Contacts of the helix formed by residues 73 - 91 (chain C) in PDB entry 2N7L
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 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C PHE* 5.3 1.8 - - - -
35C SER* 4.4 9.9 - - - +
71C THR* 3.7 2.1 + - + +
72C VAL* 1.3 73.4 - - - +
74C PHE* 1.3 53.5 + - - +
75C ASP* 2.4 38.9 + - - +
76C GLU* 2.6 40.0 + - - +
77C PHE* 2.6 39.5 + - - +
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Residues in contact with PHE 74 (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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5C TYR* 5.0 10.1 - + - -
20C PHE* 4.4 16.6 - + - -
21C LYS* 5.2 12.8 - - + -
24C PHE* 4.1 37.5 - + + -
35C SER* 5.3 1.0 + - - -
73C ASP* 1.3 76.1 + - - +
75C ASP* 1.3 63.5 + - + +
77C PHE* 3.6 4.5 - - - +
78C LEU* 2.8 56.3 + - + +
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Residues in contact with ASP 75 (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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1C MET* 4.0 27.6 - - - +
4C ILE* 5.4 2.4 - - - +
5C TYR* 4.9 9.2 + - - -
66C GLU* 5.0 5.9 - - - +
73C ASP* 2.4 22.2 + - - +
74C PHE* 1.3 82.0 - - + +
76C GLU* 1.3 68.5 + - - +
78C LEU* 3.3 7.3 + - - +
79C VAL* 3.2 32.7 + - - +
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Residues in contact with GLU 76 (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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65C ASP* 5.8 0.7 - - - +
66C GLU* 4.2 28.8 - - + +
67C ASP* 3.4 18.4 - - - +
69C SER* 4.3 0.9 + - - -
71C THR 3.0 14.1 - - - +
72C VAL* 3.4 13.7 - - + +
73C ASP* 2.6 35.9 + - - +
75C ASP* 1.3 76.8 - - - +
77C PHE* 1.3 56.4 + - - +
79C VAL* 2.9 11.6 - - - +
80C MET* 2.9 30.7 + - - +
201C CA 2.5 29.7 - - - -
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Residues in contact with PHE 77 (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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20C PHE* 3.9 23.3 - + - -
23C ALA* 5.7 2.5 - - + -
24C PHE* 3.5 40.6 - + + -
27C PHE* 4.6 24.7 - + + -
36C ILE* 4.3 27.6 - - + -
72C VAL* 3.2 12.8 - - + +
73C ASP 2.6 24.9 + - - +
74C PHE 3.6 3.6 - - - +
76C GLU* 1.3 74.8 - - - +
78C LEU* 1.3 62.5 + - - +
80C MET* 3.3 29.5 + - + +
81C MET* 3.0 36.1 + - - +
84C 4J4 5.4 1.8 - + - -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 5.9 4.9 - - + -
5C TYR* 4.4 23.6 - - + +
8C ALA* 4.7 12.6 - - + -
12C LEU* 5.5 4.0 - - + -
17C LYS* 5.3 9.9 - - - +
20C PHE* 3.9 30.3 - - + -
74C PHE* 2.8 42.7 + - + +
75C ASP* 3.5 8.3 - - - +
77C PHE* 1.3 79.1 - - - +
79C VAL* 1.3 67.2 + - + +
81C MET* 3.3 3.8 + - - +
82C VAL* 3.3 32.2 + - + +
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Residues in contact with VAL 79 (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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4C ILE* 3.8 36.3 - - + -
66C GLU* 5.2 12.8 - - + +
75C ASP* 3.3 22.2 - - - +
76C GLU* 2.9 25.6 - - - +
78C LEU* 1.3 75.7 - - + +
80C MET* 1.3 61.3 + - - +
82C VAL* 3.3 8.9 + - - +
83C ARG* 2.8 39.1 + - + +
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Residues in contact with MET 80 (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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36C ILE* 5.2 0.4 - - + -
64C VAL* 3.6 46.0 - - + +
72C VAL* 4.2 13.2 - - + -
76C GLU 2.9 20.6 + - - +
77C PHE* 3.3 41.1 - - + +
79C VAL* 1.3 78.0 - - + +
81C MET* 1.3 65.6 + - - +
83C ARG* 3.3 8.5 + - + +
84C 4J4 3.1 59.0 + - + +
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Residues in contact with MET 81 (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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12C LEU* 6.4 2.7 - - + -
20C PHE* 3.9 25.1 - - + -
23C ALA* 6.4 1.8 - - - -
77C PHE* 3.0 32.7 + - - +
78C LEU 3.7 7.4 - - - +
80C MET* 1.3 78.9 - - - +
82C VAL* 1.3 65.6 + - + +
84C 4J4 3.3 40.8 + - + +
85C MET* 3.1 45.3 + - + +
103C ALA* 6.3 2.2 - - + -
106C MET* 5.2 12.6 - - + -
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Residues in contact with VAL 82 (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 ALA* 5.4 5.6 - - + +
8C ALA* 4.1 19.7 - - + +
11C GLN* 5.2 14.4 - - + -
