Contacts of the helix formed by residues 73 - 86 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LYS* 6.4 0.4 - - - -
82A GLY* 4.8 6.5 - - - -
85A VAL* 3.1 51.8 - - + -
90A SER* 3.5 9.6 + - - +
91A PHE* 3.9 24.5 - + + -
17B PHE* 4.1 13.6 - - + +
28B VAL* 4.0 3.9 + - + +
72B ASP* 1.3 100.8 + - - +
74B GLN* 1.3 91.4 + - + +
76B PHE* 3.6 10.6 + - - +
77B LEU* 3.7 14.5 + - + +
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Residues in contact with GLN 74 (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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74A GLN* 3.3 21.8 - - - +
77A LEU 3.9 9.4 - - - +
78A ASN* 3.8 15.5 - - - +
81A GLY* 4.4 5.0 - - - -
82A GLY 4.7 0.9 + - - -
72B ASP* 4.6 0.6 - - - +
73B PHE* 1.3 101.4 - - + +
75B GLU* 1.3 57.9 + - - +
76B PHE 3.0 2.7 - - - -
77B LEU* 2.8 30.7 + - - +
78B ASN* 2.4 88.4 + - - +
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Residues in contact with GLU 75 (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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35B PHE* 4.7 0.2 - - - -
63B LEU* 4.2 19.8 - - + +
64B ASP 3.8 12.8 - - - +
65B LEU* 3.0 26.9 - - + +
67B SER* 4.0 13.1 - - - -
70B GLN 3.8 0.7 - - - +
71B LEU* 2.7 44.9 - - + +
72B ASP* 3.5 20.6 + - + +
73B PHE 4.2 0.4 - - - +
74B GLN* 1.3 76.7 - - - +
76B PHE* 1.3 50.1 + - - +
78B ASN* 3.4 8.4 - - + +
79B LEU* 2.5 44.9 + - + +
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Residues in contact with PHE 76 (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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13B LEU 5.4 0.2 - - - +
16B VAL* 3.3 41.1 - - + -
17B PHE* 3.4 37.9 - + + -
20B TYR* 4.9 1.1 - - + -
30B LEU* 3.3 30.7 - - + -
35B PHE* 3.0 53.4 - + - -
38B PHE* 3.4 21.3 - + - -
71B LEU* 4.8 2.1 - - + +
72B ASP 4.2 1.0 + - - +
73B PHE 3.6 6.7 + - - +
74B GLN 3.0 0.8 - - - -
75B GLU* 1.3 74.5 - - - +
77B LEU* 1.3 56.6 + - + +
78B ASN 2.9 1.3 - - - -
79B LEU* 2.7 3.6 + - - +
80B ILE* 2.6 45.3 + - + +
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Residues in contact with LEU 77 (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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13A LEU* 4.9 2.5 - - + -
74A GLN* 3.9 2.9 - - - +
77A LEU* 3.6 25.1 - - + +
81A GLY* 3.6 27.4 - - - +
84A ALA* 5.3 4.9 - - + -
85A VAL* 5.4 3.1 - - + -
13B LEU* 3.3 46.0 - - + +
14B ILE* 5.4 5.4 - - + +
73B PHE 3.7 10.0 + - - +
74B GLN* 2.8 38.9 + - - +
76B PHE* 1.3 76.1 - - - +
78B ASN* 1.3 51.5 + - - +
80B ILE* 4.0 4.3 - - - -
81B GLY* 2.6 35.0 + - - -
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Residues in contact with ASN 78 (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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74A GLN* 3.8 21.3 - - - +
78A ASN* 5.0 5.1 + - - +
59B MET* 4.0 4.2 - - - +
62B LYS* 5.0 16.2 + - - +
63B LEU* 6.0 0.7 - - + -
74B GLN* 2.4 54.8 + - - +
75B GLU* 3.4 9.6 - - + +
77B LEU* 1.3 67.1 - - - +
79B LEU* 1.3 66.1 + - + +
82B GLY* 2.9 24.9 + - - -
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Residues in contact with LEU 79 (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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35B PHE* 3.0 39.9 - - + -
59B MET* 3.0 34.2 - - + +
60B MET* 3.3 13.5 - - + -
62B LYS* 5.9 0.9 - - - -
63B LEU* 3.1 51.1 - - + -
71B LEU* 4.9 1.1 - - + -
