Contacts of the helix formed by residues 80 - 100 (chain C) in PDB entry 2NUP
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 PRO 80 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A GLN* 3.7 20.9 - - + +
78C ALA 3.9 4.9 - - - +
79C PHE* 1.3 106.4 - - + +
81C LYS* 1.3 69.2 + - + +
82C LYS* 2.9 26.5 - - + -
83C LEU* 3.0 41.4 + - + +
84C ALA 3.0 10.6 + - - -
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Residues in contact with LYS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C THR* 5.4 0.9 - - + +
60C THR* 6.2 0.9 - - + -
62C HIS* 3.6 30.5 - - + +
77C ALA 4.0 15.6 + - - +
78C ALA* 4.6 6.3 + - - +
79C PHE 3.2 9.1 + - - +
80C PRO* 1.3 74.3 - - - +
82C LYS* 1.3 64.3 + - + +
84C ALA* 3.4 6.9 + - - +
85C PHE* 3.0 31.6 - - + -
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Residues in contact with LYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PRO* 3.5 29.4 - - + -
81C LYS* 1.3 85.0 - - + +
83C LEU* 1.3 74.9 + - + +
84C ALA 3.6 0.2 + - - -
85C PHE* 3.9 3.8 + - - +
86C ALA* 3.7 17.7 + - - +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLN* 4.1 22.0 - - - +
79C PHE* 3.9 17.3 - - + -
80C PRO* 3.0 39.2 + - + +
82C LYS* 1.3 84.0 - - + +
84C ALA* 1.3 65.5 + - - +
86C ALA* 3.5 5.6 + - + +
87C TYR* 3.1 23.7 + - - +
126C TYR* 3.6 24.2 - - + +
132C ARG 5.7 5.2 - - - +
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS* 3.7 36.8 - - + -
73C VAL* 4.5 6.4 - - + +
75C CYS* 5.2 0.7 - - - -
79C PHE* 3.9 15.9 - - + -
80C PRO 3.0 11.5 + - - +
81C LYS 3.5 10.8 - - - +
82C LYS 3.3 0.2 - - - -
83C LEU* 1.3 78.0 - - - +
85C PHE* 1.3 62.2 + - - +
87C TYR* 3.2 12.0 - - - +
88C LEU* 3.2 24.5 + - - +
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ARG* 4.7 16.8 - - + +
52C CYS 3.8 12.3 - - - -
53C THR* 3.2 22.7 - - - -
62C HIS* 3.4 24.2 - + + -
63C TYR 3.3 26.7 - - - -
64C ILE* 3.7 18.7 - - + +
81C LYS* 3.0 27.8 + - + +
82C LYS* 3.9 4.0 + - - +
83C LEU 3.4 0.2 - - - -
84C ALA* 1.3 71.0 - - - +
86C ALA* 1.3 57.4 + - - +
87C TYR 3.1 1.6 - - - -
88C LEU* 2.9 9.3 + - + +
89C GLU* 2.7 39.4 + - + +
148C ILE* 4.5 29.2 - - + -
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LYS 3.7 12.3 + - - +
83C LEU* 3.5 12.3 + - + +
85C PHE* 1.3 77.0 - - - +
87C TYR* 1.3 60.2 + - - +
89C GLU* 3.3 7.7 + - - +
90C ASP* 2.4 35.3 + - - +
126C TYR* 3.6 18.2 - - + +
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Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 2.6 33.6 + - + -
73C VAL* 4.0 21.8 - - + -
79C PHE* 6.0 2.7 - + + -
83C LEU 3.1 13.9 + - - +
84C ALA* 3.2 14.8 - - - +
86C ALA* 1.3 78.6 - - - +
88C LEU* 1.3 65.9 + - + +
90C ASP* 3.6 3.1 + - - +
91C LEU* 3.4 35.1 + - + +
119C ILE* 3.8 9.9 - - - +
122C THR* 4.2 8.1 - - + -
123C LYS* 3.4 47.9 - - + +
126C TYR* 3.7 36.7 - + + -
127C ILE* 6.2 0.2 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 5.4 1.1 - - + -
62C HIS* 3.4 25.1 - - + +
63C TYR* 3.5 10.5 - - - +
64C ILE* 3.6 22.3 - - + +
71C TYR* 3.5 39.5 - - + +
72C LEU 4.2 3.4 - - - +
73C VAL* 4.0 21.3 - - + -
84C ALA 3.2 13.9 + - - +
85C PHE* 2.9 13.1 + - + +
87C TYR* 1.3 80.9 - - + +
89C GLU* 1.3 67.4 + - - +
91C LEU* 3.1 14.4 + - + +
92C HIS* 2.9 22.0 + - - +
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Residues in contact with GLU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ARG* 2.6 46.3 + - - +
64C ILE* 3.1 13.0 - - + +
85C PHE* 2.7 20.1 + - + +
86C ALA* 3.5 12.6 - - - +
88C LEU* 1.3 74.0 - - - +
90C ASP* 1.3 64.3 + - - +
92C HIS* 3.1 22.6 + - - +
93C SER* 3.2 16.5 + - - -
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Residues in contact with ASP 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA* 2.4 25.2 + - - +
