Contacts of the helix formed by residues 74 - 92 (chain A) in PDB entry 2NS8
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 SER 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLY 3.6 3.4 + - - -
73A GLU* 1.3 78.3 - - - +
75A TRP* 1.3 59.8 - - - +
76A GLN* 3.4 18.7 + - - +
77A ASP* 3.2 28.3 + - - +
78A PHE* 2.9 24.9 + - - +
119A PHE* 3.7 1.3 - - - -
123A GLN* 3.7 9.0 - - - +
2C SER* 6.1 4.4 - - - -
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Residues in contact with TRP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 1.3 74.1 - - - +
76A GLN* 1.3 106.3 + - + +
78A PHE* 3.9 0.7 - - - +
79A LEU* 3.1 44.7 + - + +
119A PHE* 3.5 16.8 - - + -
120A LEU* 3.7 20.0 - - + -
123A GLN* 3.2 36.8 + - + +
125A PHE* 3.4 29.2 - + - -
194A ILE* 3.7 14.6 - - + -
197A PHE* 4.0 5.4 - + + -
198A GLU* 3.5 30.7 - - + -
201A LEU* 3.6 27.5 - - + +
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 3.4 20.4 - - - +
75A TRP* 1.3 127.8 + - + +
77A ASP* 1.3 57.1 + - - +
79A LEU* 3.3 3.3 + - - +
80A ARG* 3.0 47.9 + - - +
194A ILE* 3.8 14.2 - - + +
198A GLU* 2.8 34.5 + - - +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 3.7 20.1 - - + +
74A SER* 3.2 15.6 + - - +
76A GLN* 1.3 75.8 - - - +
78A PHE* 1.3 65.1 + - - +
80A ARG* 2.9 27.8 + - - +
81A ASN* 2.7 39.0 + - - +
3C ARG* 3.6 31.3 + - - +
36C VAL* 5.8 1.4 - - - +
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Residues in contact with PHE 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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66A HIS* 3.9 9.0 - + - -
68A SER* 3.5 11.7 - - - -
69A PRO* 3.4 36.8 - - + -
73A GLU* 3.4 16.8 - - - +
74A SER 2.9 15.8 + - - +
75A TRP 3.9 1.6 - - - +
76A GLN 3.2 0.2 - - - -
77A ASP* 1.3 77.5 - - - +
79A LEU* 1.3 81.2 + - + +
81A ASN* 3.9 0.3 - - - +
82A ASN* 2.8 55.6 + - + +
116A GLN* 3.7 38.1 - - + -
119A PHE* 3.9 26.2 - + + -
120A LEU* 4.9 3.4 - - + -
134A LEU* 4.5 6.7 - - + -
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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
----------------------------------------------------------
75A TRP* 3.1 47.7 + - + +
76A GLN 3.7 3.8 - - - +
78A PHE* 1.3 103.0 - - + +
80A ARG* 1.3 63.4 + - - +
82A ASN* 3.9 4.3 - - + +
83A ALA* 3.1 25.1 + - - +
120A LEU* 4.4 12.1 - - + -
133A ALA* 4.5 18.2 - - + +
134A LEU* 4.3 19.1 - - + -
137A VAL* 4.0 24.0 - - + +
194A ILE* 4.0 16.8 - - + -
197A PHE* 6.1 0.7 - - + -
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Residues in contact with ARG 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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76A GLN* 3.0 34.9 + - - +
77A ASP* 2.9 36.3 + - - +
79A LEU* 1.3 78.0 - - - +
81A ASN* 1.3 57.9 + - - +
83A ALA* 3.3 2.3 + - - +
84A LYS* 3.0 43.6 + - + +
190A LEU* 3.8 19.4 - - + +
191A GLU* 2.8 41.7 + - - +
194A ILE* 3.3 29.6 - - + +
195A ARG* 4.0 13.1 - - - +
37C GLU* 5.3 4.9 - - - -
40C THR* 3.3 27.4 + - - +
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Residues in contact with ASN 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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66A HIS* 3.2 30.1 - - + +
73A GLU* 2.8 19.8 + - - -
77A ASP* 2.7 34.8 + - - +
80A ARG* 1.3 73.7 - - - +
82A ASN* 1.3 58.0 + - - +
84A LYS* 3.4 24.9 + - - +
85A SER* 2.9 32.2 + - - -
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Residues in contact with ASN 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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64A HIS* 3.2 27.1 + - - -
66A HIS* 2.7 30.9 + - - +
67A PHE* 3.7 10.5 + - - +
78A PHE* 2.8 38.3 + - + +
79A LEU* 3.9 5.4 - - + +
81A ASN* 1.3 74.5 - - - +
83A ALA* 1.3 56.2 + - - +
85A SER 3.4 0.2 + - - -
86A PHE* 2.8 37.1 + - - +
116A GLN* 4.3 8.5 + - - +
134A LEU* 5.3 4.5 - - - +
137A VAL* 5.5 4.4 - - + +
0H ACE 4.5 6.3 + - - +
1H TRP 5.3 1.9 + - - -
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Residues in contact with ALA 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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79A LEU 3.1 18.1 + - - +
80A ARG 3.7 3.4 - - - +
82A ASN* 1.3 75.8 + - - +
84A LYS* 1.3 59.1 + - - +
86A PHE* 3.2 6.7 + - - +
87A ARG* 2.8 30.0 + - - +
137A VAL* 3.6 16.8 - - + +
141A THR* 3.6 24.8 - - - +
