Contacts of the helix formed by residues 73 - 86 (chain A) in PDB entry 1NSH
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.1 14.0 - - + +
28A VAL* 4.0 3.7 + - + +
72A ASP* 1.3 102.1 + - - +
74A GLN* 1.3 93.3 + - + +
76A PHE* 3.6 10.0 + - - +
77A LEU* 3.7 14.9 + - - +
62B LYS* 6.4 0.2 - - - -
82B GLY* 4.8 6.3 - - - -
85B VAL* 3.1 52.7 - - + -
90B SER* 3.5 9.4 - - - +
91B PHE* 3.9 24.2 - + + -
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASP* 4.6 0.6 - - - +
73A PHE* 1.3 100.9 - - + +
75A GLU* 1.3 56.0 + - - +
76A PHE 3.0 2.9 - - - -
77A LEU* 2.8 30.6 + - - +
78A ASN* 2.4 88.3 + - - +
74B GLN* 3.3 21.8 - - - +
77B LEU 3.9 9.5 - - - +
78B ASN* 3.8 15.9 - - - +
81B GLY* 4.4 4.7 - - - -
82B GLY 4.6 0.9 + - - -
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 4.7 0.2 - - - -
63A LEU* 4.2 20.2 - - + +
64A ASP 3.8 12.8 - - - +
65A LEU* 3.0 27.9 - - + +
66A ASN 4.8 0.2 + - - -
67A SER* 4.0 13.4 - - - -
70A GLN 3.8 0.2 - - - +
71A LEU* 2.7 46.0 - - + +
72A ASP* 3.5 20.5 + - + +
73A PHE 4.2 0.8 - - - +
74A GLN* 1.3 76.4 - - - +
76A PHE* 1.3 50.5 + - - +
78A ASN* 3.4 8.2 + - + +
79A LEU* 2.5 44.8 + - - +
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU 5.4 0.7 - - - +
16A VAL* 3.3 40.6 - - + -
17A PHE* 3.4 39.9 - + + -
20A TYR* 4.9 0.7 - - + -
30A LEU* 3.3 31.2 - - + -
35A PHE* 3.0 55.6 - + - -
38A PHE* 3.4 21.8 - + - -
71A LEU* 4.8 2.0 - - + +
72A ASP 4.2 1.0 + - - +
73A PHE 3.6 6.7 + - - +
74A GLN 3.0 0.6 - - - -
75A GLU* 1.3 75.3 - - - +
77A LEU* 1.3 55.5 + - - +
78A ASN 2.9 1.3 - - - -
79A LEU* 2.7 3.8 + - - +
80A ILE* 2.6 45.1 + - + +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.3 46.7 - - + +
14A ILE* 5.4 4.7 - - + +
73A PHE 3.7 10.7 + - - +
74A GLN* 2.8 38.9 + - - +
76A PHE* 1.3 76.2 - - + +
78A ASN* 1.3 51.3 + - - +
80A ILE* 4.0 4.7 - - - -
81A GLY* 2.6 34.3 + - - -
13B LEU* 4.9 2.2 - - + -
74B GLN* 3.9 2.9 - - - +
77B LEU* 3.6 25.3 - - + +
81B GLY* 3.6 28.0 - - - +
84B ALA* 5.3 4.7 - - + -
85B VAL* 5.4 2.7 - - + -
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Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 4.0 4.4 - - - +
62A LYS* 5.0 16.2 + - - +
63A LEU* 6.0 0.9 - - + -
74A GLN* 2.4 57.1 + - - +
75A GLU* 3.4 9.2 - - - +
77A LEU* 1.3 66.9 - - - +
79A LEU* 1.3 65.5 + - + +
82A GLY* 2.9 24.6 + - - -
74B GLN* 3.8 20.6 - - - +
78B ASN* 5.0 4.3 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.0 38.6 - - + -
59A MET* 3.0 34.5 - - + +
60A MET* 3.3 13.2 - - + -
