Contacts of the helix formed by residues 69 - 79 (chain N) in PDB entry 5NSS
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 ASN 69 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65N CYS 4.7 1.1 - - - +
68N LEU* 1.3 81.2 - - - +
70N GLU* 1.3 62.1 + - - +
71N ASN* 3.5 5.4 - - + +
72N LEU* 3.8 11.9 - - + +
73N LEU* 3.0 26.2 + - - +
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Residues in contact with GLU 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N ASN* 1.3 75.0 - - - +
71N ASN* 1.3 59.9 + - - +
73N LEU* 4.0 2.5 - - - +
74N ASP* 2.9 33.6 + - - +
111N THR 5.1 7.3 + - - +
112N ALA* 5.4 4.7 - - - +
113N PRO* 4.3 31.9 - - + -
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Residues in contact with ASN 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N ASN* 4.4 2.7 - - + +
70N GLU* 1.3 79.5 - - - +
72N LEU* 1.3 50.6 + - - +
74N ASP* 4.8 2.5 - - - -
75N SER* 2.6 42.2 + - - +
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Residues in contact with LEU 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N LEU* 3.8 23.1 - - + -
69N ASN* 3.6 14.2 + - + +
70N GLU 3.2 0.8 - - - -
71N ASN* 1.3 77.6 - - - +
73N LEU* 1.3 61.1 + - - +
75N SER* 4.5 2.0 - - - -
76N GLU* 2.9 32.2 + - - +
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Residues in contact with LEU 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N CYS* 4.3 26.2 - - + +
68N LEU* 4.4 6.7 - - + +
69N ASN 3.0 18.6 + - - +
70N GLU* 4.1 2.9 - - - +
72N LEU* 1.3 75.9 - - - +
74N ASP* 1.3 58.4 + - - +
76N GLU* 4.0 2.7 - - - +
77N LEU* 2.9 32.2 + - - +
112N ALA* 6.3 3.4 - - + -
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Residues in contact with ASP 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N GLU 2.9 19.0 + - - +
71N ASN* 4.6 2.5 - - - +
73N LEU* 1.3 76.5 - - - +
75N SER* 1.3 59.0 + - - +
77N LEU* 4.2 3.8 - - - +
78N PHE* 2.9 34.2 + - + +
80N HIS* 4.8 0.6 - - - +
115N MET 6.3 0.2 - - - -
116N VAL* 4.9 19.1 - - + +
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Residues in contact with SER 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71N ASN* 2.6 24.9 + - - -
72N LEU* 4.2 2.9 - - - -
74N ASP* 1.3 76.3 - - - +
76N GLU* 1.3 58.6 + - - +
79N GLY* 2.9 9.2 + - - -
80N HIS* 2.6 44.6 + - - +
81N GLU* 3.7 29.6 - - - -
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Residues in contact with GLU 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72N LEU 2.9 20.4 + - - +
73N LEU* 4.1 3.6 - - - +
75N SER* 1.3 78.2 - - - +
77N LEU* 1.3 60.2 + - - +
79N GLY* 3.9 0.6 + - - -
94N GLY* 3.3 9.7 - - - -
95N ARG* 3.2 17.5 + - - +
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Residues in contact with LEU 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N LEU 2.9 21.6 + - - +
74N ASP* 4.2 4.3 - - - +
76N GLU* 1.3 78.2 - - - +
78N PHE* 1.3 58.5 + - + +
79N GLY 3.7 0.2 + - - -
94N GLY* 4.0 1.4 - - - -
95N ARG* 3.3 32.1 + - + -
96N PHE* 3.5 16.8 + - - +
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Residues in contact with PHE 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N ASP* 2.9 19.6 + - + +
77N LEU* 1.3 75.7 - - + +
79N GLY* 1.3 62.3 + - - +
80N HIS* 3.3 8.6 + - + +
94N GLY* 4.9 0.9 - - - -
96N PHE* 6.0 0.2 - - - -
130N GLU* 3.4 44.4 - - + +
131N ARG* 4.1 6.8 + - - +
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Residues in contact with GLY 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N SER 2.9 7.7 + - - -
76N GLU* 3.9 2.3 + - - -
77N LEU 3.4 3.6 + - - -
78N PHE* 1.3 79.6 - - - +
80N HIS* 1.3 63.7 + - - +
82N ALA* 4.8 3.6 - - - +
91N ARG 4.3 8.3 - - - +
92N HIS* 3.6 23.0 - - - +
94N GLY* 4.1 9.7 - - - -
131N ARG* 5.6 0.7 - - - -
132N VAL* 3.3 24.7 - - - +
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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