Contacts of the helix formed by residues 80 - 90 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D GLY 3.8 0.6 + - - -
79D GLY* 1.3 71.4 - - - -
81D PRO* 1.3 76.5 - - - +
82D ALA* 3.2 13.9 + - - +
83D ARG* 3.1 71.5 + - + +
84D ALA* 3.0 23.3 + - - +
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Residues in contact with PRO 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D VAL* 3.9 20.2 - - + -
79D GLY 3.5 6.5 - - - +
80D ASP* 1.3 92.7 - - - +
82D ALA* 1.3 56.9 + - - +
84D ALA* 3.3 1.9 + - - +
85D LEU* 2.9 36.9 + - - +
137D VAL* 4.3 11.0 - - + -
141D ILE* 4.0 42.2 - - + -
188D LEU* 5.0 5.6 - - + -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASP* 3.2 12.1 + - - +
81D PRO* 1.3 78.7 - - - +
83D ARG* 1.3 64.2 + - + +
85D LEU* 3.4 2.7 + - - +
86D PHE* 3.0 23.7 + - - +
184D ILE* 4.1 14.1 - - + +
188D LEU* 3.6 27.9 - - + +
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Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D GLY* 5.8 0.2 - - - -
80D ASP* 3.1 49.2 + - + +
82D ALA* 1.3 77.7 - - + +
84D ALA* 1.3 57.6 + - - +
86D PHE* 3.5 6.2 + - - +
87D ALA* 2.8 31.4 + - - +
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ARG 4.0 19.6 - - - +
72D LEU* 4.0 7.4 - - + +
74D GLU* 4.9 5.8 - - + -
75D VAL* 3.5 34.1 - - + +
79D GLY 5.6 0.2 - - - -
80D ASP 3.0 11.5 + - - +
81D PRO 3.6 1.3 - - - +
83D ARG* 1.3 73.7 - - - +
85D LEU* 1.3 66.6 + - + +
87D ALA* 3.3 6.0 + - - +
88D ALA* 2.9 26.3 + - - +
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU* 4.1 11.0 - - + -
81D PRO* 2.9 24.6 + - + +
82D ALA 3.7 3.6 - - - +
84D ALA* 1.3 76.8 - - + +
86D PHE* 1.3 57.6 + - - +
88D ALA* 3.7 0.3 - - - +
89D MSE 2.8 35.7 + - - +
134D LEU* 3.7 29.2 - - + +
137D VAL* 4.4 18.6 - - + -
138D LEU* 4.1 15.0 - - + -
153D LEU* 4.2 14.4 - - + -
184D ILE* 3.9 22.9 - - + -
187D ILE* 5.1 2.0 - - + -
188D LEU* 4.0 26.9 - - + -
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Residues in contact with PHE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ALA 3.0 17.4 + - - +
83D ARG* 3.7 6.5 - - - +
85D LEU* 1.3 74.7 - - - +
87D ALA* 1.3 63.7 + - - +
90D SER* 2.8 54.6 + - - -
177D GLU* 3.7 44.4 - - + -
180D LEU* 3.6 23.5 - - + +
181D ASP* 3.1 29.2 - - - -
184D ILE* 3.5 13.1 - - + +
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D ARG* 3.6 25.1 - - + +
83D ARG 2.8 22.3 + - - +
84D ALA* 3.3 6.5 + - - +
86D PHE* 1.3 76.3 - - + +
88D ALA* 1.3 60.4 + - - +
90D SER* 3.2 16.3 + - - -
91D GLN* 3.3 19.5 + - - +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 3.3 35.8 - - + +
71D ARG* 4.0 13.4 - - + +
72D LEU* 3.5 29.6 - - + -
84D ALA 2.9 18.0 + - - +
85D LEU 3.7 2.2 - - - +
87D ALA* 1.3 75.2 - - - +
89D MSE 1.3 76.3 + - + +
91D GLN* 3.3 8.5 + - - +
92D LEU 4.3 0.3 + - - -
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Residues in contact with MSE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 3.7 28.0 - - + -
72D LEU* 5.6 0.7 - - + -
85D LEU 2.8 23.7 + - - +
88D ALA* 1.3 79.3 - - + +
90D SER* 1.3 57.2 + - - +
91D GLN 3.0 0.2 - - - -
92D LEU* 3.0 33.4 + - + +
93D LEU* 3.9 1.9 + - - +
130D ILE* 4.1 8.5 - - + -
134D LEU* 4.1 31.4 - - + -
153D LEU* 3.9 28.9 - - + -
154D LEU* 4.3 14.8 - - - -
157D VAL* 3.7 24.1 - - + +
180D LEU* 3.9 22.0 - - + -
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D PHE* 2.8 48.4 + - - -
87D ALA* 3.2 11.8 + - - -
88D ALA 3.3 0.2 - - - -
89D MSE 1.3 71.8 - - - +
91D GLN* 1.3 68.4 + - - +
92D LEU 3.2 0.4 - - - -
93D LEU* 3.3 21.7 + - - +
95D LEU* 3.8 15.6 - - - +
99D ARG* 3.1 17.8 + - - -
180D LEU* 3.8 10.7 - - - +
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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