87C TYR 3.7 8.3 - - - +
88C LEU 3.3 0.2 - - - -
89C GLU* 1.3 76.4 - - - +
91C LEU* 1.3 63.0 + - - +
93C SER* 3.3 17.3 + - - -
94C GLU* 3.4 12.3 - - - +
118C PHE* 3.7 8.6 - - + -
122C THR* 4.2 16.8 - - + +
126C TYR* 2.9 23.6 + - - -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 3.8 28.7 - - + -
7C ILE* 4.7 5.2 - - + -
71C TYR* 4.2 13.5 - - + -
87C TYR* 3.4 34.0 + - + +
88C LEU* 3.1 17.1 + - + +
90C ASP* 1.3 78.1 - - - +
92C HIS* 1.3 54.3 + - - +
94C GLU* 3.5 1.4 - - - +
95C PHE* 2.8 36.6 + - - +
115C PHE* 3.6 27.7 - - + -
118C PHE* 3.9 14.4 - - + -
119C ILE* 3.8 18.8 - - + +
122C THR* 4.9 5.4 - - + -
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Residues in contact with HIS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.3 6.5 - - + -
66C GLU* 3.3 50.1 + - + +
67C GLN* 5.3 4.9 + - - +
71C TYR* 3.6 30.6 - + + -
88C LEU 2.9 12.6 + - - +
89C GLU* 3.1 22.3 + - - +
91C LEU* 1.3 74.9 - - - +
93C SER* 1.3 61.1 + - - +
95C PHE* 2.7 4.2 + - - -
96C ASP* 2.6 59.6 + - + +
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLU* 3.2 9.2 + - - -
90C ASP* 3.3 13.9 + - - -
92C HIS* 1.3 86.1 - - - +
94C GLU* 1.3 61.7 + - - +
96C ASP* 4.0 3.3 - - - +
97C GLU* 2.8 41.2 + - - +
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASP 3.4 6.5 + - - +
91C LEU 3.3 1.3 + - - +
93C SER* 1.3 80.2 + - - +
95C PHE* 1.3 59.7 + - - +
97C GLU* 3.6 8.7 - - - +
98C GLN* 2.9 59.6 + - + +
115C PHE* 3.9 6.7 - - + -
118C PHE* 2.8 64.9 - - + -
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Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.2 11.7 - - + -
16C LEU* 4.2 15.9 - - + -
17C ALA* 4.9 2.7 - - + -
69C VAL* 4.5 3.8 - - + -
71C TYR* 3.4 25.4 - + + +
91C LEU 2.8 16.5 + - - +
92C HIS 2.7 8.8 + - - +
94C GLU* 1.3 70.5 - - - +
96C ASP* 1.3 59.3 + - - +
98C GLN* 3.0 2.0 + - - -
99C HIS* 2.5 56.0 + + + -
100C GLY* 3.2 2.8 + - - -
103C VAL* 3.6 23.1 - - + -
112C PHE* 3.8 39.0 - + + -
115C PHE* 3.9 37.7 - + + -
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Residues in contact with ASP 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLN* 4.9 18.0 - - + +
71C TYR* 4.9 1.1 - - - +
92C HIS* 2.6 42.3 + - + +
93C SER* 4.0 4.2 - - - +
95C PHE* 1.3 75.8 - - - +
97C GLU* 1.3 62.3 + - - +
100C GLY* 2.8 31.6 + - - +
101C LYS* 3.2 26.6 + - - +
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Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C SER* 2.8 25.8 + - - +
94C GLU* 3.6 8.2 - - - +
96C ASP* 1.3 83.0 - - - +
98C GLN* 1.3 76.1 + - - +
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Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLU* 2.9 41.4 + - + +
95C PHE* 3.8 1.8 - - - +
97C GLU* 1.3 97.0 + - - +
99C HIS* 1.3 85.0 + - + +
115C PHE* 5.7 3.1 - - + -
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Residues in contact with HIS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PHE* 2.5 35.8 + + + +
98C GLN* 1.3 94.6 + - + +
100C GLY* 1.3 64.2 + - - +
101C LYS 2.9 4.8 + - - -
102C LYS* 3.0 20.4 + - - +
103C VAL* 3.3 13.1 + - - +
112C PHE* 3.2 46.8 - + + +
114C GLU 6.1 0.6 - - - -
115C PHE* 4.6 13.8 + + - +
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLN* 5.5 8.1 - - - +
95C PHE* 3.2 4.9 + - - -
96C ASP* 2.8 38.3 + - - -
98C GLN 3.8 0.2 - - - -
99C HIS* 1.3 76.9 - - - +
101C LYS* 1.3 69.5 + - - +
102C LYS 3.6 0.2 + - - -
103C VAL* 4.0 9.2 + - - +
104C PRO* 3.9 13.7 - - - +
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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
------------------------------------------------------------
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