Contacts of the helix formed by residues 72 - 81 (chain G) in PDB entry 2NOQ
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 PHE 72 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G ALA* 1.4 76.3 - - + +
73G ASP* 1.3 57.9 + - - +
74G VAL 3.1 0.2 - - - -
75G ASP* 3.3 16.8 - - + +
76G ARG* 2.7 60.9 + - + +
140G HIS* 3.4 22.9 - + + +
141G ASN* 3.7 21.5 - - + -
142G ASP 3.1 27.6 - - - -
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Residues in contact with ASP 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ILE* 2.7 27.5 - - - +
68G PHE 4.1 1.2 - - - +
69G GLY* 5.0 0.7 - - - -
70G ASP 3.4 10.1 - - - +
71G ALA 3.1 2.3 + - - +
72G PHE* 1.3 84.8 - - - +
74G VAL* 1.3 61.8 + - - +
76G ARG* 3.4 1.6 + - - +
77G ALA 3.0 11.1 + - - -
111G ILE* 5.3 0.2 - - - +
112G ALA 4.6 0.3 - - - -
113G SER* 3.1 33.3 + - - +
138G VAL* 4.2 12.1 - - - +
139G SER 5.2 1.5 - - - +
140G HIS* 4.2 14.3 - - - +
144G LEU* 2.7 41.9 - - - +
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Residues in contact with VAL 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ILE* 4.6 2.7 - - + -
69G GLY* 2.7 35.2 - - - +
70G ASP* 2.9 29.0 + - - +
71G ALA* 3.7 4.0 - - - +
73G ASP* 1.3 73.5 - - - +
75G ASP* 1.3 63.8 + - - +
77G ALA* 3.3 7.5 + - - +
78G LYS* 3.0 39.7 + - + +
84G ALA* 4.1 19.1 - - + -
85G MET 5.3 0.4 - - - +
86G SER* 5.1 9.6 - - - +
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Residues in contact with ASP 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ALA* 4.7 0.4 - - - +
72G PHE* 2.9 22.7 + - - +
74G VAL* 1.3 77.9 - - - +
76G ARG* 1.3 68.9 + - + +
78G LYS* 3.1 28.5 + - - +
79G SER* 3.0 27.6 + - - -
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Residues in contact with ARG 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G PHE* 2.7 42.6 + - + +
73G ASP 3.8 4.7 - - - +
75G ASP* 1.3 74.3 - - + +
77G ALA* 1.3 63.0 + - - +
79G SER* 3.1 11.0 + - - -
80G CYS* 3.0 33.1 + - - -
142G ASP 4.5 1.8 + - - -
143G ASP* 3.7 26.1 - - - +
144G LEU* 3.9 26.4 - - + +
145G TYR* 3.3 41.8 - - - +
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Residues in contact with ALA 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ILE* 2.9 51.1 - - + +
73G ASP 3.0 6.1 + - - -
74G VAL 3.5 8.3 - - - +
76G ARG* 1.3 77.1 - - - +
78G LYS* 1.3 61.1 + - - +
80G CYS* 3.2 5.8 + - - +
81G GLY 3.0 13.2 + - - -
82G VAL* 2.8 29.2 + - + +
84G ALA* 4.6 3.1 - - + -
144G LEU* 4.7 2.9 - - - -
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Residues in contact with LYS 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G VAL* 3.0 38.8 + - + +
75G ASP* 3.1 29.4 + - - +
77G ALA* 1.3 71.9 - - - +
79G SER* 1.3 67.3 + - - +
81G GLY* 3.0 14.1 + - - +
82G VAL 4.5 6.7 - - - +
84G ALA* 4.7 9.6 - - + -
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Residues in contact with SER 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ASP* 3.0 22.0 + - - -
76G ARG* 3.1 15.1 + - - -
78G LYS* 1.3 78.4 - - - +
80G CYS* 1.3 63.9 - - - +
81G GLY* 3.3 0.7 + - - -
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Residues in contact with CYS 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ARG* 3.0 31.0 + - - -
77G ALA* 3.4 9.4 - - - +
79G SER* 1.3 76.7 - - - +
81G GLY* 1.3 60.1 + - - +
82G VAL* 3.9 16.9 - - + +
144G LEU* 5.4 2.9 - - - -
145G TYR* 4.7 22.4 - - - -
148G VAL* 4.5 24.0 - - + -
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Residues in contact with GLY 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G ALA 3.0 3.6 + - - -
78G LYS* 3.0 15.3 + - - -
79G SER 3.1 0.9 - - - -
80G CYS* 1.3 79.0 - - - +
82G VAL* 1.3 65.1 + - - +
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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
------------------------------------------------------------
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