11.3 - - - +
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Residues in contact with VAL 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E VAL* 3.8 32.1 - - + +
55E ALA* 4.3 7.6 - - + -
56E LYS* 3.7 31.4 - - + +
59E LEU* 4.0 17.0 - - + -
91E ALA 3.6 13.2 - - - +
92E VAL 3.0 7.7 + - - +
94E ASP* 1.3 75.8 - - + +
96E TYR* 1.3 68.0 + - - +
98E GLN* 3.0 25.7 + - + +
99E TYR* 3.3 12.6 - - + -
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Residues in contact with TYR 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E LEU* 3.9 24.9 - - + +
79E ALA* 3.3 28.0 - - + +
81E VAL* 4.2 25.4 - - + -
92E VAL* 2.8 20.5 + - + +
93E ASN* 3.4 9.0 - - - +
95E VAL* 1.3 77.4 - - - +
97E LYS* 1.3 60.8 + - - +
99E TYR* 3.0 14.4 + - - +
100E PHE* 3.3 48.0 - + - -
105E PRO* 4.3 11.7 - - + +
107E ARG* 3.6 29.7 - - - +
123E ILE* 4.7 8.5 - - + -
20F PRO* 3.5 31.4 + - + -
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Residues in contact with LYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ASN* 2.9 16.3 + - - +
94E ASP* 3.2 48.2 + - - +
96E TYR* 1.3 76.7 - - - +
98E GLN* 1.3 69.1 + - - +
99E TYR 3.2 0.2 - - - -
100E PHE 3.1 22.3 - - - +
101E GLN* 4.9 3.6 + - - -
20F PRO* 3.8 30.3 - - + -
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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