75B GLU* 2.5 36.1 + - + +
76B PHE 2.7 3.6 + - - +
78B ASN* 1.3 79.4 - - + +
80B ILE* 1.3 50.4 + - - +
83B LEU* 2.8 36.4 + - - +
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Residues in contact with ILE 80 (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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6A THR* 5.1 2.5 - - + -
10A ILE* 3.0 42.2 - - + -
13B LEU* 3.1 33.2 - - + -
16B VAL* 5.9 0.2 - - + -
35B PHE* 4.1 2.4 - - + -
43B LEU* 3.4 29.6 - - + -
46B PHE* 5.0 1.8 - - + -
76B PHE* 2.6 38.0 + - + +
77B LEU* 3.9 3.8 - - - +
79B LEU* 1.3 72.9 - - - +
81B GLY* 1.3 70.6 + - - +
83B LEU* 2.9 21.8 + - + +
84B ALA 2.9 10.7 + - - +
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Residues in contact with GLY 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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74A GLN* 4.4 1.6 - - - -
77A LEU* 3.6 24.4 - - - +
13B LEU* 5.6 0.4 - - - -
77B LEU 2.6 27.9 + - - -
80B ILE* 1.3 77.0 - - - +
82B GLY* 1.3 61.6 + - - +
84B ALA* 2.9 17.9 + - - +
85B VAL* 2.9 17.5 - - - +
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Residues in contact with GLY 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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73A PHE* 4.8 6.3 - - - -
74A GLN* 4.6 2.4 + - - -
59B MET* 5.3 2.9 - - - -
62B LYS* 5.8 5.4 - - - -
78B ASN* 2.9 21.5 + - - +
79B LEU 4.2 0.2 - - - -
81B GLY* 1.3 73.7 - - - +
83B LEU* 1.3 59.3 + - - +
85B VAL* 3.0 15.4 + - - +
86B ALA* 2.9 28.0 + - - +
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Residues in contact with LEU 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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39B MET* 3.1 46.2 - - + -
46B PHE* 3.4 22.9 - - + -
55B VAL* 3.4 35.4 - - + +
56B LEU* 4.7 2.2 - - + -
59B MET* 2.9 27.6 - - + -
79B LEU 2.8 25.6 - - - +
80B ILE* 2.9 11.8 + - + +
82B GLY* 1.3 75.7 - - - +
84B ALA* 1.3 53.6 + - - +
86B ALA 2.7 2.6 + - - -
87B CYS* 2.5 37.9 + - - +
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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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10A ILE* 3.2 29.4 - - + -
14A ILE* 3.8 16.4 - - + -
77A LEU* 5.3 2.7 - - + -
46B PHE* 3.6 5.5 - - - -
80B ILE 2.9 8.0 + - - +
81B GLY* 2.9 17.1 + - - +
83B LEU* 1.3 76.2 - - - +
85B VAL* 1.3 55.7 + - + +
88B HIS* 2.7 43.1 + - - +
89B GLU 2.9 4.5 - - - +
90B SER* 5.2 0.4 - - - -
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Residues in contact with VAL 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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73A PHE* 3.1 58.8 - - + -
77A LEU* 5.4 3.1 - - + -
81B GLY 2.9 20.6 - - - +
82B GLY* 3.0 15.5 - - - +
84B ALA* 1.3 75.0 - - + +
86B ALA* 1.3 57.4 + - - +
87B CYS 3.4 0.7 - - - -
89B GLU 3.9 2.9 - - - -
90B SER* 3.5 18.2 - - - +
91B PHE* 2.8 43.0 - - + +
92B VAL* 3.7 5.0 - - - +
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Residues in contact with ALA 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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55B VAL* 3.3 40.5 - - + +
58B ARG* 5.7 5.6 - - - +
82B GLY 2.9 12.7 + - - +
83B LEU* 2.7 4.0 + - - -
85B VAL* 1.3 77.8 - - - +
87B CYS* 1.3 60.0 + - - +
92B VAL* 3.6 7.7 - - - +
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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