Contacts of the helix formed by residues 80 - 91 (chain B) in PDB entry 2NP5
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 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B ARG 3.8 5.6 + - - +
78B GLY 3.7 2.6 - - - -
79B GLY* 1.3 77.1 - - - +
81B PRO* 1.3 68.9 - - - +
82B ALA* 3.4 11.8 + - - +
83B ARG* 3.1 38.6 + - + +
84B ALA* 3.0 20.8 + - - +
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Residues in contact with PRO 81 (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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77B ARG 5.4 0.2 - - - +
79B GLY 3.7 8.1 - - - +
80B ASP* 1.3 87.1 - - - +
82B ALA* 1.3 58.5 + - + +
84B ALA* 3.2 7.5 + - + +
85B LEU* 2.8 38.8 + - + +
137B VAL* 4.4 16.2 - - + -
141B ILE* 4.0 43.3 - - + -
188B LEU* 5.1 0.7 - - + -
193B VAL* 4.6 10.8 - - + -
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Residues in contact with ALA 82 (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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80B ASP* 3.3 9.0 + - - +
81B PRO* 1.3 80.6 - - - +
83B ARG* 1.3 62.9 + - + +
85B LEU* 3.4 2.9 + - - +
86B PHE* 3.0 24.5 + - - +
184B ILE* 4.2 13.2 - - + +
188B LEU* 3.6 28.5 - - + +
193B VAL* 5.9 0.4 - - + +
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Residues in contact with ARG 83 (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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80B ASP* 3.1 39.2 + - + +
82B ALA* 1.3 77.0 - - + +
84B ALA* 1.3 58.7 + - - +
86B PHE* 3.4 9.7 + - - +
87B ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 84 (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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75B VAL* 3.9 11.2 - - + +
76B GLU 4.9 3.6 - - - -
77B ARG* 3.9 35.7 - - + +
80B ASP 3.0 12.4 + - - +
81B PRO* 3.2 11.4 + - + +
83B ARG* 1.3 73.8 - - - +
85B LEU* 1.3 66.0 + - + +
87B ALA* 3.3 3.4 + - - +
88B ALA* 2.9 25.8 + - - +
137B VAL* 5.8 3.4 - - + -
204B LMT 4.2 7.4 - - + +
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Residues in contact with LEU 85 (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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81B PRO 2.8 27.1 + - - +
82B ALA 3.7 3.8 - - - +
84B ALA* 1.3 72.5 - - - +
86B PHE* 1.3 58.5 + - - +
88B ALA* 3.8 0.6 - - - +
89B MSE 2.9 35.7 + - - +
134B LEU* 3.7 30.1 - - + -
137B VAL* 3.9 22.9 - - + -
138B LEU* 4.0 26.2 - - + -
153B LEU* 4.2 13.0 - - + -
184B ILE* 3.8 23.3 - - + -
187B ILE* 5.2 1.6 - - + -
188B LEU* 4.1 15.9 - - + -
204B LMT 4.1 8.3 - - + -
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Residues in contact with PHE 86 (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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82B ALA 3.0 18.2 + - - +
83B ARG* 3.6 11.2 - - - +
85B LEU* 1.3 75.7 - - - +
87B ALA* 1.3 63.6 + - - +
90B SER* 2.8 52.6 + - - -
177B GLU* 3.5 53.4 - - + -
180B LEU* 3.8 21.4 - - + +
181B ASP* 4.3 16.8 - - + -
184B ILE* 3.5 12.5 - - + +
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Residues in contact with ALA 87 (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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75B VAL* 4.0 18.1 - - + +
76B GLU 6.1 0.2 - - - +
83B ARG 2.9 17.6 + - - +
84B ALA* 3.3 5.1 + - - +
86B PHE* 1.3 82.0 - - + +
88B ALA* 1.3 63.4 + - - +
90B SER* 3.6 8.2 + - - -
91B GLN* 3.5 20.3 + - - +
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Residues in contact with ALA 88 (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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72B LEU* 3.3 25.8 - - + +
75B VAL* 3.8 17.0 - - + +
84B ALA 2.9 17.4 + - - +
85B LEU 3.8 1.3 - - - +
87B ALA* 1.3 73.8 - - - +
89B MSE 1.3 81.6 + - + +
91B GLN* 3.0 13.2 + - - +
92B LEU 3.9 1.4 + - - -
204B LMT 3.8 28.0 - - + -
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Residues in contact with MSE 89 (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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72B LEU* 4.5 4.5 - - + -
85B LEU 2.9 21.0 + - - +
88B ALA* 1.3 94.8 - - + +
90B SER* 1.3 56.9 + - - +
92B LEU* 2.9 46.5 + - + +
93B LEU* 3.6 9.7 + - - +
130B ILE* 4.3 12.1 - - + -
134B LEU* 3.8 31.9 - - + -
153B LEU* 3.9 24.9 - - + -
154B LEU* 4.4 6.1 - - - -
157B VAL* 3.8 24.3 - - + +
180B LEU* 3.6 25.6 - - + -
204B LMT 4.9 1.8 - - + -
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Residues in contact with SER 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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86B PHE* 2.8 48.6 + - - -
87B ALA* 3.6 9.4 - - - -
88B ALA 3.1 0.2 - - - -
89B MSE 1.3 75.3 - - - +
91B GLN* 1.3 62.9 + - - +
92B LEU 3.2 1.2 + - - -
93B LEU* 3.3 15.7 + - - +
95B LEU* 3.7 21.4 - - - +
99B ARG* 3.1 20.1 + - - -
177B GLU* 5.0 0.2 - - - +
180B LEU* 3.8 8.2 - - - +
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Residues in contact with GLN 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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68B LEU* 4.7 0.7 - - - +
71B ARG* 2.6 78.7 + - + +
72B LEU* 4.2 11.7 - - + -
75B VAL* 5.0 3.6 - - + -
87B ALA 3.5 16.0 + - - +
88B ALA* 3.0 13.6 + - - +
90B SER* 1.3 78.5 - - - +
92B LEU* 1.3 62.6 + - + +
93B LEU 3.5 0.2 - - - -
99B ARG* 3.7 32.4 + - - +
102B GLU* 4.3 1.4 - - - +
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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