Contacts of the strand formed by residues 81 - 92 (chain C) in PDB entry 3NSH
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 LYS 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C TYR* 5.4 9.2 - - + -
75C VAL 3.3 16.2 - - - +
76C PRO* 3.7 17.7 - - + -
77C TYR* 4.5 2.5 - - - -
79C GLN 5.1 8.7 - - - -
80C GLY* 1.3 75.1 - - - +
82C TRP* 1.3 67.3 + - - +
111C SER* 3.5 1.4 - - - -
112C ASP* 2.9 65.7 + - + +
113C LYS* 6.0 0.6 - - - +
114C PHE* 3.6 7.4 - - - +
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Residues in contact with TRP 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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43C ASN* 4.2 11.0 - - + -
45C ALA* 3.3 19.3 - - + +
73C VAL* 3.8 24.7 - - + -
74C TYR* 3.2 10.0 - - - +
75C VAL* 3.0 55.9 + - + +
77C TYR* 3.1 33.7 + + - -
81C LYS* 1.3 77.2 - - - +
83C GLU* 1.3 73.2 + - - +
84C GLY* 4.0 1.6 - - - -
106C ALA* 3.5 30.3 - - + -
108C ILE* 3.6 24.1 - - + +
110C GLU 3.4 12.8 - - - +
111C SER* 3.9 6.5 - - - +
114C PHE* 3.7 30.6 - + + -
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Residues in contact with GLU 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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73C VAL 3.3 11.9 - - - +
74C TYR* 3.7 11.3 - - + +
82C TRP* 1.3 83.7 - - - +
84C GLY* 1.3 60.3 + - - +
108C ILE* 3.6 2.9 - - - -
109C THR* 2.9 25.1 + - - +
110C GLU* 2.8 51.3 + - + +
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Residues in contact with GLY 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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72C GLY* 3.5 4.7 - - - -
73C VAL* 2.9 35.0 + - - +
82C TRP* 4.0 2.9 - - - -
83C GLU* 1.3 78.1 - - - +
85C GLU* 1.3 65.4 + - - +
107C ALA 3.1 13.7 - - - -
109C THR* 3.2 13.9 - - - -
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Residues in contact with GLU 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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60C ARG* 2.9 44.3 + - - +
68C ASP* 5.4 4.7 - - - +
71C LYS 3.8 7.6 - - - +
72C GLY* 5.3 2.2 - - - -
73C VAL* 4.0 1.4 - - - +
84C GLY* 1.3 79.6 - - - +
86C LEU* 1.3 67.3 + - - +
87C GLY 3.7 0.2 + - - -
105C ILE 3.6 0.7 - - - +
106C ALA* 4.4 1.6 - - - -
107C ALA* 2.9 40.1 + - - +
109C THR* 3.9 18.7 + - + +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 4.7 2.5 + - - -
68C ASP* 3.4 9.2 - - - +
69C LEU* 3.0 35.9 + - + +
70C ARG 3.9 1.6 + - - -
71C LYS* 3.0 34.5 + - + +
72C GLY 4.0 9.0 - - - +
73C VAL* 4.0 17.7 - - + -
84C GLY 4.3 0.2 - - - -
85C GLU* 1.3 72.9 - - - +
87C GLY* 1.3 57.8 + - - +
104C ASN* 5.2 2.9 - - + -
105C ILE 3.7 13.0 - - - +
106C ALA* 4.4 7.0 - - + -
135C PRO* 3.8 28.3 - - + -
139C LEU* 3.8 37.0 - - + -
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Residues in contact with GLY 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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66C TYR* 4.3 9.9 - - - -
67C ARG 3.1 14.4 - - - -
68C ASP* 4.3 1.1 - - - -
69C LEU* 3.8 13.3 - - - +
85C GLU 3.7 0.8 + - - -
86C LEU* 1.3 74.9 - - - +
88C THR* 1.3 67.3 + - - +
104C ASN* 3.6 2.3 - - - +
105C ILE* 3.0 31.7 + - - +
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Residues in contact with THR 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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66C TYR* 3.7 4.0 - - - -
67C ARG* 2.9 48.5 + - + +
69C LEU* 4.1 13.2 - - + +
87C GLY* 1.3 72.4 - - - +
89C ASP* 1.3 65.4 + - - +
102C ARG* 3.1 30.9 + - + -
103C ALA 3.3 12.3 - - - +
104C ASN* 3.4 28.9 - - - +
105C ILE* 4.5 2.7 - - - +
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Residues in contact with ASP 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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27C GLY* 3.4 11.3 - - - +
58C TYR* 2.4 33.3 + - - +
63C SER* 2.9 19.4 + - - -
65C THR* 2.7 32.6 + - - -
66C TYR* 3.7 6.8 - - - +
88C THR* 1.3 79.2 - - - +
90C LEU* 1.3 69.5 + - - +
91C VAL* 3.6 4.1 + - - +
101C VAL 3.5 0.2 - - - +
102C ARG* 3.4 13.1 - - - +
103C ALA 3.0 29.0 + - - +
105C ILE* 3.4 13.7 - - + +
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Residues in contact with LEU 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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25C THR 3.9 0.3 - - - +
26C VAL* 3.4 3.5 - - - +
27C GLY 2.8 36.3 + - - +
28C SER* 4.2 13.0 - - - +
65C THR* 4.0 24.0 - - + +
89C ASP* 1.3 80.4 + - - +
91C VAL* 1.3 59.9 + - - +
100C THR* 3.8 24.9 - - + -
101C VAL 3.4 3.4 - - - +
102C ARG* 3.8 37.9 - - + +
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Residues in contact with VAL 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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24C MET* 3.6 31.6 - - + -
25C THR 3.3 10.5 - - - +
26C VAL* 4.1 8.3 - - + -
44C PHE* 4.0 24.2 - - + -
89C ASP 3.7 10.8 - - - +
90C LEU* 1.3 80.9 - - - +
92C SER* 1.3 69.8 + - - +
100C THR* 3.4 6.0 - - - -
101C VAL* 2.9 35.9 + - - +
103C ALA* 4.1 14.8 - - + -
105C ILE* 4.3 2.9 - - + -
142C PHE* 3.8 16.4 - - + -
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Residues in contact with SER 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C MET* 3.4 8.3 - - - +
25C THR* 2.8 54.9 + - - +
91C VAL* 1.3 75.4 - - - +
93C ILE* 1.3 66.6 + - - +
94C PRO* 3.9 2.2 - - - +
99C VAL 3.2 23.8 - - - -
100C THR* 3.8 10.2 + - - +
101C VAL* 5.7 0.7 - - - -
142C PHE* 6.1 0.7 - - - -
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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