12C LEU* 4.0 26.9 - - + -
78C LEU* 3.3 24.0 + - + +
79C VAL* 3.3 11.1 + - - +
81C MET* 1.3 78.7 - - + +
83C ARG* 1.3 63.3 + - + +
85C MET* 3.1 17.9 + - + +
86C LYS* 3.2 26.0 + - + +
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Residues in contact with ARG 83 (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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79C VAL* 2.8 26.4 + - + +
80C MET* 3.6 7.9 - - + +
82C VAL* 1.3 76.2 - - + +
84C 4J4 1.3 54.3 + - - +
86C LYS* 3.2 43.2 - - - +
87C ASP* 2.7 48.8 + - + +
90C GLU* 5.6 4.4 + - - -
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Residues in contact with 4J4 84 (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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27C PHE* 5.7 3.8 - + - -
36C ILE* 3.7 28.5 - - + -
41C LEU* 3.8 31.2 - - + -
45C MET* 5.8 7.0 - - + -
60C MET* 4.6 13.6 - - + -
61C ILE* 3.6 31.9 - - - -
64C VAL* 3.7 45.1 - - + -
72C VAL* 4.7 3.4 - - - -
77C PHE* 5.4 2.2 - + - -
80C MET* 3.1 40.4 + - + +
81C MET* 3.5 37.1 - - + +
82C VAL 3.2 0.4 - - - -
83C ARG* 1.3 75.4 + - - +
85C MET* 1.3 73.2 + - - +
87C ASP* 4.0 6.3 - - - -
88C ASP* 2.9 51.6 + - - +
100C ARG* 5.8 11.7 + - - -
101C ILE* 5.2 18.2 - - + -
103C ALA* 3.9 24.8 - - + +
106C MET* 4.3 25.8 - - + +
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Residues in contact with MET 85 (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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11C GLN* 5.9 7.0 - - + +
12C LEU* 4.9 21.8 - - + -
16C GLN* 5.5 10.5 - - - +
81C MET* 3.1 36.8 + - + +
82C VAL* 3.1 12.7 + - + +
84C 4J4 1.3 85.9 + - - +
86C LYS* 1.3 63.0 + - - +
88C ASP* 3.9 3.4 - - - +
89C SER* 3.3 19.9 + - - -
103C ALA* 5.8 8.1 - - + -
107C MET* 5.5 11.4 - - + -
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Residues in contact with LYS 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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11C GLN* 4.8 17.0 - - + +
82C VAL* 3.2 19.6 + - + +
83C ARG* 3.2 56.9 - - - +
85C MET* 1.3 77.5 - - - +
87C ASP* 1.3 66.3 + - - +
89C SER* 3.2 7.4 + - - -
90C GLU* 2.8 34.3 + - - +
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Residues in contact with ASP 87 (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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83C ARG* 2.7 36.7 + - + +
84C 4J4 3.8 6.8 - - - +
86C LYS* 1.3 76.5 - - + +
88C ASP* 1.3 66.5 - - - +
90C GLU* 3.3 10.4 + - - +
91C ASN* 3.0 28.4 + - - +
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Residues in contact with ASP 88 (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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84C 4J4 2.9 43.7 + - - +
85C MET* 3.9 4.3 - - - +
87C ASP* 1.3 82.8 - - - +
89C SER* 1.3 60.7 + - - +
91C ASN* 2.8 28.1 - - - +
92C LEU* 4.3 6.3 - - - +
103C ALA* 4.5 9.7 + - - +
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Residues in contact with SER 89 (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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85C MET 3.3 11.8 + - - -
86C LYS* 3.2 12.4 + - - -
88C ASP* 1.3 81.5 - - - +
90C GLU* 1.3 63.0 + - - +
92C LEU* 3.7 22.7 - - - +
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Residues in contact with GLU 90 (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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83C ARG* 5.6 4.3 + - - -
86C LYS* 2.8 21.8 + - - +
87C ASP* 3.6 11.1 - - - +
89C SER* 1.3 74.2 - - - +
91C ASN* 1.3 59.0 + - + +
92C LEU* 3.3 6.4 + - - +
93C TYR* 4.5 10.8 + - - +
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Residues in contact with ASN 91 (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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87C ASP* 3.0 22.0 + - - +
88C ASP* 2.8 17.0 - - - +
89C SER 3.3 0.2 - - - -
90C GLU* 1.3 74.1 - - + +
92C LEU* 1.3 59.0 + - - +
93C TYR* 3.3 26.7 - - - -
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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
------------------------------------------------------------
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