62A LYS* 5.9 0.9 - - - -
63A LEU* 3.1 51.6 - - + -
71A LEU* 4.9 1.1 - - + -
75A GLU* 2.5 37.2 + - + +
76A PHE 2.7 3.6 + - - +
78A ASN* 1.3 79.3 - - + +
80A ILE* 1.3 50.5 + - - +
83A LEU* 2.8 36.9 + - - +
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.1 33.4 - - + -
16A VAL* 5.9 0.2 - - + -
35A PHE* 4.1 2.7 - - + -
43A LEU* 3.4 29.2 - - + -
46A PHE* 5.0 1.6 - - + -
76A PHE* 2.6 38.0 + - + +
77A LEU* 3.9 4.3 - - - +
79A LEU* 1.3 73.1 - - - +
81A GLY* 1.3 70.9 + - - +
83A LEU* 2.9 22.2 + - + +
84A ALA 2.9 11.1 + - - +
6B THR* 5.1 2.9 - - + -
10B ILE* 3.0 41.5 - - + -
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 5.6 0.4 - - - -
77A LEU 2.6 26.9 + - - -
80A ILE* 1.3 77.7 - - - +
82A GLY* 1.3 62.9 + - - +
84A ALA* 2.9 18.1 + - - +
85A VAL* 2.9 17.3 - - - +
74B GLN* 4.4 1.3 - - - -
77B LEU* 3.6 24.8 - - - +
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 5.3 3.4 - - - -
62A LYS* 5.8 5.2 - - - -
77A LEU 3.9 0.2 + - - -
78A ASN* 2.9 21.7 + - - +
79A LEU 4.2 0.2 - - - -
81A GLY* 1.3 73.3 - - - +
83A LEU* 1.3 59.8 + - - +
85A VAL* 3.0 16.1 + - - +
86A ALA* 2.9 27.4 + - - +
73B PHE* 4.8 6.3 - - - -
74B GLN* 4.7 2.2 + - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 3.1 45.8 - - + -
46A PHE* 3.4 23.3 - - + -
55A VAL* 3.4 36.1 - - + +
56A LEU* 4.7 2.0 - - - -
59A MET* 2.9 27.6 - - + -
79A LEU 2.8 25.4 - - - +
80A ILE* 2.9 11.9 + - + +
82A GLY* 1.3 75.4 - - - +
84A ALA* 1.3 53.3 + - - +
86A ALA 2.7 2.8 + - - -
87A CYS* 2.5 37.6 + - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.6 5.3 - - - -
80A ILE 2.9 7.6 + - - +
81A GLY* 2.9 16.9 + - - +
83A LEU* 1.3 76.2 - - - +
85A VAL* 1.3 56.8 + - + +
88A HIS* 2.7 42.1 + - - +
89A GLU 2.9 4.2 - - - +
90A SER* 5.2 0.7 - - - -
10B ILE* 3.2 28.9 - - + -
14B ILE* 3.8 17.3 - - + -
77B LEU* 5.3 2.9 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLY 2.9 20.0 - - - +
82A GLY* 3.0 15.9 - - - +
84A ALA* 1.3 74.9 - - + +
86A ALA* 1.3 57.6 + - - +
87A CYS 3.4 0.4 - - - -
89A GLU 3.9 2.5 - - - -
90A SER* 3.5 18.2 - - - +
91A PHE* 2.8 43.2 - - + +
92A VAL* 3.7 5.3 - - - +
73B PHE* 3.1 59.0 - - + -
77B LEU* 5.4 3.1 - - + -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.3 40.2 - - + +
58A ARG* 5.7 5.4 - - - +
82A GLY 2.9 13.5 + - - +
83A LEU* 2.7 4.1 + - - -
85A VAL* 1.3 77.2 - - - +
87A CYS* 1.3 60.2 + - - +
92A VAL* 3.6 7.9 - - - +
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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