186A PHE* 4.1 3.4 - - + -
190A LEU* 3.7 17.9 - - + -
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Residues in contact with LYS 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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80A ARG* 3.0 27.8 + - + +
81A ASN* 3.7 26.5 + - - +
83A ALA* 1.3 75.5 - - - +
85A SER* 1.3 57.5 + - - +
87A ARG* 3.2 9.8 - - - +
88A ASN* 3.0 36.6 + - - +
186A PHE* 4.2 8.7 - - + -
187A LEU* 3.7 31.2 - - + -
190A LEU* 4.7 3.8 - - + -
37C GLU* 2.8 34.6 + - + +
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Residues in contact with SER 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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63A HIS 3.5 9.2 + - - +
64A HIS* 2.8 25.0 + - - -
65A THR* 3.0 13.5 + - - -
66A HIS* 3.0 26.7 + - - -
81A ASN 2.9 18.8 + - - -
82A ASN 3.6 1.8 - - - -
84A LYS* 1.3 75.5 - - - +
86A PHE* 1.3 63.6 + - - -
88A ASN* 3.4 10.7 + - - +
89A ALA* 3.1 17.7 + - - +
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Residues in contact with PHE 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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60A LEU* 4.1 16.6 - - + -
64A HIS* 3.3 10.9 + - + -
82A ASN* 2.8 20.4 + - - +
83A ALA* 3.4 7.0 - - - +
85A SER* 1.3 74.7 - - - +
87A ARG* 1.3 65.8 + - - +
89A ALA* 3.1 2.6 + - - +
90A LEU* 2.9 59.2 + - + +
100A HIS* 4.4 6.7 - + + -
138A GLY* 3.9 25.1 - - - -
141A THR* 3.7 19.1 - - + -
142A LEU* 4.5 9.0 - - + -
0H ACE 3.7 39.3 - - + +
1H TRP* 4.4 7.0 - - - -
2H THR* 4.7 7.9 - - + -
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Residues in contact with ARG 87 (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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83A ALA 2.8 16.1 + - - +
84A LYS* 3.2 12.3 - - - +
86A PHE* 1.3 72.8 - - - +
88A ASN* 1.3 60.5 + - - +
90A LEU* 3.1 4.9 + - - +
91A LEU* 2.8 54.6 + - + +
141A THR* 3.8 10.7 - - + +
144A SER* 5.5 1.6 - - - -
145A VAL* 3.9 19.1 - - + +
148A ASP* 3.9 18.4 + - - -
182A ALA* 4.3 3.6 - - - +
183A GLU* 3.7 53.1 + - - +
186A PHE* 3.3 43.4 - - - +
6E TYR* 5.5 1.0 + - - -
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Residues in contact with ASN 88 (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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63A HIS* 4.3 10.0 - - + +
84A LYS* 3.0 24.9 + - - +
85A SER* 3.6 10.2 - - - +
86A PHE 3.3 0.2 - - - -
87A ARG* 1.3 81.9 + - - +
89A ALA* 1.3 58.0 + - - +
91A LEU* 3.2 11.5 + - - +
92A SER* 2.9 30.5 + - - -
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Residues in contact with ALA 89 (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* 2.6 43.1 - - + +
60A LEU* 4.1 13.2 - - + -
63A HIS* 3.6 30.7 + - + -
64A HIS* 4.0 12.3 - - + +
85A SER 3.1 9.3 + - - +
86A PHE 3.1 8.4 + - - +
88A ASN* 1.3 76.6 - - - +
90A LEU* 1.3 55.8 + - - +
92A SER* 2.7 7.4 + - - -
100A HIS* 5.0 0.2 - - - -
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Residues in contact with LEU 90 (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* 4.2 3.8 - - - -
86A PHE* 2.9 48.2 + - + +
87A ARG 3.6 4.5 - - - +
89A ALA* 1.3 76.4 - - - +
91A LEU* 1.3 58.3 + - - +
92A SER 3.5 0.3 + - - -
96A GLY* 3.3 16.9 - - - -
97A ALA* 4.2 9.2 - - - +
100A HIS* 3.4 42.4 - - + +
141A THR* 4.2 2.9 - - + +
142A LEU* 3.8 31.2 - - + -
145A VAL* 3.8 25.8 - - + -
149A GLN* 3.1 17.5 + - - -
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Residues in contact with LEU 91 (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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87A ARG* 2.8 61.9 + - + +
88A ASN* 3.2 10.9 + - - +
90A LEU* 1.3 70.3 - - - +
92A SER* 1.3 63.8 + - - +
93A HIS* 3.2 8.8 + - - +
145A VAL* 3.6 23.8 - - + -
148A ASP* 5.0 11.9 - - + +
149A GLN* 3.8 14.8 + - + +
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Residues in contact with SER 92 (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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18A ASN* 4.8 3.8 + - - -
59A MET* 2.9 12.6 - - - +
63A HIS* 3.5 35.9 - - - -
88A ASN 2.9 11.5 + - - -
89A ALA 2.7 20.4 + - - -
91A LEU* 1.3 77.8 - - - +
93A HIS* 1.3 70.6 + - - +
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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